downloading reverse dependencies ‘BIGDAWG’, ‘haplo.ccs’, ‘IFP’,
  ‘pould’, ‘SNPassoc’, ‘asymLD’, ‘gaawr2’, ‘gap’

trying URL 'file:///data/Repositories/CRAN/src/contrib/BIGDAWG_3.0.3.tar.gz'
trying URL 'file:///data/Repositories/CRAN/src/contrib/haplo.ccs_1.3.3.tar.gz'
trying URL 'file:///data/Repositories/CRAN/src/contrib/IFP_0.2.4.tar.gz'
trying URL 'file:///data/Repositories/CRAN/src/contrib/pould_1.0.1.tar.gz'
trying URL 'file:///data/Repositories/CRAN/src/contrib/SNPassoc_2.1-2.tar.gz'
trying URL 'file:///data/Repositories/CRAN/src/contrib/asymLD_0.1.tar.gz'
trying URL 'file:///data/Repositories/CRAN/src/contrib/gaawr2_0.0.5.tar.gz'
trying URL 'file:///data/Repositories/CRAN/src/contrib/gap_1.9.tar.gz'

installing dependencies ‘BIGDAWG’, ‘BLR’, ‘BradleyTerry2’, ‘DOT’,
  ‘EnsDb.Hsapiens.v75’, ‘ensembldb’, ‘genetics’, ‘GMMAT’,
  ‘haplo.stats’, ‘HardyWeinberg’, ‘httr’, ‘pedigree’, ‘pedigreemm’,
  ‘poisbinom’, ‘powerEQTL’, ‘regress’, ‘SNPassoc’,
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘valr’, ‘VariantAnnotation’

also installing the dependencies ‘AnnotationFilter’, ‘ProtGenerics’, ‘HaploSim’, ‘cpp11bigwig’

begin installing package ‘AnnotationFilter’
begin installing package ‘ProtGenerics’
begin installing package ‘HaploSim’
begin installing package ‘cpp11bigwig’
begin installing package ‘poisbinom’
begin installing package ‘httr’
begin installing package ‘BLR’
begin installing package ‘GMMAT’
begin installing package ‘HardyWeinberg’
begin installing package ‘powerEQTL’
begin installing package ‘regress’
begin installing package ‘BradleyTerry2’
begin installing package ‘DOT’
begin installing package ‘genetics’
begin installing package ‘pedigreemm’
begin installing package ‘haplo.stats’
* installing *source* package ‘DOT’ ...
** this is package ‘DOT’ version ‘0.1’
** package ‘DOT’ 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 (DOT)
* installing *source* package ‘regress’ ...
** this is package ‘regress’ version ‘1.3-22’
** package ‘regress’ 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 (regress)
* installing *source* package ‘powerEQTL’ ...
** this is package ‘powerEQTL’ version ‘0.3.6’
** package ‘powerEQTL’ 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 (powerEQTL)
* installing *source* package ‘BLR’ ...
** this is package ‘BLR’ version ‘1.6’
** package ‘BLR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpW2tqlG/R.INSTALLc5e05477a506c/BLR/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 init.c -o init.o
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 sample_betas.c -o sample_betas.o
gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o BLR.so init.o sample_betas.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpW2tqlG/R.INSTALLc5e05477a506c/BLR/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BLR/00new/BLR/libs
** R
** data
** demo
** 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
** 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 (BLR)
* installing *source* package ‘HaploSim’ ...
** this is package ‘HaploSim’ version ‘1.8.4.2’
** package ‘HaploSim’ 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 (HaploSim)
begin installing package ‘pedigree’
* installing *source* package ‘ProtGenerics’ ...
** this is package ‘ProtGenerics’ version ‘1.42.0’
** 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 ‘genetics’ ...
** this is package ‘genetics’ version ‘1.3.8.1.3’
** package ‘genetics’ 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 (genetics)
* installing *source* package ‘httr’ ...
** this is package ‘httr’ version ‘1.4.8’
** package ‘httr’ 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 (httr)
begin installing package ‘VariantAnnotation’
begin installing package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
* installing *source* package ‘BradleyTerry2’ ...
** this is package ‘BradleyTerry2’ version ‘1.1.3’
** package ‘BradleyTerry2’ 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 (BradleyTerry2)
* installing *source* package ‘pedigreemm’ ...
** this is package ‘pedigreemm’ version ‘0.3-5’
** package ‘pedigreemm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0Jg6yC/R.INSTALLc5e164f3f9c7e/pedigreemm/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 init.c -o init.o
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 pedigree.c -o pedigree.o
gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o pedigreemm.so init.o pedigree.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0Jg6yC/R.INSTALLc5e164f3f9c7e/pedigreemm/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pedigreemm/00new/pedigreemm/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** 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 (pedigreemm)
* installing *source* package ‘pedigree’ ...
** this is package ‘pedigree’ version ‘1.4.2’
** package ‘pedigree’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpTmtNIu/R.INSTALLc63741a19dacf/pedigree/src'
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Pedigree.cpp -o Pedigree.o
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 pedigree_init.c -o pedigree_init.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o pedigree.so Pedigree.o pedigree_init.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpTmtNIu/R.INSTALLc63741a19dacf/pedigree/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pedigree/00new/pedigree/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 (pedigree)
* installing *source* package ‘AnnotationFilter’ ...
** this is package ‘AnnotationFilter’ version ‘1.34.0’
** 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 ‘poisbinom’ ...
** this is package ‘poisbinom’ version ‘1.0.2’
** package ‘poisbinom’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp7UrHxt/R.INSTALLc5e02769db4ec/poisbinom/src'
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/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   -c RcppExports.cpp -o RcppExports.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -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++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/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   -c poisbinom.cpp -o poisbinom.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o poisbinom.so RcppExports.o init.o poisbinom.o -lfftw3 -lm -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp7UrHxt/R.INSTALLc5e02769db4ec/poisbinom/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-poisbinom/00new/poisbinom/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 (poisbinom)
* installing *source* package ‘haplo.stats’ ...
** this is package ‘haplo.stats’ version ‘1.9.8.2’
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOpSmfd/R.INSTALLc5e1421933170/haplo.stats/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 groupsum.c -o groupsum.o
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 haplo.stats_init.c -o haplo.stats_init.o
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 haplo_em_pin.c -o haplo_em_pin.o
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 louis_info.c -o louis_info.o
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 seqhap.c -o seqhap.o
gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o haplo.stats.so groupsum.o haplo.stats_init.o haplo_em_pin.o louis_info.o seqhap.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOpSmfd/R.INSTALLc5e1421933170/haplo.stats/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-haplo.stats/00new/haplo.stats/libs
** 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
** 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 (haplo.stats)
begin installing package ‘BIGDAWG’
begin installing package ‘SNPassoc’
* installing *source* package ‘cpp11bigwig’ ...
** this is package ‘cpp11bigwig’ version ‘0.1.3’
** package ‘cpp11bigwig’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1Xf0hK/R.INSTALLc5e0050e798d7/cpp11bigwig/src'
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cpp11.cpp -o cpp11.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cpp11bigwig.cpp -o cpp11bigwig.o
(cd libBigWig; make)
make[2]: Entering directory '/home/hornik/tmp/scratch/Rtmp1Xf0hK/R.INSTALLc5e0050e798d7/cpp11bigwig/src/libBigWig'
gcc -c -Wall -O3 -DNOCURL -fpic bwRead.c -o bwRead.o
gcc -c -Wall -O3 -DNOCURL -fpic bwStats.c -o bwStats.o
gcc -c -Wall -O3 -DNOCURL -fpic bwValues.c -o bwValues.o
gcc -c -Wall -O3 -DNOCURL -fpic bwWrite.c -o bwWrite.o
gcc -c -Wall -O3 -DNOCURL -fpic io.c -o io.o
ar rcs libBigWig.a bwRead.o bwStats.o bwValues.o bwWrite.o io.o
make[2]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1Xf0hK/R.INSTALLc5e0050e798d7/cpp11bigwig/src/libBigWig'
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o cpp11bigwig.so cpp11.o cpp11bigwig.o -L./libBigWig -lBigWig -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1Xf0hK/R.INSTALLc5e0050e798d7/cpp11bigwig/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-cpp11bigwig/00new/cpp11bigwig/libs
** 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
** 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 (cpp11bigwig)
begin installing package ‘valr’
* installing *source* package ‘HardyWeinberg’ ...
** this is package ‘HardyWeinberg’ version ‘1.7.9’
** package ‘HardyWeinberg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6X1NmS/R.INSTALLc5dfe4baf1584/HardyWeinberg/src'
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/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   -c HWxChromosomal.cpp -o HWxChromosomal.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/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   -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/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   -c SNPHWEX.cpp -o SNPHWEX.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/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   -c support.cpp -o support.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o HardyWeinberg.so HWxChromosomal.o RcppExports.o SNPHWEX.o support.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6X1NmS/R.INSTALLc5dfe4baf1584/HardyWeinberg/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-HardyWeinberg/00new/HardyWeinberg/libs
** 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
** 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 (HardyWeinberg)
* installing *source* package ‘SNPassoc’ ...
** this is package ‘SNPassoc’ version ‘2.1-2’
** package ‘SNPassoc’ 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 (SNPassoc)
* installing *source* package ‘BIGDAWG’ ...
** this is package ‘BIGDAWG’ version ‘3.0.3’
** package ‘BIGDAWG’ 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 (BIGDAWG)
* installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ...
** this is package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ version ‘3.22.1’
** 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 (TxDb.Hsapiens.UCSC.hg19.knownGene)
* installing *source* package ‘GMMAT’ ...
** this is package ‘GMMAT’ version ‘1.5.0’
** package ‘GMMAT’ successfully unpacked and MD5 sums checked
** using staged installation
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 g++-15 -std=gnu++20 accepts -g... yes
checking how to run the C++ preprocessor... g++-15 -std=gnu++20 -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 for ZSTD_decompress in -lzstd... yes
checking zstd.h usability... yes
checking zstd.h presence... yes
checking for zstd.h... yes
configure: Will use system-wide zstd library
checking for libdeflate_zlib_decompress in -ldeflate... yes
checking libdeflate.h usability... yes
checking libdeflate.h presence... yes
checking for libdeflate.h... yes
configure: Will use system-wide libdeflate library
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQfkfkh/R.INSTALLc5df917faaff4/GMMAT/src'
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fitglmm.cpp -o fitglmm.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o GMMAT.so fitglmm.o registerDynamicSymbol.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -lz -lbz2 -lzstd -ldeflate -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQfkfkh/R.INSTALLc5df917faaff4/GMMAT/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-GMMAT/00new/GMMAT/libs
** 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
** 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 (GMMAT)
* installing *source* package ‘ensembldb’ ...
** this is package ‘ensembldb’ version ‘2.34.0’
** 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)
begin installing package ‘EnsDb.Hsapiens.v75’
* installing *source* package ‘VariantAnnotation’ ...
** this is package ‘VariantAnnotation’ version ‘1.56.0’
** package ‘VariantAnnotation’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpIUYuW5/R.INSTALLc641562cd836c/VariantAnnotation/src'
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c IRanges_stubs.c -o IRanges_stubs.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c XVector_stubs.c -o XVector_stubs.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c dna_hash.c -o dna_hash.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c rle.c -o rle.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c strhash.c -o strhash.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c utilities.c -o utilities.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c vcffile.c -o vcffile.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c vcftype.c -o vcftype.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c writevcf.c -o writevcf.o
gcc-15 -shared -L/home/hornik/tmp/R/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/4.6/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIUYuW5/R.INSTALLc641562cd836c/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)
* installing *source* package ‘valr’ ...
** this is package ‘valr’ version ‘0.9.1’
** package ‘valr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpo2Jub3/R.INSTALLc66cf37b4d445/valr/src'
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bed12toexons.cpp -o bed12toexons.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c closest.cpp -o closest.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c complement.cpp -o complement.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c coverage.cpp -o coverage.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cpp11.cpp -o cpp11.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dist.cpp -o dist.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c flank.cpp -o flank.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c gcoverage.cpp -o gcoverage.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c intersect.cpp -o intersect.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c makewindows.cpp -o makewindows.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c merge.cpp -o merge.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c partition.cpp -o partition.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c random.cpp -o random.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c shuffle.cpp -o shuffle.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c subtract.cpp -o subtract.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o valr.so bed12toexons.o closest.o complement.o coverage.o cpp11.o dist.o flank.o gcoverage.o intersect.o makewindows.o merge.o partition.o random.o shuffle.o subtract.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpo2Jub3/R.INSTALLc66cf37b4d445/valr/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-valr/00new/valr/libs
** 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
** 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 (valr)
* installing *source* package ‘EnsDb.Hsapiens.v75’ ...
** this is package ‘EnsDb.Hsapiens.v75’ version ‘2.99.0’
** 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 (EnsDb.Hsapiens.v75)

checking haplo.stats_1.9.8.2.tar.gz ...
checking BIGDAWG_3.0.3.tar.gz ...
checking haplo.ccs_1.3.3.tar.gz ...
checking IFP_0.2.4.tar.gz ...
checking pould_1.0.1.tar.gz ...
checking SNPassoc_2.1-2.tar.gz ...
checking asymLD_0.1.tar.gz ...
checking gaawr2_0.0.5.tar.gz ...
checking gap_1.9.tar.gz ...

Depends:
Package: haplo.stats
  Depends: R (>= 4.4.0), methods, stats, graphics, arsenal
  Imports: rms

Timings:
              user system elapsed
haplo.stats 303.88 10.054 315.849

Results:
Check status summary:
                  NOTE OK
  Source packages    1  0
  Reverse depends    1  7

Check results summary:
haplo.stats ... NOTE
* checking CRAN incoming feasibility ... [4s/5s] NOTE
rdepends_asymLD ... OK
rdepends_BIGDAWG ... OK
rdepends_gaawr2 ... OK
rdepends_gap ... OK
rdepends_haplo.ccs ... OK
rdepends_IFP ... OK
rdepends_pould ... NOTE
* checking Rd files ... [0s/0s] NOTE
rdepends_SNPassoc ... OK

Check results changes:
Package: asymLD
Check: CRAN incoming feasibility
Old result: NOTE

Package: BIGDAWG
Check: CRAN incoming feasibility
Old result: NOTE

Package: IFP
Check: CRAN incoming feasibility
Old result: NOTE