downloading reverse dependencies ... downloading batchLLM_0.2.0.tar.gz ... ok downloading inDAGO_1.0.0.tar.gz ... ok downloading Spectran_1.0.6.tar.gz ... ok downloading vvshiny_0.1.1.tar.gz ... ok installing dependencies ‘bigtabulate’, ‘colorSpec’, ‘gemini.R’, ‘gghighlight’, ‘HTSFilter’, ‘openai’, ‘Rfastp’, ‘rhub’, ‘Rsubread’, ‘shinytoastr’, ‘ShortRead’, ‘spsComps’, ‘spsUtil’, ‘upsetjs’ also installing the dependencies ‘biganalytics’, ‘hwriter’ begin installing package ‘biganalytics’ begin installing package ‘hwriter’ begin installing package ‘shinytoastr’ begin installing package ‘spsUtil’ begin installing package ‘openai’ begin installing package ‘gemini.R’ begin installing package ‘HTSFilter’ begin installing package ‘Rfastp’ begin installing package ‘Rsubread’ begin installing package ‘upsetjs’ begin installing package ‘colorSpec’ begin installing package ‘gghighlight’ begin installing package ‘rhub’ * installing *source* package ‘hwriter’ ... ** this is package ‘hwriter’ version ‘1.3.2.1’ ** package ‘hwriter’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hwriter) begin installing package ‘ShortRead’ * installing *source* package ‘colorSpec’ ... ** this is package ‘colorSpec’ version ‘1.8-0’ ** package ‘colorSpec’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (colorSpec) * installing *source* package ‘shinytoastr’ ... ** this is package ‘shinytoastr’ version ‘2.2.0’ ** package ‘shinytoastr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (shinytoastr) begin installing package ‘spsComps’ * installing *source* package ‘openai’ ... ** this is package ‘openai’ version ‘0.4.1’ ** package ‘openai’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (openai) * installing *source* package ‘upsetjs’ ... ** this is package ‘upsetjs’ version ‘1.11.1’ ** package ‘upsetjs’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (upsetjs) * installing *source* package ‘gemini.R’ ... ** this is package ‘gemini.R’ version ‘0.16.0’ ** package ‘gemini.R’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gemini.R) * installing *source* package ‘spsUtil’ ... ** this is package ‘spsUtil’ version ‘0.2.2’ ** package ‘spsUtil’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spsUtil) * installing *source* package ‘gghighlight’ ... ** this is package ‘gghighlight’ version ‘0.5.0’ ** package ‘gghighlight’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gghighlight) * installing *source* package ‘spsComps’ ... ** this is package ‘spsComps’ version ‘0.3.4.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spsComps) * installing *source* package ‘rhub’ ... ** this is package ‘rhub’ version ‘2.0.1’ ** package ‘rhub’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhub) * installing *source* package ‘biganalytics’ ... ** this is package ‘biganalytics’ version ‘1.1.22’ ** package ‘biganalytics’ successfully unpacked and MD5 sums checked ** using staged installation checking for Sun Studio compiler... no checking for OS... Linux ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjOJtEO/R.INSTALL3ccc9379860647/biganalytics/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c biganalytics_init.c -o biganalytics_init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c binit.cpp -o binit.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from binit.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hash.cpp -o hash.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from hash.cpp:2: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kmeans.cpp -o kmeans.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from kmeans.cpp:32: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c summary_stat.cpp -o summary_stat.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from summary_stat.cpp:7: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o biganalytics.so biganalytics_init.o binit.o hash.o kmeans.o summary_stat.o -lrt -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjOJtEO/R.INSTALL3ccc9379860647/biganalytics/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-biganalytics/00new/biganalytics/libs ** R ** byte-compile and prepare package for lazy loading Creating a generic function for ‘apply’ from package ‘base’ in package ‘biganalytics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biganalytics) begin installing package ‘bigtabulate’ * installing *source* package ‘HTSFilter’ ... ** this is package ‘HTSFilter’ version ‘1.48.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (HTSFilter) * installing *source* package ‘bigtabulate’ ... ** this is package ‘bigtabulate’ version ‘1.1.9’ ** package ‘bigtabulate’ successfully unpacked and MD5 sums checked ** using staged installation checking for Sun Studio compiler... no checking for OS... Linux ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmprbUcVf/R.INSTALL3cd49e2b919186/bigtabulate/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bigtabulate.cpp -o bigtabulate.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from bigtabulate.cpp:7: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = BreakMapper]’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper]’ 150 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = Mapper; Y = BreakMapper]’ 205 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = BreakMapper; T = Mapper]’ 283 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bigtabulate.cpp:438:26: required from ‘SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = double; MatrixAccessorType = MatrixAccessor; SEXP = SEXPREC*]’ 438 | mappers.push_back( MapperPtr( | ^~~~~~~~~~ 439 | new BreakMapper( breaks[i][0], breaks[i][1], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 | breaks[i][2], INTEGER(useNA)[0] > 0 ) ) ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigtabulate.cpp:772:24: required from here 772 | return TAPPLY( MatrixAccessor( REAL(numericMatrix), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 773 | static_cast(Rf_nrows(numericMatrix)) ), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 774 | columns, breaks, returnTable, useNA, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 775 | returnSummary, processColumns, summaryNARM, splitcol, splitlist ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type ‘BreakMapper’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 44 | delete x; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = IndexMapper]’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper]’ 150 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = Mapper; Y = IndexMapper]’ 205 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = IndexMapper; T = Mapper]’ 283 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bigtabulate.cpp:445:26: required from ‘SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = double; MatrixAccessorType = MatrixAccessor; SEXP = SEXPREC*]’ 445 | mappers.push_back( MapperPtr( | ^~~~~~~~~~ 446 | new IndexMapper( RData(vec), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 | RData(vec) + vecLen, INTEGER(useNA)[0] > 0 ) ) ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigtabulate.cpp:772:24: required from here 772 | return TAPPLY( MatrixAccessor( REAL(numericMatrix), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 773 | static_cast(Rf_nrows(numericMatrix)) ), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 774 | columns, breaks, returnTable, useNA, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 775 | returnSummary, processColumns, summaryNARM, splitcol, splitlist ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type ‘IndexMapper’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 44 | delete x; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = BreakMapper]’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper]’ 150 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = Mapper; Y = BreakMapper]’ 205 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = BreakMapper; T = Mapper]’ 283 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bigtabulate.cpp:438:26: required from ‘SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = int; MatrixAccessorType = MatrixAccessor; SEXP = SEXPREC*]’ 438 | mappers.push_back( MapperPtr( | ^~~~~~~~~~ 439 | new BreakMapper( breaks[i][0], breaks[i][1], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 | breaks[i][2], INTEGER(useNA)[0] > 0 ) ) ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigtabulate.cpp:782:21: required from here 782 | return TAPPLY( MatrixAccessor( INTEGER(numericMatrix), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 783 | static_cast(Rf_nrows(numericMatrix)) ), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 784 | columns, breaks, returnTable, useNA, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 785 | returnSummary, processColumns, summaryNARM, splitcol, splitlist ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type ‘BreakMapper’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 44 | delete x; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = IndexMapper]’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:150:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper]’ 150 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = Mapper; Y = IndexMapper]’ 205 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = IndexMapper; T = Mapper]’ 283 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bigtabulate.cpp:445:26: required from ‘SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = int; MatrixAccessorType = MatrixAccessor; SEXP = SEXPREC*]’ 445 | mappers.push_back( MapperPtr( | ^~~~~~~~~~ 446 | new IndexMapper( RData(vec), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 | RData(vec) + vecLen, INTEGER(useNA)[0] > 0 ) ) ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigtabulate.cpp:782:21: required from here 782 | return TAPPLY( MatrixAccessor( INTEGER(numericMatrix), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 783 | static_cast(Rf_nrows(numericMatrix)) ), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 784 | columns, breaks, returnTable, useNA, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 785 | returnSummary, processColumns, summaryNARM, splitcol, splitlist ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type ‘IndexMapper’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 44 | delete x; | ^~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bigtabulate_init.c -o bigtabulate_init.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o bigtabulate.so bigtabulate.o bigtabulate_init.o -lrt -lm -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmprbUcVf/R.INSTALL3cd49e2b919186/bigtabulate/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-bigtabulate/00new/bigtabulate/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bigtabulate) * installing *source* package ‘Rsubread’ ... ** this is package ‘Rsubread’ version ‘2.22.1’ ** using staged installation @@@@@ The operating system is Linux. ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpkRzTMN/R.INSTALL3ccca511e0f370/Rsubread/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c HelperFunctions.c -o HelperFunctions.o HelperFunctions.c: In function ‘get_contig_fasta’: HelperFunctions.c:236:74: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 236 | unsigned int this_size = HashTableGet( tab -> size_table, chro ) - NULL; | ^ HelperFunctions.c: In function ‘read_contig_fasta’: HelperFunctions.c:310:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 310 | HashTablePut(tab -> size_table , mem_chro, NULL + inner_cursor); | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMbase-index.c -o LRMbase-index.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMchro-event.c -o LRMchro-event.o LRMchro-event.c: In function ‘LRMevents_build_entries’: LRMchro-event.c:87:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 87 | int * entries_list = LRMHashTableGet(context -> events_realignment, NULL+sidepos); | ^ LRMchro-event.c:97:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 97 | LRMHashTablePut(context -> events_realignment , NULL+sidepos, entries_list); | ^ LRMchro-event.c:120:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 120 | LRMHashTablePut(context -> events_realignment, NULL+sidepos, entries_list); | ^ LRMchro-event.c: In function ‘LRMevents_search’: LRMchro-event.c:213:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 213 | int * event_here = LRMHashTableGet(context -> events_realignment, NULL + testing_pos); | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMfile-io.c -o LRMfile-io.o LRMfile-io.c: In function ‘LRMgenerate_bam_record’: LRMfile-io.c:275:89: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 275 | int chro_number = LRMHashTableGet(context->sam_bam_chromosome_table, chro_name) - NULL; | ^ LRMfile-io.c: In function ‘LRMwrite_chunk_compress_bam_block’: LRMfile-io.c:349:22: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 349 | bam_buf[9] = 0xff; // OS | ^~~~ LRMfile-io.c: In function ‘LRMload_offsets’: LRMfile-io.c:437:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 437 | LRMHashTablePut(context->sam_bam_chromosome_table, chro_name, NULL + chromosome_no + 1); | ^ LRMfile-io.c:437:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 437 | LRMHashTablePut(context->sam_bam_chromosome_table, chro_name, NULL + chromosome_no + 1); | ^ LRMfile-io.c:440:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 440 | LRMHashTablePut(context->chromosome_size_table, chro_name, NULL + (this_offset - last_end + 16 - context->current_index_padding * 2)); | ^ LRMfile-io.c:441:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 441 | LRMArrayListPush(context->chromosome_size_list, NULL + this_offset); | ^ LRMfile-io.c: In function ‘LRMsambam_write_header’: LRMfile-io.c:477:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 477 | int chro_length = LRMHashTableGet(context -> chromosome_size_table, chro_name) - NULL; | ^ LRMfile-io.c:513:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 513 | int chro_length = LRMHashTableGet(context -> chromosome_size_table, chro_name) - NULL; | ^ LRMfile-io.c: In function ‘LRMlocate_gene_position’: LRMfile-io.c:611:112: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 611 | while(n+jump_ns < total_offsets && LRMArrayListGet(context->chromosome_size_list, n + jump_ns) - NULL <= linear) | ^ LRMfile-io.c:619:73: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 619 | if ( (LRMArrayListGet(context->chromosome_size_list, n) - NULL) > linear) | ^ LRMfile-io.c:622:94: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 622 | if(n>0)(*pos) -= (LRMArrayListGet(context->chromosome_size_list, n-1)-NULL); | ^ LRMfile-io.c: In function ‘LRMlocate_chro_length’: LRMfile-io.c:640:112: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 640 | while(n+jump_ns < total_offsets && LRMArrayListGet(context->chromosome_size_list, n + jump_ns) - NULL <= linear) | ^ LRMfile-io.c:648:73: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 648 | if ( (LRMArrayListGet(context->chromosome_size_list, n) - NULL) > linear) { | ^ LRMfile-io.c:650:88: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 650 | (* end_pos) = LRMArrayListGet(context->chromosome_size_list, n)-NULL; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMhashtable.c -o LRMhashtable.o LRMhashtable.c: In function ‘LRMpointerHashFunction’: LRMhashtable.c:737:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 737 | return ((srUInt_64)( pointer - NULL )) ; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMhelper.c -o LRMhelper.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMseek-zlib.c -o LRMseek-zlib.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_wrapper.c -o R_wrapper.o R_wrapper.c: In function ‘R_try_cell_barcode_wrapper’: R_wrapper.c:119:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 119 | int rv = (void*)c_argv[7]-NULL; | ^ R_wrapper.c:120:44: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 120 | int tested_reads = (void*)c_argv[8]-NULL; | ^ R_wrapper.c:121:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 121 | int sample_good_reads = (void*)c_argv[9]-NULL; | ^ R_wrapper.c:122:48: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 122 | int cell_good_reads = (void*)c_argv[10]-NULL; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RsimReads.c -o RsimReads.o RsimReads.c: In function ‘Rgen_one_read_here’: RsimReads.c:71:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 71 | int trans_len = HashTableGet(grc->transcript_lengths, seq_name)-NULL-1; | ^ RsimReads.c: In function ‘Rgrc_put_new_trans’: RsimReads.c:114:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 114 | HashTablePut( grc->transcript_lengths, strdup(seq_name) , NULL+lbuf_len +1); | ^ RsimReads.c:114:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 114 | HashTablePut( grc->transcript_lengths, strdup(seq_name) , NULL+lbuf_len +1); | ^ RsimReads.c: In function ‘init_grc_by_file’: RsimReads.c:144:92: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 144 | HashTablePut(grc -> expression_levels, strdup(input_order_transcript_names[xk1]), NULL +1); | ^ RsimReads.c:155:125: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 155 | int ov = HashTableGet( grc -> expression_levels, input_order_transcript_names[input_order_transcript_per_read[xk1]-1] ) -NULL; | ^ RsimReads.c:158:125: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 158 | HashTablePutReplace(grc -> expression_levels, input_order_transcript_names[input_order_transcript_per_read[xk1]-1], NULL+ov, 0); | ^ RsimReads.c:183:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 183 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ RsimReads.c:185:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 185 | if(seq_exp>1)HashTablePut(seq_duplicate_tab, md5mem, 1+NULL); | ^ RsimReads.c:241:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 241 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c SNPCalling.c -o SNPCalling.o SNPCalling.c: In function ‘put_hash_to_pile’: SNPCalling.c:229:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 229 | int base_N_qual = cursor->value - NULL; | ^ SNPCalling.c:230:51: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 230 | int POI_pos = cursor->key - NULL - 100; | ^ SNPCalling.c: In function ‘read_tmp_block’: SNPCalling.c:383:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 383 | unsigned int original_value = HashTableGet(merge_table,NULL+POI_pos)-NULL; | ^ SNPCalling.c:383:109: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 383 | unsigned int original_value = HashTableGet(merge_table,NULL+POI_pos)-NULL; | ^ SNPCalling.c:388:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 388 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c:388:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 388 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c:403:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 403 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c:403:101: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 403 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c: In function ‘process_snp_votes’: SNPCalling.c:939:109: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 939 | long long int indel_no = HashTableGet(parameters -> cigar_event_table, event_token) - NULL; | ^ SNPCalling.c:943:114: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 943 | long long int tmpv = HashTableGet(parameters -> cigar_event_table, event_token2) - NULL; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c aligner.c -o aligner.o aligner.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c atgcContent.c -o atgcContent.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c build-sam-index.c -o build-sam-index.o build-sam-index.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cell-counts.c -o cell-counts.o In file included from cell-counts.c:19: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ cell-counts.c: In function ‘cellCounts_cell_barcode_tabel_destroy’: cell-counts.c:269:15: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 269 | if(((a-NULL) & 0xfffffffff0000000llu ) ==IMPOSSIBLE_MEMORY_SPACE )return; | ^ cell-counts.c: In function ‘cellCounts_make_barcode_HT_table’: cell-counts.c:288:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 288 | HashTablePut(cct_context -> cell_barcode_head_tail_table, strdup(bc), NULL+xx1+IMPOSSIBLE_MEMORY_SPACE); | ^ cell-counts.c:288:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 288 | HashTablePut(cct_context -> cell_barcode_head_tail_table, strdup(bc), NULL+xx1+IMPOSSIBLE_MEMORY_SPACE); | ^ cell-counts.c:301:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 301 | ArrayListPush(array_of_codes, NULL+xx1); | ^ cell-counts.c: In function ‘sheet_convert_ss_to_arr’: cell-counts.c:672:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 672 | hashed_arr -> appendix1 = NULL+ cct_context -> sample_id_to_name -> numOfElements; // One-based | ^ cell-counts.c:681:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 681 | push_arr[0] = NULL + lane_sample_int; | ^ cell-counts.c:682:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 682 | push_arr[1] = NULL + cct_context -> sample_id_to_name -> numOfElements; | ^ cell-counts.c:684:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 684 | push_arr[3] = NULL + (sbc_lane_sample[1]!=NULL && strlen(sbc_lane_sample[1])>12); | ^ cell-counts.c:686:78: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 686 | HashTablePut(cct_context -> lineno1B_to_sampleno1B_tab , NULL+line_no_in_sheet, NULL + cct_context -> sample_id_to_name -> numOfElements); | ^ cell-counts.c:686:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 686 | HashTablePut(cct_context -> lineno1B_to_sampleno1B_tab , NULL+line_no_in_sheet, NULL + cct_context -> sample_id_to_name -> numOfElements); | ^ cell-counts.c: In function ‘cellCounts_sample_SamBam_writers_new_files’: cell-counts.c:801:50: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 801 | HashTablePut(fp_tab, NULL+x1+1 , wtrptr); | ^ cell-counts.c:801:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 801 | HashTablePut(fp_tab, NULL+x1+1 , wtrptr); | ^ cell-counts.c: In function ‘features_load_one_line’: cell-counts.c:918:101: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 918 | int access_n = HashTableGet(cct_context -> chromosome_table.read_name_to_index, chro_name ) - NULL; | ^ cell-counts.c: In function ‘cellCounts_find_or_insert_gene_name’: cell-counts.c:988:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 988 | srInt_64 gene_number = HashTableGet(genetable, feature_name) - NULL; | ^ cell-counts.c:993:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 993 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ cell-counts.c:993:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 993 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ cell-counts.c: In function ‘cellCounts_load_annotations’: cell-counts.c:1295:128: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1295 | chro_stub -> chro_number = HashTableGet(cct_context -> chromosome_table.read_name_to_index, seq_name ) - NULL -1; | ^ cell-counts.c: In function ‘cellCounts_get_cellbarcode_no’: cell-counts.c:1741:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1741 | srInt_64 xint = xrawarr - NULL; | ^ cell-counts.c:1752:77: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1752 | int bcno = ArrayListGet(rawarr, xx2)-NULL; | ^ cell-counts.c:1755:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1755 | if(ArrayListGet(ret, xx3)==NULL+bcno){ | ^ cell-counts.c:1761:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1761 | if(!found)ArrayListPush(ret, NULL+bcno); | ^ cell-counts.c:1770:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1770 | int tbcn = ArrayListGet(ret,xx1)-NULL; | ^ cell-counts.c: In function ‘cellCounts_build_read_bin’: cell-counts.c:1807:107: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1807 | if(chro_name) refID = HashTableGet(cct_context -> chromosome_table.read_name_to_index, chro_name) - NULL - 1; | ^ cell-counts.c: In function ‘cellCounts_vote_and_add_count’: cell-counts.c:1991:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1991 | sample_no = HashTableGet(cct_context -> lineno1B_to_sampleno1B_tab, NULL+lineno)-NULL; | ^ cell-counts.c:1991:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1991 | sample_no = HashTableGet(cct_context -> lineno1B_to_sampleno1B_tab, NULL+lineno)-NULL; | ^ cell-counts.c:2030:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2030 | }else sample_bam_2fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+(sample_no-1) + 1); // sample_id-1: 0,1,2,... | ^ cell-counts.c:2030:9: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2030 | }else sample_bam_2fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+(sample_no-1) + 1); // sample_id-1: 0,1,2,... | ^ cell-counts.c:2030:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2030 | }else sample_bam_2fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+(sample_no-1) + 1); // sample_id-1: 0,1,2,... | ^ cell-counts.c: In function ‘cellCounts_run_in_thread’: cell-counts.c:2117:38: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2117 | int thread_no = parameters[1]-NULL; | ^ cell-counts.c:2118:33: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2118 | int task = parameters[2]-NULL; | ^ cell-counts.c: In function ‘cellCounts_run_maybe_threads’: cell-counts.c:2155:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2155 | thr_parameters[1] = NULL+current_thread_no; | ^ cell-counts.c:2156:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2156 | thr_parameters[2] = NULL+task; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_cell’: cell-counts.c:3542:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3542 | int sample_id = app1[3]-NULL; | ^ cell-counts.c:3536:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3551:41: note: in expansion of macro ‘ADD_count_hash’ 3551 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:3536:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3551:41: note: in expansion of macro ‘ADD_count_hash’ 3551 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:3536:163: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3551:41: note: in expansion of macro ‘ADD_count_hash’ 3551 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:3536:165: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3551:41: note: in expansion of macro ‘ADD_count_hash’ 3551 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:3536:193: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3551:41: note: in expansion of macro ‘ADD_count_hash’ 3551 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:3566:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3566 | HashTablePut(filtered_CGU_table, strdup(replaced_key), NULL-1); | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_step’: cell-counts.c:3536:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3688:66: note: in expansion of macro ‘ADD_count_hash’ 3688 | else if(is_UMI_step2 && str0->cellbc>=0) ADD_count_hash(str0->cellbc,str0->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:3536:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3688:66: note: in expansion of macro ‘ADD_count_hash’ 3688 | else if(is_UMI_step2 && str0->cellbc>=0) ADD_count_hash(str0->cellbc,str0->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:3536:163: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3688:66: note: in expansion of macro ‘ADD_count_hash’ 3688 | else if(is_UMI_step2 && str0->cellbc>=0) ADD_count_hash(str0->cellbc,str0->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:3536:165: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3688:66: note: in expansion of macro ‘ADD_count_hash’ 3688 | else if(is_UMI_step2 && str0->cellbc>=0) ADD_count_hash(str0->cellbc,str0->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:3536:193: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3536 | #define ADD_count_hash(bc,gn,no) HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) ) | ^ cell-counts.c:3688:66: note: in expansion of macro ‘ADD_count_hash’ 3688 | else if(is_UMI_step2 && str0->cellbc>=0) ADD_count_hash(str0->cellbc,str0->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_do_one_batch_tab_to_struct_list_compare’: cell-counts.c:3745:47: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3745 | int sort_by_geneid_then_umi = app1[1] - NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_tab_to_struct_list’: cell-counts.c:3773:29: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3773 | int supp_reads = val-NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_write_UMIs’: cell-counts.c:3795:20: warning: wrong type argument to decrement [-Wpointer-arith] 3795 | vcell_gene --; | ^~ cell-counts.c: In function ‘cellCounts_merge_batches_worker’: cell-counts.c:3805:35: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3805 | int my_worker_id = vpp[2] - NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch’: cell-counts.c:3985:143: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3985 | srInt_64 this_batch_size_and_no = ArrayListGet(file_size_list, file_size_list->numOfElements-1 -this_batch_sorted_idx)-NULL; | ^ cell-counts.c:3963:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3963 | srInt_64 supp_reads = HashTableGet(supp_reads_SCGU, my_key)-NULL; \ | ^ cell-counts.c:4036:41: note: in expansion of macro ‘ADD_key_struct’ 4036 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:3964:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3964 | if(1>supp_reads) HashTablePut(supp_reads_SCGU, strdup(my_key), NULL+1); \ | ^ cell-counts.c:4036:41: note: in expansion of macro ‘ADD_key_struct’ 4036 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:3965:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3965 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:4036:41: note: in expansion of macro ‘ADD_key_struct’ 4036 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:3965:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3965 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:4036:41: note: in expansion of macro ‘ADD_key_struct’ 4036 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:3963:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3963 | srInt_64 supp_reads = HashTableGet(supp_reads_SCGU, my_key)-NULL; \ | ^ cell-counts.c:4041:33: note: in expansion of macro ‘ADD_key_struct’ 4041 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:3964:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3964 | if(1>supp_reads) HashTablePut(supp_reads_SCGU, strdup(my_key), NULL+1); \ | ^ cell-counts.c:4041:33: note: in expansion of macro ‘ADD_key_struct’ 4041 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:3965:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3965 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:4041:33: note: in expansion of macro ‘ADD_key_struct’ 4041 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:3965:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3965 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:4041:33: note: in expansion of macro ‘ADD_key_struct’ 4041 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:4069:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4069 | app1[1] = NULL+1; | ^ cell-counts.c:4076:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4076 | app1[1] = NULL+0; | ^ cell-counts.c:4120:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4120 | if(umi == NULL-1) umi="-----------------------------------------"; | ^ cell-counts.c:4141:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4141 | return NULL + removed_UMIs; | ^ cell-counts.c: In function ‘cellCounts_save_BAM_result’: cell-counts.c:4154:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4154 | void ** fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+sample_id); | ^ cell-counts.c: In function ‘cellCounts_merged_write_sparse_unique_genes’: cell-counts.c:4187:26: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4187 | int cellbcP1 = ky-NULL; | ^ cell-counts.c:4188:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4188 | if(used_cellnoP1_tab && !HashTableGet(used_cellnoP1_tab, NULL+cellbcP1))return; | ^ cell-counts.c:4194:131: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4194 | if(!HashTableGet(unique_geneno1B_tab, ArrayListGet(g2ul,x1))) HashTablePut(unique_geneno1B_tab, geneno1B_ptr, NULL+1); | ^ cell-counts.c: In function ‘cellCounts_merged_write_sparse_matrix’: cell-counts.c:4234:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4234 | int gene_index_0B = ArrayListGet(unique_NZ_genenosP1_list, x2) - NULL-1; | ^ cell-counts.c:4240:71: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4240 | srInt_64 cellno = ArrayListGet(used_cell_barcodes, x1)-NULL; | ^ cell-counts.c:4246:71: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4246 | srInt_64 cellno = ArrayListGet(used_cell_barcodes, x1)-NULL; | ^ cell-counts.c:4247:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4247 | HashTable * geneno1B_to_UMIs = HashTableGet(cellP1_to_geneP1_to_umis_tab, NULL+1+cellno); | ^ cell-counts.c:4247:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4247 | HashTable * geneno1B_to_UMIs = HashTableGet(cellP1_to_geneP1_to_umis_tab, NULL+1+cellno); | ^ cell-counts.c:4250:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4250 | int geneno1B = ArrayListGet(unique_NZ_genenosP1_list, x2)-NULL; | ^ cell-counts.c:4251:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4251 | int this_umis = HashTableGet(geneno1B_to_UMIs, NULL+geneno1B) -NULL; | ^ cell-counts.c:4251:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4251 | int this_umis = HashTableGet(geneno1B_to_UMIs, NULL+geneno1B) -NULL; | ^ cell-counts.c: In function ‘cellCounts_merged_45K_to_90K_sum_SUM_Level2’: cell-counts.c:4265:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4265 | HashTablePut(summed_gene_to_umis, GeneNo1B, vUMIs + (HashTableGet(summed_gene_to_umis, GeneNo1B)-NULL)); | ^ cell-counts.c:4265:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4265 | HashTablePut(summed_gene_to_umis, GeneNo1B, vUMIs + (HashTableGet(summed_gene_to_umis, GeneNo1B)-NULL)); | ^ cell-counts.c: In function ‘cellCounts_merged_45K_to_90K_sum_WRT’: cell-counts.c:4282:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4282 | unsigned char * gene_name = cct_context -> gene_name_array[ kyGeneID - NULL-1 ]; | ^ cell-counts.c:4283:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4283 | fprintf(ofp, "%s\t%u\n", gene_name, (unsigned int) (valUMIs-NULL)); | ^ cell-counts.c: In function ‘cellCounts_merged_write_nozero_geneids_WRT’: cell-counts.c:4314:71: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4314 | unsigned char* gene_symbol = cct_context -> gene_name_array [k-NULL-1]; | ^ cell-counts.c: In function ‘cellCounts_merged_to_tables_write_build_UMIcount_in’: cell-counts.c:4333:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4333 | tab -> counter1 += (val-NULL); | ^ cell-counts.c: In function ‘cellCounts_merged_to_tables_write_build_UMIcounts’: cell-counts.c:4338:25: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4338 | int cell_no = ky-NULL-1; | ^ cell-counts.c:4343:48: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4343 | HashTablePut(cellbcP1_to_umis_tab, NULL+1+cell_no, NULL+geneP1_to_counts_tab -> counter1); | ^ cell-counts.c:4343:50: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4343 | HashTablePut(cellbcP1_to_umis_tab, NULL+1+cell_no, NULL+geneP1_to_counts_tab -> counter1); | ^ cell-counts.c:4343:64: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4343 | HashTablePut(cellbcP1_to_umis_tab, NULL+1+cell_no, NULL+geneP1_to_counts_tab -> counter1); | ^ cell-counts.c: In function ‘cellCounts_merged_ambient_rescure’: cell-counts.c:4359:129: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4359 | srInt_64 median_umis = HashTableGet(cellnoP1_to_umis_tab, ArrayListGet(sorted_bcno_p1 , (high_conf_cells-1)/2))-NULL; | ^ cell-counts.c:4366:100: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4366 | srInt_64 this_bc_umis = HashTableGet(cellnoP1_to_umis_tab, this_bc_pnt_p1) - NULL; | ^ cell-counts.c:4373:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4373 | ArrayListPush(this_sample_ambient_rescure_candi, this_bc_pnt_p1-1); | ^ cell-counts.c:4378:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4378 | ArrayListPush(this_sample_45k_90k_barcode_no_P0, ArrayListGet(sorted_bcno_p1 , x1)-1 ); | ^ cell-counts.c: In function ‘cellCounts_merged_bootstrap_a_sample’: cell-counts.c:4401:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4401 | srInt_64 this_umis = HashTableGet(cellnoP1_to_umis_tab, cellbc_p1_ptr )-NULL; | ^ cell-counts.c:4403:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4403 | ArrayListPush(highconf_cellbc_list, ArrayListGet( sorted_idx, x1 ) - 1 ); | ^ cell-counts.c:4414:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4414 | srInt_64 this_umis = HashTableGet( cellnoP1_to_umis_tab, cellbc_p1_ptr )-NULL; | ^ cell-counts.c:4415:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4415 | ArrayListPush(resampled_list_of_umis,NULL+this_umis); | ^ cell-counts.c:4418:159: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4418 | srInt_64 UMIs_30th_div10 = ArrayListGet(resampled_list_of_umis, resampled_list_of_umis -> numOfElements - SCRNA_BOOTSTRAP_HIGH_INDEX) -NULL; | ^ cell-counts.c:4423:95: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4423 | srInt_64 this_umis = ArrayListGet(resampled_list_of_umis, lli)-NULL; | ^ cell-counts.c:4435:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4435 | ArrayListPush(highconf_cellbc_list, last_ptr - 1 ); | ^ cell-counts.c:4437:75: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4437 | last_umi_no = HashTableGet(cellnoP1_to_umis_tab ,last_ptr)-NULL; | ^ cell-counts.c: In function ‘cellCounts_merged_to_tables_write’: cell-counts.c:4475:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4475 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:4475:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4475 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:4475:104: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4475 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:4475:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4475 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:4480:126: warning: wrong type argument to decrement [-Wpointer-arith] 4480 | for(xk1=0; xk1numOfElements; xk1++) all_barcode_index_list->elementList[xk1]--; | ^~ cell-counts.c: In function ‘cellCounts_do_cellbc_batches’: cell-counts.c:4546:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4546 | ArrayListPush(file_size_list, NULL+( batchsize<<20 | xk1)); | ^ cell-counts.c:4568:31: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4568 | vpp[1] = NULL + xk1; | ^ cell-counts.c:4577:39: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4577 | removed_umis += (pret - NULL); | ^ cell-counts.c:4618:31: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4618 | vpp[2] = NULL + xk1; | ^ cell-counts.c:4643:112: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4643 | HashTable *gene_tab = HashTableGet(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1); | ^ cell-counts.c:4643:122: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4643 | HashTable *gene_tab = HashTableGet(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1); | ^ cell-counts.c:4646:98: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4646 | HashTablePut(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1, gene_tab); | ^ cell-counts.c:4646:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4646 | HashTablePut(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1, gene_tab); | ^ cell-counts.c:4648:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4648 | HashTablePut(gene_tab, NULL+gene_no0B+1 , NULL+umis); | ^ cell-counts.c:4648:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4648 | HashTablePut(gene_tab, NULL+gene_no0B+1 , NULL+umis); | ^ cell-counts.c:4648:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4648 | HashTablePut(gene_tab, NULL+gene_no0B+1 , NULL+umis); | ^ cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’: cell-counts.c:1622:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized] 1622 | if(search_start>0xffffff00) return; | ^ cell-counts.c:1611:30: note: ‘search_start’ was declared here 1611 | unsigned int search_start, search_end, search_block_id; | ^~~~~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-bigtable.c -o core-bigtable.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-indel.c -o core-indel.o In file included from core-indel.c:34: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ core-indel.c: In function ‘anti_support_thread_run’: core-indel.c:223:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 223 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:223:136: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 223 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:223:141: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 223 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:225:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut( atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:225:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut( atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:225:125: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut( atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:247:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 247 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:247:144: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 247 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:247:149: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 247 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:249:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 249 | HashTablePut( atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:249:123: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 249 | HashTablePut( atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:249:133: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 249 | HashTablePut( atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c: In function ‘anti_support_add_count’: core-indel.c:263:21: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 263 | int eno = ky-NULL-1; | ^ core-indel.c:265:51: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 265 | event_body -> anti_supporting_reads+= (va - NULL); | ^ core-indel.c: In function ‘remove_neighbour’: core-indel.c:579:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 579 | unsigned int * res = HashTableGet(event_table, NULL+pos); | ^ core-indel.c:590:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 590 | HashTableRemove(event_table, NULL+pos); | ^ core-indel.c: In function ‘localPointerCmp_forEventEntry’: core-indel.c:609:50: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 609 | unsigned int v1 = (unsigned int)(pointer1-NULL); | ^ core-indel.c:610:50: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 610 | unsigned int v2 = (unsigned int)(pointer2-NULL); | ^ core-indel.c: In function ‘localPointerHashFunction_forEventEntry’: core-indel.c:616:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 616 | unsigned int v = (pointer-NULL); | ^ core-indel.c: In function ‘init_indel_tables’: core-indel.c:672:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 672 | indel_context -> local_reassembly_pileup_files -> appendix1 = NULL + max_open_file * 2/ 3; | ^ core-indel.c: In function ‘sort_junction_entry_table’: core-indel.c:920:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 920 | HashTablePut(indel_context -> event_entry_table, NULL + last_scannping_pos, id_list); | ^ core-indel.c: In function ‘do_juncs_add_feature’: core-indel.c:1240:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1240 | int access_n = HashTableGet( global_context -> chromosome_table.read_name_to_index, chro_name ) - NULL; | ^ core-indel.c: In function ‘put_new_event’: core-indel.c:1397:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1397 | unsigned int * id_list = HashTableGet(event_table, NULL+sides[xk1]); | ^ core-indel.c:1403:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1403 | HashTablePut(event_table , NULL+sides[xk1] , id_list); | ^ core-indel.c: In function ‘search_event’: core-indel.c:1439:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1439 | unsigned int * res = HashTableGet(event_table, NULL+pos); | ^ core-indel.c: In function ‘insert_pileup_read’: core-indel.c:2550:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2550 | unsigned int next_jump_array = HashTableGet(current_table ,NULL+next_key_prefix) - NULL; | ^ core-indel.c:2550:106: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2550 | unsigned int next_jump_array = HashTableGet(current_table ,NULL+next_key_prefix) - NULL; | ^ core-indel.c:2558:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2558 | HashTablePut(current_table, NULL + next_key_prefix , NULL + next_jump_array); | ^ core-indel.c:2558:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2558 | HashTablePut(current_table, NULL + next_key_prefix , NULL + next_jump_array); | ^ core-indel.c: In function ‘finalise_db_graph’: core-indel.c:2587:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2587 | next_moves = HashTableGet(de_brujin_graph , NULL + current_key) - NULL; | ^ core-indel.c:2587:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2587 | next_moves = HashTableGet(de_brujin_graph , NULL + current_key) - NULL; | ^ core-indel.c: In function ‘rectify_read_text’: core-indel.c:2814:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2814 | char * neighbour_read_text = HashTableGet(block_context->read_sequence_table,NULL+neighbour_read_key); | ^ core-indel.c: In function ‘search_window_once’: core-indel.c:2903:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2903 | char * start_read_txt = HashTableGet(block_context->read_sequence_table,NULL+starter_read_key); | ^ core-indel.c:2907:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2907 | int start_read_pos = HashTableGet(block_context->read_position_table, NULL+starter_read_key) - NULL ; | ^ core-indel.c:2907:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2907 | int start_read_pos = HashTableGet(block_context->read_position_table, NULL+starter_read_key) - NULL ; | ^ core-indel.c:2976:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2976 | int next_read_pos = HashTableGet(block_context->read_position_table, NULL+test_next_read_key) - NULL; | ^ core-indel.c:2976:127: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2976 | int next_read_pos = HashTableGet(block_context->read_position_table, NULL+test_next_read_key) - NULL; | ^ core-indel.c:2991:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2991 | char * next_read_txt = HashTableGet(block_context->read_sequence_table,NULL+test_next_read_key); | ^ core-indel.c:3034:127: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3034 | +(unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ core-indel.c:3034:147: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3034 | +(unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ core-indel.c:3056:128: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3056 | + (unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ core-indel.c:3056:148: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3056 | + (unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ core-indel.c:3089:140: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3089 | char *prev_read_txt = HashTableGet(block_context->read_sequence_table,NULL+test_prev_read_key); | ^ core-indel.c:3179:92: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3179 | char * next_read_txt = HashTableGet(block_context->read_sequence_table,NULL+test_next_read_key); | ^ core-indel.c: In function ‘finalise_pileup_file’: core-indel.c:3981:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3981 | HashTablePut(read_position_table, NULL + read_hashed_key, NULL+first_base_pos+1); | ^ core-indel.c:3981:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3981 | HashTablePut(read_position_table, NULL + read_hashed_key, NULL+first_base_pos+1); | ^ core-indel.c:3981:110: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3981 | HashTablePut(read_position_table, NULL + read_hashed_key, NULL+first_base_pos+1); | ^ core-indel.c:3982:64: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3982 | HashTablePut(read_sequence_table, NULL + read_hashed_key, sequence_for_hash); | ^ core-indel.c:3983:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3983 | HashTablePut(read_quality_table, NULL + read_hashed_key, NULL + qual_of_this_read); | ^ core-indel.c:3983:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3983 | HashTablePut(read_quality_table, NULL + read_hashed_key, NULL + qual_of_this_read); | ^ core-indel.c:4052:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4052 | char * start_read_txt = HashTableGet(block_context.read_sequence_table,NULL+starter_read_key); | ^ core-indel.c: In function ‘destroy_pileup_table’: core-indel.c:4316:38: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4316 | if(fp != NULL+1) | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-interface-aligner.c -o core-interface-aligner.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-interface-subjunc.c -o core-interface-subjunc.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-junction.c -o core-junction.o In file included from core-junction.c:32: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ core-junction.c: In function ‘find_donor_receptor’: core-junction.c:2099:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) | ^~ core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ core-junction.c: In function ‘find_translocation_brk_PQR’: core-junction.c:5725:59: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5725 | int event_no = event_ptr_list_A1[candA1i] - NULL; | ^ core-junction.c:5738:72: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5738 | unsigned int event_no_P = event_ptr_list_A1[candBrkPi] - NULL; | ^ core-junction.c:5761:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5761 | unsigned int event_no_Q = event_ptr_list_Q[candQi] - NULL; | ^ core-junction.c:5779:84: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5779 | unsigned int event_no_R = event_ptr_list_R[candRi] - NULL; | ^ core-junction.c: In function ‘finalise_translocations’: core-junction.c:6025:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6025 | subread_read_number_t frag_S_no = (s_ptrs[cand_i] - NULL)/ 2; | ^ core-junction.c:6026:72: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6026 | int frag_S_is_read_B = (s_ptrs[cand_i] - NULL) % 2; | ^ core-junction.c: In function ‘finalise_inversions’: core-junction.c:6210:91: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6210 | subread_read_number_t frag_S_no = (s_ptrs[cand_i] - NULL)/2; | ^ core-junction.c:6211:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6211 | int frag_S_larger_read = (s_ptrs[cand_i] - NULL)%2; | ^ core-junction.c:6295:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6295 | int event_no_Y = s1_ptrs[cand_Y] - NULL; | ^ core-junction.c:6305:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6305 | int event_no_Z = s1_ptrs[cand_Z] - NULL; | ^ core-junction.c: In function ‘build_breakpoint_tables’: core-junction.c:6479:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6479 | if(index_table) bktable_append(index_table, chro_name_left, chro_pos_left, NULL + xk1); | ^ core-junction.c:6480:99: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6480 | if(index_table) bktable_append(index_table, chro_name_right, chro_pos_right, NULL + xk1); | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core.c -o core.o In file included from core.c:55: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ core.c: In function ‘write_single_fragment’: core.c:1909:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1909 | bktable_append(&global_context -> funky_table_BC, rec1 -> chro, rec1 -> offset , NULL + (2*pair_number)); | ^ core.c:1910:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1910 | bktable_append(&global_context -> funky_table_BC, rec2 -> chro, rec2 -> offset , NULL + (2*pair_number+1)); | ^ core.c:1910:25: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1910 | bktable_append(&global_context -> funky_table_BC, rec2 -> chro, rec2 -> offset , NULL + (2*pair_number+1)); | ^~~~~~~~~~~~~~ core.c:1914:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1914 | bktable_append(&global_context -> funky_table_DE, rec1 -> chro, rec1 -> offset , NULL + (2*pair_number + (rec1 -> offset > rec2 -> offset ? 1:0))); | ^ core.c:1915:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1915 | bktable_append(&global_context -> funky_table_DE, rec2 -> chro, rec2 -> offset , NULL + (2*pair_number + (rec1 -> offset < rec2 -> offset ? 1:0))); | ^ core.c: In function ‘do_anno_bitmap_add_feature’: core.c:3927:99: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3927 | HashTablePut(global_context -> annotation_chro_table, memstrcpy( chro_name ), NULL+1); | ^ core.c:3930:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3930 | int access_n = HashTableGet( global_context -> chromosome_table.read_name_to_index, chro_name ) - NULL; | ^ core.c: In function ‘test_PE_and_same_chro_align’: core.c:4816:16: warning: ISO C forbids ‘return’ with expression, in function returning void [-Wpedantic] 4816 | return test_PE_and_same_chro_cigars(global_context, res1 -> first_base_position, res2 -> first_base_position, is_exonic_regions, is_PE_distance, is_same_chromosome , read_len_1 , read_len_2, res1 -> cigar_string, res2 -> cigar_string, read_name, res_tlen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ core.c:4815:6: note: declared here 4815 | void test_PE_and_same_chro_align(global_context_t * global_context , realignment_result_t * res1, realignment_result_t * res2, int * is_exonic_regions, int * is_PE_distance, int * is_same_chromosome, int read_len_1, int read_len_2, char * read_name, int *res_tlen){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c detection-calls.c -o detection-calls.o detection-calls.c: In function ‘DTCload_fasta’: detection-calls.c:95:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 95 | HashTablePut(context -> chro_length_table, curr_chro_mem , NULL + base_current_chro_len); | ^ detection-calls.c:136:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 136 | HashTablePut(context -> chro_length_table, curr_chro_mem , NULL + base_current_chro_len); | ^ detection-calls.c: In function ‘DTCprint_lentab_items’: detection-calls.c:160:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 160 | SUBREADprintf("%s => %ld\n", (char*)key, (long)(hashed_obj - NULL)); | ^ detection-calls.c: In function ‘DTCtotal_GC_bases’: detection-calls.c:168:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 168 | unsigned int chro_len = HashTableGet(context -> chro_length_table, chro) - NULL; | ^ detection-calls.c:175:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 175 | chro_len = HashTableGet(context -> chro_length_table, tna) - NULL; | ^ detection-calls.c:182:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 182 | chro_len = HashTableGet(context -> chro_length_table, tna) - NULL; | ^ detection-calls.c: In function ‘DTCparse_GTF_and_Genome’: detection-calls.c:413:148: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 413 | DTCanno_fill_gap(context, current_chro_name_in_anno, top_end + 1, HashTableGet(context -> chro_length_table, current_chro) - NULL - 1); | ^ detection-calls.c: In function ‘DTCwrite_annotations’: detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ detection-calls.c:155:109: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c detectionCall.c -o detectionCall.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c detectionCallAnnotation.c -o detectionCallAnnotation.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c exon-algorithms.c -o exon-algorithms.o exon-algorithms.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c exon-align-indel.c -o exon-align-indel.o exon-align-indel.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c exon-align.c -o exon-align.o exon-align.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c flattenAnnotations.c -o flattenAnnotations.o flattenAnnotations.c: In function ‘flatAnno_do_anno_chop_one_array’: flattenAnnotations.c:167:75: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 167 | if(ArrayListGet(edge_before_me_List,findi)-NULL == search_tag){ | ^ flattenAnnotations.c:172:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 172 | if(0==found) ArrayListPush(edge_before_me_List, NULL+search_tag); | ^ flattenAnnotations.c:180:77: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 180 | int an_edge_before_me = edge_before_me_List-> elementList[i]-NULL; | ^ flattenAnnotations.c:215:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 215 | curr_2i[0] = edge_before_me_List -> elementList[i] -NULL; | ^ flattenAnnotations.c:216:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 216 | curr_2i[1] = edge_before_me_List -> elementList[i+1] -NULL-1; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fullscan.c -o fullscan.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fusion-align.c -o fusion-align.o fusion-align.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gen_rand_reads.c -o gen_rand_reads.o gen_rand_reads.c: In function ‘gen_a_read_from_one_transcript’: gen_rand_reads.c:206:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 206 | int actual_transcript_len = HashTableGet(grc->transcript_lengths, trans_name) - NULL; | ^ gen_rand_reads.c: In function ‘calc_N_from_M’: gen_rand_reads.c:299:132: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 299 | unsigned long long space_end = ArrayListGet(grc->transcript_hitting_space, grc->transcript_hitting_space->numOfElements -1)-NULL; | ^ gen_rand_reads.c:303:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 303 | unsigned long long thisv = ArrayListGet(grc->transcript_hitting_space, ti) - NULL; | ^ gen_rand_reads.c: In function ‘convert_hitting_space_to_num_of_reads’: gen_rand_reads.c:339:132: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 339 | unsigned long long space_end = ArrayListGet(grc->transcript_hitting_space, grc->transcript_hitting_space->numOfElements -1)-NULL; | ^ gen_rand_reads.c:349:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 349 | int seq_len = HashTableGet(grc-> transcript_lengths, seq_name)-NULL; | ^ gen_rand_reads.c:350:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 350 | unsigned long long thisv = ArrayListGet(grc->transcript_hitting_space, read_i) - NULL; | ^ gen_rand_reads.c:366:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 366 | ArrayListPush(rescure_hitting_space, NULL+to_rescure_read_top); | ^ gen_rand_reads.c:367:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 367 | ArrayListPush(num_of_frags_per_transcript, NULL+expected_reads); | ^ gen_rand_reads.c:382:122: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 382 | unsigned long long expected_reads = ArrayListGet(num_of_frags_per_transcript, this_transcript_no)-NULL; | ^ gen_rand_reads.c:384:92: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 384 | num_of_frags_per_transcript->elementList[this_transcript_no] = NULL+expected_reads; | ^ gen_rand_reads.c: In function ‘grc_gen’: gen_rand_reads.c:412:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 412 | int seq_len = HashTableGet(grc-> transcript_lengths, seq_name)-NULL; | ^ gen_rand_reads.c:413:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 413 | unsigned long long expected_reads = ArrayListGet(num_of_frags_per_transcript, read_i)-NULL; | ^ gen_rand_reads.c:423:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 423 | ArrayListPush(per_transcript_reads_hitting_space, NULL+total_read_top); | ^ gen_rand_reads.c: In function ‘grc_summary_fasta’: gen_rand_reads.c:531:85: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 531 | long dupval = HashTableGet(seq_duplicate_tab,md5mem)-NULL; | ^ gen_rand_reads.c:533:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 533 | HashTablePutReplace( seq_duplicate_tab, md5mem, NULL+dupval , 0); | ^ gen_rand_reads.c:540:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 540 | HashTablePut( seq_length_tab, seq_name, NULL+seq_len); | ^ gen_rand_reads.c:562:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 562 | HashTablePut(name_duplicate_tab, seq_name, NULL+1); | ^ gen_rand_reads.c:581:69: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 581 | long dupval = HashTableGet(seq_duplicate_tab,md5mem)-NULL; | ^ gen_rand_reads.c:583:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 583 | HashTablePutReplace( seq_duplicate_tab, md5mem, NULL+dupval ,0); | ^ gen_rand_reads.c:592:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 592 | HashTablePut( seq_length_tab, seq_name, NULL+seq_len); | ^ gen_rand_reads.c:601:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 601 | long md5repeated = HashTableGet(seq_duplicate_tab, md5str) - NULL; | ^ gen_rand_reads.c:603:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 603 | long seqlen = HashTableGet(seq_length_tab,seqnam)-NULL; | ^ gen_rand_reads.c:605:51: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 605 | HashTablePut(reprs_tab,md5str,NULL+1); | ^ gen_rand_reads.c: In function ‘grc_put_new_trans’: gen_rand_reads.c:627:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 627 | HashTablePut(grc-> transcript_lengths, seq_name, NULL+ seq_len); | ^ gen_rand_reads.c:628:95: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 628 | unsigned long long this_seq_exp_10000 = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gen_rand_reads.c:636:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 636 | ArrayListPush(grc->transcript_hitting_space, NULL+*linear_space_top); | ^ gen_rand_reads.c: In function ‘grc_load_env’: gen_rand_reads.c:696:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 696 | HashTablePut(grc->expression_levels, seqname_buf, NULL+seqexp_int+1); | ^ gen_rand_reads.c:696:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 696 | HashTablePut(grc->expression_levels, seqname_buf, NULL+seqexp_int+1); | ^ gen_rand_reads.c:771:94: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 771 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gen_rand_reads.c:773:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 773 | if(seq_exp>1)HashTablePut(seq_duplicate_tab, md5mem, 1+NULL); | ^ gen_rand_reads.c:829:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 829 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gene-algorithms.c -o gene-algorithms.o gene-algorithms.c: In function ‘linear_gene_position’: gene-algorithms.c:425:67: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 425 | n = HashTableGet(offsets -> read_name_to_index, chro_name)-NULL; | ^ gene-algorithms.c: In function ‘find_and_explain_indel’: gene-algorithms.c:768:93: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 768 | *(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xff ; | ^~~~ gene-algorithms.c: In function ‘explain_indel_in_middle’: gene-algorithms.c:918:93: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘253’ to ‘-3’ [-Woverflow] 918 | *(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xfd; | ^~~~ gene-algorithms.c:945:93: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘254’ to ‘-2’ [-Woverflow] 945 | *(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xfe ; | ^~~~ gene-algorithms.c: In function ‘load_offsets’: gene-algorithms.c:1355:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1355 | HashTablePut(offsets->read_name_to_index, read_name_mem , NULL + 1 + n); | ^ gene-algorithms.c:1355:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1355 | HashTablePut(offsets->read_name_to_index, read_name_mem , NULL + 1 + n); | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gene-value-index.c -o gene-value-index.o gene-value-index.c: In function ‘is_offset_in_chro’: gene-value-index.c:85:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding )) | ^~ In file included from gene-value-index.h:24, from gene-value-index.c:25: subread.h:153:24: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 153 | #define SUBREADprintf msgqu_printf | ^~~~~~~~~~~~ gene-value-index.c:87:41: note: in expansion of macro ‘SUBREADprintf’ 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hashtable.c -o hashtable.o hashtable.c: In function ‘ArrayListToLookupTable_Int’: hashtable.c:43:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 43 | for(x1 = 0; x1 < arr->numOfElements; x1++) HashTablePut(ret, ArrayListGet(arr, x1)+1, NULL+x1+1); | ^ hashtable.c:43:99: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 43 | for(x1 = 0; x1 < arr->numOfElements; x1++) HashTablePut(ret, ArrayListGet(arr, x1)+1, NULL+x1+1); | ^ hashtable.c:43:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 43 | for(x1 = 0; x1 < arr->numOfElements; x1++) HashTablePut(ret, ArrayListGet(arr, x1)+1, NULL+x1+1); | ^ hashtable.c: In function ‘ArrayListSort_compare’: hashtable.c:169:75: warning: ISO C forbids initialization between function pointer and ‘void *’ [-Wpedantic] 169 | int (*comp_elems)(void * L_elem, void * R_elem, ArrayList * me) = sortdata[1]; | ^~~~~~~~ hashtable.c: In function ‘ArrayListSort_merge’: hashtable.c:188:75: warning: ISO C forbids initialization between function pointer and ‘void *’ [-Wpedantic] 188 | int (*comp_elems)(void * L_elem, void * R_elem, ArrayList * me) = sortdata[1]; | ^~~~~~~~ hashtable.c: In function ‘ArrayListSort’: hashtable.c:214:21: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 214 | sortdata[1] = compare_L_minus_R?compare_L_minus_R:ArrayListSort_comp_pntr; | ^ hashtable.c: In function ‘ArrayListLLUComparison’: hashtable.c:227:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 227 | srUInt_64 lint = L_elem-NULL; | ^ hashtable.c:228:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 228 | srUInt_64 rint = R_elem-NULL; | ^ hashtable.c: In function ‘ArrayListFindNextDent’: hashtable.c:236:35: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 236 | if( list -> elementList[h]- NULL <= value_less_than_dent )return -1l; | ^ hashtable.c:239:55: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 239 | srUInt_64 mv = list -> elementList[m] - NULL; | ^ hashtable.c:247:46: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 247 | for(; m>=0 && list -> elementList[m] - NULL >= value_less_than_dent; m--); | ^ hashtable.c:250:44: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 250 | if( list -> elementList[m] - NULL > value_less_than_dent )return m; | ^ hashtable.c: In function ‘HashTableInc’: hashtable.c:321:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 321 | HashTablePut(tab, key, oldv+1); | ^ hashtable.c:322:21: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 322 | return oldv - NULL+1; | ^ hashtable.c: In function ‘pointerHashFunction’: hashtable.c:987:36: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 987 | return (srUInt_64)(pointer - NULL); | ^ hashtable.c: In function ‘HashTableSortedIndexes’: hashtable.c:1089:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1089 | appx[1]=NULL+larger_value_first; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c index-builder.c -o index-builder.o index-builder.c: In function ‘save_none_informative’: index-builder.c:78:40: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 78 | unsigned int subread_int = key - NULL; | ^ index-builder.c:79:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 79 | int repeats = hashed_obj - NULL; | ^ index-builder.c: In function ‘build_gene_index’: index-builder.c:349:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 349 | int is_no_info = HashTableGet(huge_table, NULL+1+int_key)-NULL; | ^ index-builder.c:349:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 349 | int is_no_info = HashTableGet(huge_table, NULL+1+int_key)-NULL; | ^ index-builder.c:349:90: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 349 | int is_no_info = HashTableGet(huge_table, NULL+1+int_key)-NULL; | ^ index-builder.c: In function ‘scan_gene_index’: index-builder.c:678:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 678 | HashTablePut(huge_table,NULL+1+ current_bucket -> item_keys[j], NULL+current_bucket -> item_values [j]); | ^ index-builder.c:678:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 678 | HashTablePut(huge_table,NULL+1+ current_bucket -> item_keys[j], NULL+current_bucket -> item_values [j]); | ^ index-builder.c:678:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 678 | HashTablePut(huge_table,NULL+1+ current_bucket -> item_keys[j], NULL+current_bucket -> item_values [j]); | ^ index-builder.c: In function ‘check_and_convert_FastA’: index-builder.c:905:90: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 905 | int is_exist = HashTableGet(rep_name_table , line_buf+1) - NULL; | ^ index-builder.c:915:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 915 | HashTablePut(rep_name_table, keymem, NULL+1); | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c input-blc.c -o input-blc.o input-blc.c: In function ‘iBLC_guess_scan’: input-blc.c:128:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 128 | ArrayListPush(tilelist, NULL+tmpi); | ^ input-blc.c:149:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 149 | scancon -> cbcl_tile_numbers[ii] = ArrayListGet(tilelist,ii) - NULL; | ^ input-blc.c: In function ‘iCache_continuous_read_lanes’: input-blc.c:508:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 508 | ArrayListPush(tfp -> list_mapped_qscore, NULL+tov); | ^ input-blc.c:520:117: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 520 | HashTablePut(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit, NULL+seek_start); | ^ input-blc.c:520:135: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 520 | HashTablePut(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit, NULL+seek_start); | ^ input-blc.c:521:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 521 | HashTablePut(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit, NULL+1+reads_in_tile); | ^ input-blc.c:521:127: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 521 | HashTablePut(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit, NULL+1+reads_in_tile); | ^ input-blc.c:521:129: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 521 | HashTablePut(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit, NULL+1+reads_in_tile); | ^ input-blc.c:537:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 537 | int this_tile_reads = HashTableGet(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit) - NULL -1; | ^ input-blc.c:537:129: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 537 | int this_tile_reads = HashTableGet(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit) - NULL -1; | ^ input-blc.c:538:132: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 538 | srInt_64 next_tile_start_off = HashTableGet(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit) - NULL; | ^ input-blc.c:538:146: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 538 | srInt_64 next_tile_start_off = HashTableGet(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit) - NULL; | ^ input-blc.c:558:130: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 558 | nch = (nch & 3) | (4*(tfp -> list_mapped_qscore -> elementList[ nch >>2 ]-NULL)); | ^ input-blc.c:577:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 577 | np1 = HashTableGet(tfp -> digit4_to_compressed_start_of_next, NULL+new_4digit); | ^ input-blc.c:580:59: warning: unused variable ‘npos’ [-Wunused-variable] 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); | ^~~~ input-blc.c: In function ‘input_BLC_parse_SampleSheet’: input-blc.c:1002:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1002 | entry[0] = NULL + lane_no; | ^ input-blc.c:1004:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1004 | entry[2] = NULL + stat1_line; // the N-th line in the file , 1 based | ^ input-blc.c: In function ‘iCache_write_supIdx_result’: input-blc.c:1126:53: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1126 | fprintf(ofp, "%s\t%d\n", (char*)ky, (int)(va-NULL)); | ^ input-blc.c: In function ‘iCache_copy_sample_table_2_list’: input-blc.c:1139:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1139 | push_arr[0] = NULL + lane_sample_int; | ^ input-blc.c:1140:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1140 | push_arr[1] = NULL + cbclist -> numOfElements+1; | ^ input-blc.c:1140:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1140 | push_arr[1] = NULL + cbclist -> numOfElements+1; | ^ input-blc.c: In function ‘iCache_get_cell_no’: input-blc.c:1171:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1171 | srInt_64 xint = xrawarr - NULL; | ^ input-blc.c:1182:77: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1182 | int bcno = ArrayListGet(rawarr, xx2)-NULL; | ^ input-blc.c:1185:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1185 | if(ArrayListGet(ret, xx3)==NULL+bcno){ | ^ input-blc.c:1191:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1191 | if(!found)ArrayListPush(ret, NULL+bcno); | ^ input-blc.c:1200:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1200 | int tbcn = ArrayListGet(ret,xx1)-NULL; | ^ input-blc.c: In function ‘iCache_delete_bcb_key’: input-blc.c:1218:15: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1218 | if(((k-NULL) & 0xFFFFFFFFF0000000llu)!= IMPOSSIBLE_MEMORY_ADDRESS) ArrayListDestroy(k); | ^ input-blc.c: In function ‘do_R_try_cell_barcode_files’: input-blc.c:1248:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1248 | argv[7]=NULL+rv; | ^ input-blc.c:1249:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1249 | argv[8]=NULL+tested_reads; | ^ input-blc.c:1250:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1250 | argv[9]=NULL+valid_sample_index; | ^ input-blc.c:1251:22: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1251 | argv[10]=NULL+valid_cell_barcode; | ^ input-blc.c: In function ‘cacheBCL_quality_test’: input-blc.c:1425:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1425 | HashTablePut(cell_barcode_table, strdup(bcbstr), NULL+IMPOSSIBLE_MEMORY_ADDRESS+xx1); | ^ input-blc.c:1425:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1425 | HashTablePut(cell_barcode_table, strdup(bcbstr), NULL+IMPOSSIBLE_MEMORY_ADDRESS+xx1); | ^ input-blc.c:1440:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1440 | ArrayListPush(array_of_codes, NULL+xx1); | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c input-files.c -o input-files.o input-files.c: In function ‘get_temp_file_pointer’: input-files.c:1536:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1536 | if(temp_file_pointer == NULL || temp_file_pointer == NULL + 1) { | ^ input-files.c:1550:64: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1550 | int maximum_open_file = fp_table -> appendix1 - NULL; | ^ input-files.c:1555:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1555 | HashTablePut(fp_table, key_name , NULL + 1); | ^ input-files.c: In function ‘my_fclose’: input-files.c:1565:28: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1565 | if(fp && fp != NULL+1) | ^ input-files.c: In function ‘add_cigar_indel_event’: input-files.c:1681:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1681 | int exist_indel_count = HashTableGet(event_table_ptr, event_token) - NULL; | ^ input-files.c:1688:85: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1688 | srInt_64 t64v = (HashTableGet(event_table_ptr, event_token)-NULL); | ^ input-files.c:1708:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1708 | memset(event_table_ptr->appendix2 + event_space_max_size * sizeof(short), 0, sizeof(short) * event_space_max_size); | ^ input-files.c:1718:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1718 | HashTablePut(event_table_ptr, token_1, NULL+1); | ^ input-files.c:1722:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1722 | HashTablePutReplace(event_table_ptr, event_token, NULL+exist_indel_count+1, 0); | ^ input-files.c:1722:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1722 | HashTablePutReplace(event_table_ptr, event_token, NULL+exist_indel_count+1, 0); | ^ input-files.c:1731:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1731 | HashTablePut(event_table_ptr, token_2, NULL + ((0xff & (0x80 + indels)) | ((indel_event_id_long&0xffffff) << 8))); | ^ input-files.c: In function ‘destroy_cigar_event_table’: input-files.c:1758:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1758 | srInt_64 tmpv = cursor -> value - NULL; | ^ input-files.c: In function ‘break_SAM_file’: input-files.c:1885:38: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1885 | fp_table -> appendix1 = NULL + max_open_file * 2/ 3; | ^ input-files.c: In function ‘SAM_pairer_create’: input-files.c:2609:22: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 2609 | old_sig_TERM = signal (SIGTERM, REPAIR_SIGINT_hook); | ^ input-files.c:2610:21: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 2610 | old_sig_INT = signal (SIGINT, REPAIR_SIGINT_hook); | ^ input-files.c: In function ‘SAM_pairer_destroy’: input-files.c:2699:26: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 2699 | signal (SIGTERM, old_sig_TERM); | ^~~~~~~~~~~~ In file included from input-files.c:21: /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ input-files.c:2700:25: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 2700 | signal (SIGINT, old_sig_INT); | ^~~~~~~~~~~ /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ input-files.c: In function ‘SAM_pairer_get_next_read_BIN’: input-files.c:3126:112: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3126 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c:3126:116: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3126 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c: In function ‘online_register_contig’: input-files.c:3169:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3169 | signed int refId = HashTableGet(pairer->sam_contig_number_table, ref) - NULL - 1; | ^ input-files.c:3176:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3176 | HashTablePut(pairer->sam_contig_number_table, mem_ref, NULL + refId + 1); | ^ input-files.c:3176:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3176 | HashTablePut(pairer->sam_contig_number_table, mem_ref, NULL + refId + 1); | ^ input-files.c: In function ‘reduce_SAM_to_BAM’: input-files.c:3228:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3228 | signed int refID = HashTableGet(pairer->sam_contig_number_table, ref) - NULL - 1; | ^ input-files.c:3252:86: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3252 | mate_refID = HashTableGet(pairer->sam_contig_number_table, mate_ref) - NULL - 1; | ^ input-files.c:3277:39: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 3277 | bin_tmp[bin_ptr ++] = 0xff; | ^~~~ input-files.c:3278:39: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 3278 | bin_tmp[bin_ptr ++] = 0xff; | ^~~~ input-files.c:3244:13: warning: unused variable ‘seq_len’ [-Wunused-variable] 3244 | int seq_len = qual - seq - 1; | ^~~~~~~ input-files.c: In function ‘SAM_pairer_make_dummy’: input-files.c:3683:37: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 3683 | out_bin2[36 + len_name+1] = 0xff; | ^~~~ input-files.c: In function ‘SAM_pairer_rescure_orphants_max_FP’: input-files.c:4236:43: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4236 | int thread_no = (int)(param_ptr[1]-NULL); | ^ input-files.c: In function ‘SAM_pairer_thread_run’: input-files.c:4523:43: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4523 | int thread_no = (int)(param_ptr[1]-NULL), is_disk_full = 0; | ^ input-files.c: In function ‘SAM_pairer_finish_margins’: input-files.c:4597:34: warning: wrong type argument to increment [-Wpointer-arith] 4597 | tab -> appendix2 ++; | ^~ input-files.c:4616:32: warning: wrong type argument to decrement [-Wpointer-arith] 4616 | }else tab -> appendix2 --; | ^~ input-files.c: In function ‘SAM_pairer_run_once’: input-files.c:4647:47: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4647 | init_params[1] = (void *)(NULL+x1); | ^ input-files.c:4668:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4668 | init_params[1] = (void *)(NULL+x1); | ^ input-files.c: In function ‘SAM_pairer_fix_format’: input-files.c:4863:50: warning: variable ‘readname’ set but not used [-Wunused-but-set-variable] 4863 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; | ^~~~~~~~ input-files.c: In function ‘SAM_nosort_thread_run’: input-files.c:5159:43: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5159 | int thread_no = (int)(param_ptr[1]-NULL); | ^ input-files.c: In function ‘SAM_nosort_run_once’: input-files.c:5271:47: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5271 | init_params[1] = (void *)(NULL+x1); | ^ input-files.c:5437:104: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5437 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c:5437:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5437 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c: In function ‘sort_SAM_create’: input-files.c:5678:22: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 5678 | old_sig_TERM = signal (SIGTERM, SAM_SORT_SIGINT_hook); | ^ input-files.c:5679:21: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 5679 | old_sig_INT = signal (SIGINT, SAM_SORT_SIGINT_hook); | ^ input-files.c: In function ‘sort_SAM_finalise’: input-files.c:5817:65: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 5817 | old_line_mem[0]=0xff; | ^~~~ input-files.c:6048:26: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 6048 | signal (SIGTERM, old_sig_TERM); | ^~~~~~~~~~~~ /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ input-files.c:6049:25: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 6049 | signal (SIGINT, old_sig_INT); | ^~~~~~~~~~~ /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c interval_merge.c -o interval_merge.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c long-hashtable.c -o long-hashtable.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c longread-mapping.c -o longread-mapping.o longread-mapping.c: In function ‘LRM_thread_runner’: longread-mapping.c:350:27: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 350 | int thid = argv[1]-NULL; | ^ longread-mapping.c:351:27: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 351 | int task = argv[2]-NULL; | ^ longread-mapping.c: In function ‘LRMstart_thread’: longread-mapping.c:391:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 391 | th_args[1] = NULL + th_id; | ^ longread-mapping.c:392:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 392 | th_args[2] = NULL + task; | ^ longread-mapping.c: In function ‘LRMis_gap_in_used_gap’: longread-mapping.c:636:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 636 | unsigned int used_start = LRMArrayListGet(iteration_context -> chain_used_gaps, xxi) - NULL; | ^ longread-mapping.c:637:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 637 | unsigned int used_end = LRMArrayListGet(iteration_context -> chain_used_gaps, xxi+1) - NULL; | ^ longread-mapping.c: In function ‘LRMbuild_chains’: longread-mapping.c:968:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 968 | LRMArrayListPush(iteration_context -> chain_used_gaps, NULL+this_gap_start_corr); | ^ longread-mapping.c:969:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 969 | LRMArrayListPush(iteration_context -> chain_used_gaps, NULL+this_gap_end_corr); | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mergeVCF.c -o mergeVCF.o mergeVCF.c: In function ‘do_find_common’: mergeVCF.c:219:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 219 | int repeat_times = HashTableGet(extra_count_table, ky) - NULL; | ^ mergeVCF.c:222:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 222 | HashTablePut(extra_count_table, ky, NULL+1); | ^ mergeVCF.c:225:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut(extra_qual_table, ky, NULL + qual + 1); | ^ mergeVCF.c:225:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut(extra_qual_table, ky, NULL + qual + 1); | ^ mergeVCF.c:235:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 235 | int repeat_times = HashTableGet(extra_count_table, ky) - NULL; | ^ mergeVCF.c:238:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 238 | int old_qual = HashTableGet(extra_qual_table, ky) - NULL - 1; | ^ mergeVCF.c:240:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 240 | HashTablePutReplace(extra_count_table, ky, NULL + repeat_times, 0); | ^ mergeVCF.c:251:104: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 251 | HashTablePutReplace(extra_qual_table, ky, NULL + 1 + qual, 0); | ^ mergeVCF.c:251:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 251 | HashTablePutReplace(extra_qual_table, ky, NULL + 1 + qual, 0); | ^ mergeVCF.c:277:54: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 277 | int counts = cursor -> value - NULL; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c processExons.c -o processExons.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c propmapped.c -o propmapped.o propmapped.c: In function ‘get_FP_by_read_name’: propmapped.c:248:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 248 | FILE * ret = HashTableGet(context -> split_fp_table, NULL+1+(int)(hash_key)); | ^ propmapped.c:248:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 248 | FILE * ret = HashTableGet(context -> split_fp_table, NULL+1+(int)(hash_key)); | ^ propmapped.c:258:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 258 | HashTablePut(context -> split_fp_table, NULL+1+(int)(hash_key), ret); | ^ propmapped.c:258:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 258 | HashTablePut(context -> split_fp_table, NULL+1+(int)(hash_key), ret); | ^ propmapped.c: In function ‘prop_PE’: propmapped.c:409:91: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 409 | int old_OK = HashTableGet(rname_table, read_name) - NULL; | ^ propmapped.c:416:98: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 416 | HashTablePut(rname_table, read_name, NULL+2); | ^ propmapped.c:419:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 419 | HashTablePut(rname_table, read_name, NULL + new_OK + 1); | ^ propmapped.c:419:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 419 | HashTablePut(rname_table, read_name, NULL + new_OK + 1); | ^ propmapped.c:435:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 435 | if(cursor -> value == NULL+2) context -> mapped_reads++; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c qualityScores.c -o qualityScores.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read-repair.c -o read-repair.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c readSummary.c -o readSummary.o readSummary.c: In function ‘load_feature_info’: readSummary.c:1260:134: warning: non-ISO-standard escape sequence, '\E' 1260 | SUBREADprintf("\Error: the feature on the %d-th line has zero coordinate or zero lengths\n\n", lineno); | ^ readSummary.c: In function ‘find_or_insert_gene_name’: readSummary.c:1409:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1409 | srInt_64 gene_number = HashTableGet(genetable, feature_name) - NULL; | ^ readSummary.c:1415:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1415 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ readSummary.c:1415:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1415 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ readSummary.c: In function ‘add_bin_new_tags’: readSummary.c:2644:47: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2644 | int intv = vals[tagi] - NULL; | ^ readSummary.c: In function ‘compress_read_detail_BAM’: readSummary.c:2706:38: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 2706 | bam_buf[9] = 0xff; // OS | ^~~~ readSummary.c: In function ‘write_read_details_FP’: readSummary.c:2799:29: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2799 | vals[1]=NULL+feature_count; | ^ readSummary.c: In function ‘warning_anno_BAM_chromosomes’: readSummary.c:2830:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2830 | HashTablePut(BAM_chro_tab, BAM_chro, NULL+1); | ^ readSummary.c:2838:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2838 | HashTablePut(ANNO_chro_tab, global_context -> exontable_chr[x1], NULL+1); | ^ readSummary.c: In function ‘add_fragment_supported_junction’: readSummary.c:3463:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3463 | srInt_64 count_junc = count_ptr - NULL; | ^ readSummary.c:3464:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3464 | HashTablePut(junction_counting_table, this_key, NULL+count_junc + 1); | ^ readSummary.c:3464:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3464 | HashTablePut(junction_counting_table, this_key, NULL+count_junc + 1); | ^ readSummary.c:3475:48: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3475 | count_junc = count_ptr - NULL; | ^ readSummary.c:3476:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3476 | HashTablePut(splicing_point_table, lr_key, NULL + count_junc + 1); | ^ readSummary.c:3476:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3476 | HashTablePut(splicing_point_table, lr_key, NULL + count_junc + 1); | ^ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3900:58: warning: variable ‘assignment_target_number’ set but not used [-Wunused-but-set-variable] 3900 | srInt_64 assignment_target_number = tmp_voter_id; | ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘fc_thread_merge_results’: readSummary.c:4046:93: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4046 | globval += (cursor -> value - NULL); | ^ readSummary.c:4046:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4046 | globval += (cursor -> value - NULL); | ^~ readSummary.c:4064:93: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4064 | globval += (cursor -> value - NULL); | ^ readSummary.c:4064:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4064 | globval += (cursor -> value - NULL); | ^~ readSummary.c:4123:69: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4123 | globval += (cursor -> value - NULL); | ^ readSummary.c:4123:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4123 | globval += (cursor -> value - NULL); | ^~ readSummary.c:4143:69: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4143 | globval += (cursor -> value - NULL); | ^ readSummary.c:4143:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4143 | globval += (cursor -> value - NULL); | ^~ readSummary.c:3970:32: warning: unused variable ‘sample_i’ [-Wunused-variable] 3970 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ readSummary.c: In function ‘determine_jcount_gene_transcript_report’: readSummary.c:5420:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5420 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ readSummary.c:5420:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5420 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ readSummary.c:5423:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5423 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5423:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5423 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5448:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5448 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ readSummary.c:5448:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5448 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ readSummary.c:5451:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5451 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5451:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5451 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5461:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5461 | int edge1_ptr = HashTableGet(edge1P1_table, edge1_txnid)-NULL; | ^ readSummary.c:5463:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5463 | int edge2_ptr = HashTableGet(edge2P1_table, edge1_txnid)-NULL; | ^ readSummary.c:5465:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5465 | int exonno_1 = HashTableGet(edge1exonNo_table, edge1_txnid)-NULL-1; | ^ readSummary.c:5466:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5466 | int exonno_2 = HashTableGet(edge2exonNo_table, edge1_txnid)-NULL-1; | ^ readSummary.c:5478:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5478 | HashTablePut(out_gene_tab, txnptr -> gene_name, NULL+1); | ^ readSummary.c:5479:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5479 | HashTablePut(out_txn_tab, txnptr -> transcript_id, NULL+1); | ^ readSummary.c:5510:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5510 | srInt_64 edge_dist = HashTableGet(this_side_olay_tab, this_side_txn_id)-NULL; | ^ readSummary.c:5513:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5513 | HashTablePut(this_side_reported_genes, txn_ptr -> gene_name, NULL+1); | ^ readSummary.c: In function ‘find_nearest_gene_dist’: readSummary.c:5603:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5603 | HashTablePut(gene_name_tab, gene_name, NULL+1); | ^ readSummary.c: In function ‘fc_write_final_junctions’: readSummary.c:5651:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5651 | unsigned int old_supp = HashTableGet(merged_splicing_table, ky) - NULL; | ^ readSummary.c:5652:62: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5652 | old_supp += (cursor -> value - NULL); | ^ readSummary.c:5653:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5653 | HashTablePut(merged_splicing_table, ky, NULL+old_supp); | ^ readSummary.c:5671:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5671 | HashTablePut(merged_junction_table, ky, NULL+1); | ^ readSummary.c:5831:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5831 | srInt_64 count = HashTableGet(junc_table, key_list[ky_i]) - NULL; | ^ readSummary.c:5724:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 5724 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ readSummary.c:5700:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5700:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5698:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 5698 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ readSummary.c: In function ‘readSummary’: readSummary.c:5971:52: warning: variable ‘scrna_total_BAM_no’ set but not used [-Wunused-but-set-variable] 5971 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; | ^~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3833:66: warning: ‘longest_overlap_score’ may be used uninitialized [-Wmaybe-uninitialized] 3833 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:3602:51: note: ‘longest_overlap_score’ was declared here 3602 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c removeDupReads.c -o removeDupReads.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sam2bed.c -o sam2bed.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sambam-file.c -o sambam-file.o sambam-file.c: In function ‘SamBam_writer_write_header’: sambam-file.c:1282:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1282 | char * chro_name = HashTableGet(writer -> chromosome_id_table, NULL + 1 + header_ptr); | ^ sambam-file.c:1282:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1282 | char * chro_name = HashTableGet(writer -> chromosome_id_table, NULL + 1 + header_ptr); | ^ sambam-file.c:1283:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1283 | unsigned int chro_len = HashTableGet(writer -> chromosome_len_table, NULL + 1 + header_ptr) - NULL - 1; | ^ sambam-file.c:1283:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1283 | unsigned int chro_len = HashTableGet(writer -> chromosome_len_table, NULL + 1 + header_ptr) - NULL - 1; | ^ sambam-file.c:1283:109: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1283 | unsigned int chro_len = HashTableGet(writer -> chromosome_len_table, NULL + 1 + header_ptr) - NULL - 1; | ^ sambam-file.c: In function ‘SamBam_writer_add_chromosome’: sambam-file.c:1408:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1408 | HashTablePut(writer -> chromosome_name_table, chro_name_space, NULL+1+chro_id); | ^ sambam-file.c:1408:78: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1408 | HashTablePut(writer -> chromosome_name_table, chro_name_space, NULL+1+chro_id); | ^ sambam-file.c:1409:57: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1409 | HashTablePut(writer -> chromosome_id_table, NULL+1+chro_id, chro_name_space); | ^ sambam-file.c:1409:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1409 | HashTablePut(writer -> chromosome_id_table, NULL+1+chro_id, chro_name_space); | ^ sambam-file.c:1410:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c:1410:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c:1410:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c:1410:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c: In function ‘SamBam_writer_add_read’: sambam-file.c:1746:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1746 | int refID = HashTableGet(writer -> chromosome_name_table, chro_name) - NULL - 1; | ^ sambam-file.c:1752:91: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1752 | nextRefID = HashTableGet(writer -> chromosome_name_table, next_chro_name) - NULL - 1; | ^ sambam-file.c: In function ‘SamBam_writer_sort_bins_to_BAM_test_bins’: sambam-file.c:1946:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1946 | ArrayListPush(win16k_list, NULL+ this_Vpos); | ^ sambam-file.c:1950:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1950 | ArrayList * this_bin_chunks = HashTableGet(bin_tab, NULL+binno+1); | ^ sambam-file.c:1950:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1950 | ArrayList * this_bin_chunks = HashTableGet(bin_tab, NULL+binno+1); | ^ sambam-file.c:1953:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1953 | HashTablePut(bin_tab, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:1953:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1953 | HashTablePut(bin_tab, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:1954:45: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1954 | ArrayListPush(bin_list, NULL+binno); | ^ sambam-file.c:1962:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1962 | diff -=(this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] - NULL)>>16; | ^ sambam-file.c:1964:101: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1964 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements -1] = NULL+this_Vpos + block_len+4; | ^ sambam-file.c:1964:112: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1964 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements -1] = NULL+this_Vpos + block_len+4; | ^ sambam-file.c:1964:123: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1964 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements -1] = NULL+this_Vpos + block_len+4; | ^ sambam-file.c:1972:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1972 | ArrayListPush(this_bin_chunks, NULL + this_Vpos); | ^ sambam-file.c:1973:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1973 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + block_len+4); | ^ sambam-file.c:1973:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1973 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + block_len+4); | ^ sambam-file.c:1973:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1973 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + block_len+4); | ^ sambam-file.c: In function ‘SamBam_writer_sorted_compress’: sambam-file.c:1981:37: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1981 | int this_thread_no = vptr[1]-NULL; | ^ sambam-file.c: In function ‘SamBam_thread_wait_merge_write’: sambam-file.c:2015:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2015 | HashTablePut(writer -> block_no_p1_to_vpos_tab, NULL+1+writer -> writer_threads[thread_no].bam_block_no, NULL+fpos); | ^ sambam-file.c:2015:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2015 | HashTablePut(writer -> block_no_p1_to_vpos_tab, NULL+1+writer -> writer_threads[thread_no].bam_block_no, NULL+fpos); | ^ sambam-file.c:2015:126: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2015 | HashTablePut(writer -> block_no_p1_to_vpos_tab, NULL+1+writer -> writer_threads[thread_no].bam_block_no, NULL+fpos); | ^ sambam-file.c: In function ‘SamBam_writer_merge_chunks’: sambam-file.c:2173:45: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2173 | ll[0] = ArrayListGet(chs, i)-NULL; | ^ sambam-file.c:2174:47: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2174 | ll[1] = ArrayListGet(chs, i+1)-NULL; | ^ sambam-file.c:2181:32: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2181 | ArrayListPush(chs, NULL+ll0[0]); | ^ sambam-file.c:2182:32: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2182 | ArrayListPush(chs, NULL+ll0[1]); | ^ sambam-file.c:2185:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2185 | long long last_end = ArrayListGet(chs, chs -> numOfElements-1) -NULL; | ^ sambam-file.c:2192:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2192 | chs-> elementList[chs -> numOfElements-1] = NULL+max(ll_this[1],last_end); | ^ sambam-file.c:2194:48: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2194 | ArrayListPush(chs, NULL+ll_this[0]); | ^ sambam-file.c:2195:48: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2195 | ArrayListPush(chs, NULL+ll_this[1]); | ^ sambam-file.c: In function ‘SamBam_writer_optimize_bins_level’: sambam-file.c:2211:53: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2211 | int binno = ArrayListGet(bin_arr, i)-NULL; | ^ sambam-file.c:2213:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2213 | ArrayList * old_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2213:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2213 | ArrayList * old_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2215:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2215 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(old_bin_arr)); | ^ sambam-file.c:2215:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2215 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(old_bin_arr)); | ^ sambam-file.c:2216:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2216 | ArrayListPush(new_arrs, NULL+binno); | ^ sambam-file.c:2224:53: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2224 | int binno = ArrayListGet(bin_arr, i)-NULL; | ^ sambam-file.c:2226:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2226 | ArrayList * small_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2226:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2226 | ArrayList * small_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2233:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2233 | long long this_start = ArrayListGet(small_bin_arr, j)-NULL; | ^ sambam-file.c:2234:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2234 | long long this_end = ArrayListGet(small_bin_arr, j+1)-NULL; | ^ sambam-file.c:2243:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2243 | ArrayList * parent_bin_arr = HashTableGet(new_tab, NULL+1+parent_binno); | ^ sambam-file.c:2243:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2243 | ArrayList * parent_bin_arr = HashTableGet(new_tab, NULL+1+parent_binno); | ^ sambam-file.c:2246:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2246 | HashTablePut(new_tab, NULL+1+parent_binno, parent_bin_arr); | ^ sambam-file.c:2246:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2246 | HashTablePut(new_tab, NULL+1+parent_binno, parent_bin_arr); | ^ sambam-file.c:2247:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2247 | ArrayListPush(new_arrs, NULL+parent_binno); | ^ sambam-file.c:2253:51: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2253 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(small_bin_arr)); | ^ sambam-file.c:2253:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2253 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(small_bin_arr)); | ^ sambam-file.c:2254:54: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2254 | ArrayListPush(new_arrs, NULL + binno); | ^ sambam-file.c:2260:54: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2260 | int binno = ArrayListGet(new_arrs, i)-NULL; | ^ sambam-file.c:2262:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2262 | ArrayList * large_bin_arr = HashTableGet(new_tab, NULL+1+binno); | ^ sambam-file.c:2262:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2262 | ArrayList * large_bin_arr = HashTableGet(new_tab, NULL+1+binno); | ^ sambam-file.c: In function ‘SamBam_write_BAI_for_1chr’: sambam-file.c:2317:60: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2317 | int bin_no = ArrayListGet(*bins_list, bini)-NULL; | ^ sambam-file.c:2318:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2318 | ArrayList * chunks_list = HashTableGet(*bin_chunks_table, NULL+ bin_no+1); | ^ sambam-file.c:2318:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2318 | ArrayList * chunks_list = HashTableGet(*bin_chunks_table, NULL+ bin_no+1); | ^ sambam-file.c:2325:84: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2325 | long long int Voff_st = ArrayListGet(chunks_list, chunk_i) - NULL; | ^ sambam-file.c:2326:86: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2326 | long long int Voff_en = ArrayListGet(chunks_list, chunk_i+1) - NULL; | ^ sambam-file.c:2298:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2327:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2327 | SAMBAM_Block2Vpos(Voff_st); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2327:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2327 | SAMBAM_Block2Vpos(Voff_st); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2327:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2327 | SAMBAM_Block2Vpos(Voff_st); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2328:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2328 | SAMBAM_Block2Vpos(Voff_en); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2328:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2328 | SAMBAM_Block2Vpos(Voff_en); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2328:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2328 | SAMBAM_Block2Vpos(Voff_en); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2336:72: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2336 | long long int Voff = ArrayListGet(*win16k_list , bini) - NULL; | ^ sambam-file.c:2298:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2337:17: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2337 | SAMBAM_Block2Vpos(Voff); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2337:17: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2337 | SAMBAM_Block2Vpos(Voff); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2337:17: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2337 | SAMBAM_Block2Vpos(Voff); | ^~~~~~~~~~~~~~~~~ sambam-file.c: In function ‘SamBam_writer_sort_bins_to_BAM’: sambam-file.c:2397:35: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2397 | thparam[1] = NULL + thread_i; | ^ sambam-file.c: In function ‘simple_bam_writer_update_index’: sambam-file.c:2531:107: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2531 | struct simple_bam_writer_index_per_chro * index_chro = HashTableGet(writer -> index_per_chro, NULL+chro_no+1); | ^ sambam-file.c:2531:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2531 | struct simple_bam_writer_index_per_chro * index_chro = HashTableGet(writer -> index_per_chro, NULL+chro_no+1); | ^ sambam-file.c:2534:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2534 | HashTablePut(writer -> index_per_chro, NULL+chro_no+1, index_chro); | ^ sambam-file.c:2534:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2534 | HashTablePut(writer -> index_per_chro, NULL+chro_no+1, index_chro); | ^ sambam-file.c:2546:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2546 | ArrayListPush(win16k_list, NULL+ this_Vpos); | ^ sambam-file.c:2549:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2549 | ArrayList * this_bin_chunks = HashTableGet(index_chro -> index_binP1_table, NULL+binno+1); | ^ sambam-file.c:2549:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2549 | ArrayList * this_bin_chunks = HashTableGet(index_chro -> index_binP1_table, NULL+binno+1); | ^ sambam-file.c:2552:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2552 | HashTablePut(index_chro -> index_binP1_table, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:2552:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2552 | HashTablePut(index_chro -> index_binP1_table, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:2553:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2553 | ArrayListPush(index_chro -> index_binP0_list, NULL+binno); | ^ sambam-file.c:2560:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2560 | diff -=(this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] - NULL)>>16; | ^ sambam-file.c:2562:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2562 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] = NULL+this_Vpos + binlen + 4; | ^ sambam-file.c:2562:113: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2562 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] = NULL+this_Vpos + binlen + 4; | ^ sambam-file.c:2562:122: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2562 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] = NULL+this_Vpos + binlen + 4; | ^ sambam-file.c:2568:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2568 | ArrayListPush(this_bin_chunks, NULL + this_Vpos); | ^ sambam-file.c:2569:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2569 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + binlen+4); | ^ sambam-file.c:2569:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2569 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + binlen+4); | ^ sambam-file.c:2569:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2569 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + binlen+4); | ^ sambam-file.c: In function ‘simple_bam_write_compressed_block’: sambam-file.c:2574:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2574 | if(block_number >= 0)HashTablePut(writer -> bam_blockP1_to_offset0B_table, NULL+1+block_number, NULL+ftello(writer -> bam_FP)); | ^ sambam-file.c:2574:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2574 | if(block_number >= 0)HashTablePut(writer -> bam_blockP1_to_offset0B_table, NULL+1+block_number, NULL+ftello(writer -> bam_FP)); | ^ sambam-file.c:2574:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2574 | if(block_number >= 0)HashTablePut(writer -> bam_blockP1_to_offset0B_table, NULL+1+block_number, NULL+ftello(writer -> bam_FP)); | ^ sambam-file.c: In function ‘simple_bam_write’: sambam-file.c:2591:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2591 | bin += concatinate_binlen; | ^~ sambam-file.c: In function ‘simple_bam_close’: sambam-file.c:2635:113: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2635 | struct simple_bam_writer_index_per_chro *this_idx = HashTableGet(writer -> index_per_chro , NULL+1+chri); | ^ sambam-file.c:2635:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2635 | struct simple_bam_writer_index_per_chro *this_idx = HashTableGet(writer -> index_per_chro , NULL+1+chri); | ^ sambam-file.c:2647:93: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2647 | int binno = ArrayListGet(this_idx -> index_binP0_list, bini)-NULL; | ^ sambam-file.c:2648:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2648 | ArrayList * bingaps = HashTableGet(this_idx -> index_binP1_table, NULL+1+binno); | ^ sambam-file.c:2648:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2648 | ArrayList * bingaps = HashTableGet(this_idx -> index_binP1_table, NULL+1+binno); | ^ sambam-file.c:2653:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2653 | srInt_64 rposone, vposone = ArrayListGet(bingaps , gapi)-NULL; | ^ sambam-file.c:2625:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2654:41: note: in expansion of macro ‘vpos_to_rpos’ 2654 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:117: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2654:41: note: in expansion of macro ‘vpos_to_rpos’ 2654 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:134: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2654:41: note: in expansion of macro ‘vpos_to_rpos’ 2654 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2661:106: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2661 | srInt_64 rposone, vposone = ArrayListGet(this_idx -> win16k_list , bini )-NULL; | ^ sambam-file.c:2625:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2662:33: note: in expansion of macro ‘vpos_to_rpos’ 2662 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:117: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2662:33: note: in expansion of macro ‘vpos_to_rpos’ 2662 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:134: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2662:33: note: in expansion of macro ‘vpos_to_rpos’ 2662 | vpos_to_rpos; | ^~~~~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seek-zlib.c -o seek-zlib.o seek-zlib.c: In function ‘seekgz_open’: seek-zlib.c:136:45: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘139’ to ‘-117’ [-Woverflow] 136 | fp -> in_zipped_buffer[1] = 0x8b; | ^~~~ seek-zlib.c: In function ‘seekgz_load_1_block’: seek-zlib.c:327:75: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 327 | int zipped_data_used = (void *)fp -> stem.next_in - old_next_in; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sorted-hashtable.c -o sorted-hashtable.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sublog.c -o sublog.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.22.1\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tx-unique.c -o tx-unique.o tx-unique.c: In function ‘txunique_process_gene_chro’: tx-unique.c:292:101: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 292 | int old_all_bases = HashTableGet(context -> result_table, hash_key) - NULL; | ^ tx-unique.c:294:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 294 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + total_bases); | ^ tx-unique.c:294:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 294 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + total_bases); | ^ tx-unique.c:298:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 298 | old_all_bases = HashTableGet(context -> result_table, hash_key) - NULL; | ^ tx-unique.c:300:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 300 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + unique_bases); | ^ tx-unique.c:300:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 300 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + unique_bases); | ^ tx-unique.c: In function ‘txunique_process_write_gene’: tx-unique.c:320:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 320 | int all_bases = HashTableGet(context -> result_table, hash_key)-NULL-1; | ^ tx-unique.c:322:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 322 | int unique_bases = HashTableGet(context -> result_table, hash_key)-NULL-1; | ^ gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpkRzTMN/R.INSTALL3ccca511e0f370/Rsubread/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rsubread/00new/Rsubread/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsubread) * installing *source* package ‘ShortRead’ ... ** this is package ‘ShortRead’ version ‘1.66.0’ ** using staged installation checking for gcc... gcc-14 -std=gnu23 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-14 -std=gnu23 accepts -g... yes checking for gcc-14 -std=gnu23 option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc-14 -std=gnu23 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of unsigned long... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpuupozm/R.INSTALL3ccf376352f6c7/ShortRead/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_ShortRead.c -o R_init_ShortRead.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c alphabet.c -o alphabet.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c count.c -o count.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io.c -o io.o io.c: In function ‘read_prb_as_character’: io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=] 227 | error("could not read file '%f'", translateChar(STRING_ELT(fname, 0))); | ~^ | | | double | %s io.c: In function ‘_read_solexa_export_file’: io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 658 | error("invalid 'strand' field '%s', %s:%d", | ~^ | | | char * | %d 659 | *elt[13], fname, lineno); | ~~~~~~~~ | | | int io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 676 | error("invalid 'filtering' field '%s', %s:%d", | ~^ | | | char * | %d 677 | *elt[21], fname, lineno); | ~~~~~~~~ | | | int gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_bowtie.c -o io_bowtie.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_soap.c -o io_soap.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’: readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35 | (void) fread( seq_name, sizeof(char), name_len, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | (void) fread( &seq_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_maq_map.cc -o read_maq_map.o In file included from read_maq_map.cc:13: maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sampler.c -o sampler.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trim.c -o trim.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util.c -o util.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c xsnap.c -o xsnap.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpuupozm/R.INSTALL3ccf376352f6c7/ShortRead/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ShortRead/00new/ShortRead/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ShortRead) * installing *source* package ‘Rfastp’ ... ** this is package ‘Rfastp’ version ‘1.18.0’ ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqxhOqi/R.INSTALL3ccca36e3e60c/Rfastp/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c main_fastp.cpp -o main_fastp.o In file included from main_fastp.cpp:9: FASTP/util.h: In function ‘std::string reverse(const std::string&)’: FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos >&, bool, bool)’: FASTP/adaptertrimmer.cpp:58:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 58 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos, long int>&, int)’: FASTP/evaluator.cpp:108:25: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 108 | if(seq.length() >= seqlen-1) { | ~~~~~~~~~~~~~^~~~~~~~~~~ FASTP/evaluator.cpp:74:10: warning: variable ‘reachedEOF’ set but not used [-Wunused-but-set-variable] 74 | bool reachedEOF = false; | ^~~~~~~~~~ FASTP/evaluator.cpp: In member function ‘std::string Evaluator::evalAdapterAndReadNumDepreciated(long int&)’: FASTP/evaluator.cpp:304:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 304 | if(counts[i] >= repeatReq) { | ~~~~~~~~~~^~~~~~~~~~~~ FASTP/evaluator.cpp:308:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 308 | for(int s=0; s >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 336 | for(int i=0; isecond > largest) { | ~~~~~~~~~~~~~^~~~~~~~~ FASTP/evaluator.cpp: In member function ‘std::string Evaluator::evalAdapterAndReadNum(long int&, bool)’: FASTP/evaluator.cpp:479:21: warning: unused variable ‘data’ [-Wunused-variable] 479 | const char* data = r->mSeq.mStr.c_str(); | ^~~~ FASTP/evaluator.cpp:549:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 549 | for(int s=0; smSeq.mStr.c_str(); | ^~~~ FASTP/evaluator.cpp:601:21: warning: unused variable ‘data’ [-Wunused-variable] 601 | const char* data = r->mSeq.mStr.c_str(); | ^~~~ FASTP/evaluator.cpp: In static member function ‘static std::string Evaluator::matchKnownAdapter(std::string)’: FASTP/evaluator.cpp:643:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 643 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 643 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos >&, std::string, int)’: FASTP/filter.cpp:239:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 239 | for(int i=0; i&)’: FASTP/filterresult.cpp:43:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 43 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 75 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 45 | for(int i=0; ichildren[base] == NULL) { | ^~~~ FASTP/nucleotidetree.cpp:50:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | curNode->children[base] = new NucleotideNode(); | ^~~~ FASTP/nucleotidetree.cpp:51:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | curNode->children[base]->base = seq[i]; | ^~~~ FASTP/nucleotidetree.cpp:53:27: warning: array subscript has type ‘char’ [-Wchar-subscripts] 53 | curNode->children[base]->count++; | ^~~~ FASTP/nucleotidetree.cpp:54:37: warning: array subscript has type ‘char’ [-Wchar-subscripts] 54 | curNode = curNode->children[base]; | ^~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FASTP/options.cpp -o FASTP/options.o In file included from FASTP/options.cpp:4: FASTP/util.h: In function ‘std::string reverse(const std::string&)’: FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 360 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 376 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 406 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 417 | for(int i=0; i > Options::makeListFromFileByLine(std::string)’: FASTP/options.cpp:486:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 486 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 41 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 120 | for(int q=0;q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 21 | for(int c=0;c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 313 | for(int p = i; p < seq.length() + i && p < mEvaluatedSeqLen; p++) { | ~~^~~~~~~~~~~~~~~~~~ FASTP/stats.cpp: In member function ‘void Stats::reportHtmlORA(std::ofstream&, std::string, std::string)’: FASTP/stats.cpp:551:9: warning: unused variable ‘displayed’ [-Wunused-variable] 551 | int displayed = 0; | ^~~~~~~~~ FASTP/stats.cpp: In member function ‘void Stats::reportHtmlContents(std::ofstream&, std::string, std::string)’: FASTP/stats.cpp:850:35: warning: array subscript has type ‘char’ [-Wchar-subscripts] 850 | count = mBaseContents[b]; | ^ FASTP/stats.cpp: In static member function ‘static Stats* Stats::merge(std::vector&)’: FASTP/stats.cpp:888:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 888 | for(int t=0; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 898 | for(int t=0; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 96 | while(num.size() < mOptions->split.digits) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from FASTP/writer.h:11, from FASTP/threadconfig.h:9, from FASTP/threadconfig.cpp:1: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: ‘FAILED_TYPES’ defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FASTP/umiprocessor.cpp -o FASTP/umiprocessor.o FASTP/umiprocessor.cpp: In member function ‘void UmiProcessor::addUmiToName(Read*, std::string)’: FASTP/umiprocessor.cpp:70:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | for(int i=0; imName.length(); i++) { | ~^~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FASTP/unittest.cpp -o FASTP/unittest.o In file included from FASTP/evaluator.h:8, from FASTP/unittest.cpp:12: FASTP/util.h: In function ‘std::string reverse(const std::string&)’: FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(int pos=0; pos= 4.0.0), shiny (>= 1.5.0) Imports: assertthat, stringr, glue (>= 1.4.0), magrittr, shinytoastr, shinyAce, htmltools, utils, R6, crayon Timings: user system elapsed spsComps 31.442 3.688 49.632 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 2 2 Check results summary: spsComps ... OK rdepends_batchLLM ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_inDAGO ... OK rdepends_Spectran ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_vvshiny ... OK