installing dependencies ‘SeqArray’, ‘SeqVarTools’

also installing the dependency ‘GWASExactHW’

begin installing package ‘GWASExactHW’
begin installing package ‘SeqArray’
* installing *source* package ‘GWASExactHW’ ...
** this is package ‘GWASExactHW’ version ‘1.2’
** package ‘GWASExactHW’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-7) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLfP3FM/R.INSTALL1bd14925b073af/GWASExactHW/src'
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c SNPHWE.c -o SNPHWE.o
gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o GWASExactHW.so SNPHWE.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLfP3FM/R.INSTALL1bd14925b073af/GWASExactHW/src'
installing to /home/hornik/tmp/CRAN_special_noSuggests/Library/00LOCK-GWASExactHW/00new/GWASExactHW/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 (GWASExactHW)
* installing *source* package ‘SeqArray’ ...
** this is package ‘SeqArray’ version ‘1.50.0’
** package ‘SeqArray’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-7) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGNilAw/R.INSTALL1bd14747575148/SeqArray/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ConvToGDS.cpp -o ConvToGDS.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c FileMerge.cpp -o FileMerge.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GetData.cpp -o GetData.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Index.cpp -o Index.o
Index.cpp: In member function ‘void SeqArray::CProgress::ShowProgress()’:
Index.cpp:1273:66: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1273 |                                 if (R_Process_StatusFName.size() < *R_Process_Count) return;
      |                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Methods.cpp -o Methods.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_SeqArray.c -o R_SeqArray.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ReadBySample.cpp -o ReadBySample.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ReadByUnit.cpp -o ReadByUnit.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ReadByVariant.cpp -o ReadByVariant.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SeqArray.cpp -o SeqArray.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pkg_test.cpp -o pkg_test.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c samtools_ext.c -o samtools_ext.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DUSING_R -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c vectorization.cpp -o vectorization.o
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGNilAw/R.INSTALL1bd14747575148/SeqArray/src'
installing to /home/hornik/tmp/CRAN_special_noSuggests/Library/00LOCK-SeqArray/00new/SeqArray/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 (SeqArray)
begin installing package ‘SeqVarTools’
* installing *source* package ‘SeqVarTools’ ...
** this is package ‘SeqVarTools’ version ‘1.48.0’
** package ‘SeqVarTools’ 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 (SeqVarTools)

checking GMMAT_1.5.0.tar.gz ...

Depends:
Package: GMMAT
  Depends: R (>= 3.2.0)
  Imports: Rcpp, CompQuadForm, foreach, parallel, Matrix, methods,
    data.table
  LinkingTo: Rcpp, RcppArmadillo

Timings:
         user system elapsed
GMMAT 144.098  9.637 155.592

Results:
Check status summary:
                  NOTE
  Source packages    1

Check results summary:
GMMAT ... NOTE
* checking CRAN incoming feasibility ... [5s/5s] NOTE