[ Started: 2022-04-26 16:41:34 ] cli (3.2.0 -> 3.3.0 ) [CRAN] ps (1.6.0 -> 1.7.0 ) [CRAN] rmarkdown (2.13 -> 2.14 ) [CRAN] parallelly (1.31.0 -> 1.31.1 ) [CRAN] future (1.24.0 -> 1.25.0 ) [CRAN] future.apply (1.8.1 -> 1.9.0 ) [CRAN] BiocManager (1.30.16 -> 1.30.17) [CRAN] testthat (3.1.3 -> 3.1.4 ) [CRAN] ridge (NA -> 3.3 ) [CRAN] Installing 9 packages: cli, ps, rmarkdown, parallelly, future, future.apply, BiocManager, testthat, ridge trying URL 'https://cloud.r-project.org/src/contrib/cli_3.3.0.tar.gz' Content type 'application/x-gzip' length 495823 bytes (484 KB) ================================================== downloaded 484 KB trying URL 'https://cloud.r-project.org/src/contrib/ps_1.7.0.tar.gz' Content type 'application/x-gzip' length 125455 bytes (122 KB) ================================================== downloaded 122 KB trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.14.tar.gz' Content type 'application/x-gzip' length 3241807 bytes (3.1 MB) ================================================== downloaded 3.1 MB trying URL 'https://cloud.r-project.org/src/contrib/parallelly_1.31.1.tar.gz' Content type 'application/x-gzip' length 121211 bytes (118 KB) ================================================== downloaded 118 KB trying URL 'https://cloud.r-project.org/src/contrib/future_1.25.0.tar.gz' Content type 'application/x-gzip' length 359794 bytes (351 KB) ================================================== downloaded 351 KB trying URL 'https://cloud.r-project.org/src/contrib/future.apply_1.9.0.tar.gz' Content type 'application/x-gzip' length 64200 bytes (62 KB) ================================================== downloaded 62 KB trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.17.tar.gz' Content type 'application/x-gzip' length 287948 bytes (281 KB) ================================================== downloaded 281 KB trying URL 'https://cloud.r-project.org/src/contrib/testthat_3.1.4.tar.gz' Content type 'application/x-gzip' length 700919 bytes (684 KB) ================================================== downloaded 684 KB trying URL 'https://cloud.r-project.org/src/contrib/ridge_3.3.tar.gz' Content type 'application/x-gzip' length 144986 bytes (141 KB) ================================================== downloaded 141 KB * installing *source* package ‘cli’ ... ** package ‘cli’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c ansi.c -o ansi.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c cleancall.c -o cleancall.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c diff.c -o diff.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c errors.c -o errors.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c md5.c -o md5.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress-altrep.c -o progress-altrep.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress.c -o progress.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c sha256.c -o sha256.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c thread.c -o thread.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c tty.c -o tty.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c utf8.c -o utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c win-utf8.c -o win-utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c winfiles.c -o winfiles.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o init.o md5.o progress-altrep.o progress.o sha256.o thread.o tty.o utf8.o win-utf8.o winfiles.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-cli/00new/cli/libs ** 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 ** 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 (cli) * installing *source* package ‘ps’ ... ** package ‘ps’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -std=gnu99 -Wall -pedantic -L/usr/local/lib -Wall px.c -o px gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c api-common.c -o api-common.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c common.c -o common.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c extra.c -o extra.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c dummy.c -o dummy.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c error-codes.c -o error-codes.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c posix.c -o posix.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c api-posix.c -o api-posix.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c linux.c -o linux.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c api-linux.c -o api-linux.o api-linux.c: In function ‘psll_get_cpu_aff’: api-linux.c:1139:9: warning: ‘pid’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1139 | if (sched_getaffinity(pid, setsize, mask) == 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o ps.so init.o api-common.o common.o extra.o dummy.o error-codes.o posix.o api-posix.o linux.o api-linux.o -L/opt/R-rc/lib/R/lib -lR installing via 'install.libs.R' to /home/omnipath/local/R/00LOCK-ps/00new/ps ** 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 (ps) * installing *source* package ‘rmarkdown’ ... ** package ‘rmarkdown’ 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 (rmarkdown) * installing *source* package ‘parallelly’ ... ** package ‘parallelly’ 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 (parallelly) * installing *source* package ‘BiocManager’ ... ** package ‘BiocManager’ 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 (BiocManager) * installing *source* package ‘ridge’ ... ** package ‘ridge’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... unsupported checking for gcc option to enable C99 features... none needed checking for gsl-config... /usr/bin/gsl-config checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for gsl/gsl_version.h... yes configure: creating ./config.status config.status: creating R/linearRidgeGenotypes.R config.status: creating R/linearRidgeGenotypesPredict.R config.status: creating R/logisticRidgeGenotypes.R config.status: creating R/logisticRidgeGenotypesPredict.R config.status: creating src/Makevars config.status: creating src/config.h ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c ReadInData.c -o ReadInData.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c commonFunctions.c -o commonFunctions.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c computeLinearRidge.c -o computeLinearRidge.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c computePvals.c -o computePvals.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c coordinateDescent.c -o coordinateDescent.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c linear.c -o linear.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c linearFunctions.c -o linearFunctions.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c logistic.c -o logistic.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c logisticFunctions.c -o logisticFunctions.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c registration.c -o registration.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c regression_wrapper_function.c -o regression_wrapper_function.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c ridgeRegressionFunctions.c -o ridgeRegressionFunctions.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c thin.c -o thin.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o ridge.so ReadInData.o commonFunctions.o computeLinearRidge.o computePvals.o coordinateDescent.o linear.o linearFunctions.o logistic.o logisticFunctions.o registration.o regression_wrapper_function.o ridgeRegressionFunctions.o thin.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-ridge/00new/ridge/libs ** R ** data ** 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 ** 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 (ridge) * installing *source* package ‘future’ ... ** package ‘future’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (future) * installing *source* package ‘testthat’ ... ** package ‘testthat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c reassign.c -o reassign.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -Wall -pedantic -c test-catch.cpp -o test-catch.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -Wall -pedantic -c test-example.cpp -o test-example.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -Wall -pedantic -c test-runner.cpp -o test-runner.o g++ -std=gnu++14 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o testthat.so init.o reassign.o test-catch.o test-example.o test-runner.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-testthat/00new/testthat/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 (testthat) * installing *source* package ‘future.apply’ ... ** package ‘future.apply’ 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 (future.apply) The downloaded source packages are in ‘/tmp/RtmpKIMaRG/downloaded_packages’ [ Finished: 2022-04-26 16:42:57 ]