downloading reverse dependencies ... downloading SpatialVx_1.0-3.tar.gz ... ok downloading CNVScope_3.7.2.tar.gz ... ok installing dependencies ‘BSgenome.Hsapiens.UCSC.hg19’, ‘distillery’, ‘GenomicInteractions’, ‘HiCseg’, ‘InteractionSet’, ‘jointseg’, ‘rslurm’, ‘smatr’, ‘smoothie’, ‘SpatialVx’, ‘turboEM’ Warning: package ‘HiCseg’ is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘AnnotationFilter’, ‘ProtGenerics’, ‘VariantAnnotation’, ‘ensembldb’, ‘biovizBase’, ‘acnr’, ‘Gviz’ begin installing package ‘AnnotationFilter’ begin installing package ‘ProtGenerics’ begin installing package ‘acnr’ begin installing package ‘VariantAnnotation’ begin installing package ‘smoothie’ begin installing package ‘smatr’ begin installing package ‘turboEM’ begin installing package ‘distillery’ begin installing package ‘InteractionSet’ begin installing package ‘rslurm’ begin installing package ‘BSgenome.Hsapiens.UCSC.hg19’ * installing *source* package ‘acnr’ ... ** package ‘acnr’ 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 (acnr) begin installing package ‘jointseg’ * installing *source* package ‘smoothie’ ... ** 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 (smoothie) * installing *source* package ‘rslurm’ ... ** package ‘rslurm’ 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 (rslurm) * installing *source* package ‘distillery’ ... ** package ‘distillery’ 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 (distillery) * installing *source* package ‘ProtGenerics’ ... ** package ‘ProtGenerics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘smooth’ in package ‘ProtGenerics’ ** 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 (ProtGenerics) * installing *source* package ‘smatr’ ... ** package ‘smatr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (smatr) * installing *source* package ‘turboEM’ ... ** package ‘turboEM’ successfully unpacked and MD5 sums checked ** 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 (turboEM) begin installing package ‘SpatialVx’ * installing *source* package ‘jointseg’ ... ** package ‘jointseg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfYGPOr/R.INSTALL3fee3136ded26e/jointseg/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c Heap.cpp -o Heap.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c Node.cpp -o Node.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c Rwrappers.cc -o Rwrappers.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c colibri.cc -o colibri.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c liste.cc -o liste.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o jointseg.so Heap.o Node.o Rwrappers.o colibri.o init.o liste.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfYGPOr/R.INSTALL3fee3136ded26e/jointseg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-jointseg/00new/jointseg/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 (jointseg) * installing *source* package ‘AnnotationFilter’ ... ** package ‘AnnotationFilter’ 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 (AnnotationFilter) begin installing package ‘ensembldb’ * installing *source* package ‘SpatialVx’ ... ** package ‘SpatialVx’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (SpatialVx) * installing *source* package ‘InteractionSet’ ... ** package ‘InteractionSet’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpj8MFCX/R.INSTALL3fed3c48b20520/InteractionSet/src' g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c box_bounds.cpp -o box_bounds.o box_bounds.cpp: In function ‘SEXPREC* get_box_bounds(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: box_bounds.cpp:10:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 10 | if (npts!=Adex.size()) { | ~~~~^~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c detect_overlaps.cpp -o detect_overlaps.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c init.cpp -o init.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c link_overlaps.cpp -o link_overlaps.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c overlap_utils.cpp -o overlap_utils.o g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o InteractionSet.so box_bounds.o detect_overlaps.o init.o link_overlaps.o overlap_utils.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpj8MFCX/R.INSTALL3fed3c48b20520/InteractionSet/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-InteractionSet/00new/InteractionSet/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 (InteractionSet) * installing *source* package ‘ensembldb’ ... ** package ‘ensembldb’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘.cds_for_id2’ in package ‘ensembldb’ ** 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 (ensembldb) * installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ... ** 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 (BSgenome.Hsapiens.UCSC.hg19) * installing *source* package ‘VariantAnnotation’ ... ** package ‘VariantAnnotation’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp34oYBt/R.INSTALL3fed28403c894b/VariantAnnotation/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o In file included from vcftype.h:8, from writevcf.h:4, from R_init_VariantAnnotation.c:3: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dna_hash.c -o dna_hash.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rle.c -o rle.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strhash.c -o strhash.o In file included from strhash.c:2: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ strhash.c:5:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 5 | khash_t(strhash) *_strhash_new() | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utilities.c -o utilities.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcffile.c -o vcffile.o In file included from vcftype.h:8, from vcffile.c:4: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ vcffile.c:22:27: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | static khash_t(WARNINGS) *vcfwarn_new() | ^~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcftype.c -o vcftype.o In file included from vcftype.h:8, from vcftype.c:1: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c writevcf.c -o writevcf.o In file included from vcftype.h:8, from writevcf.h:4, from writevcf.c:1: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp34oYBt/R.INSTALL3fed28403c894b/VariantAnnotation/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** 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 (VariantAnnotation) begin installing package ‘biovizBase’ * installing *source* package ‘biovizBase’ ... ** package ‘biovizBase’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpKEPvFV/R.INSTALL3ff10847781eb5/biovizBase/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_biovizBase.c -o R_init_biovizBase.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bin_offsets.c -o bin_offsets.o bin_offsets.c: In function ‘scan_bam_bin_offsets’: bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign] 57 | if (strncmp(b, "BAI\1", 4)) | ^ | | | Rbyte * {aka unsigned char *} In file included from /home/hornik/tmp/R-d-gcc-14/include/R_ext/RS.h:34, from /home/hornik/tmp/R-d-gcc-14/include/Rdefines.h:38, from bin_offsets.h:1, from bin_offsets.c:3: /usr/include/string.h:159:33: note: expected ‘const char *’ but argument is of type ‘Rbyte *’ {aka ‘unsigned char *’} 159 | extern int strncmp (const char *__s1, const char *__s2, size_t __n) | ~~~~~~~~~~~~^~~~ gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpKEPvFV/R.INSTALL3ff10847781eb5/biovizBase/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-biovizBase/00new/biovizBase/libs ** 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 ** 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 (biovizBase) begin installing package ‘Gviz’ * installing *source* package ‘Gviz’ ... ** package ‘Gviz’ successfully unpacked and MD5 sums checked ** 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 (Gviz) begin installing package ‘GenomicInteractions’ * installing *source* package ‘GenomicInteractions’ ... ** package ‘GenomicInteractions’ successfully unpacked and MD5 sums checked ** 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 (GenomicInteractions) checking smoothie_1.0-4.tar.gz ... checking SpatialVx_1.0-3.tar.gz ... checking CNVScope_3.7.2.tar.gz ... Depends: Package: smoothie Depends: R (>= 3.0.0) Timings: user system elapsed smoothie 15.252 2.476 19.54 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 0 2 Check results summary: smoothie ... NOTE * checking CRAN incoming feasibility ... [5s/6s] NOTE rdepends_CNVScope ... OK rdepends_SpatialVx ... OK