starting phase `separate-from-pid1' build process now running as PID 18 phase `separate-from-pid1' succeeded after 0.0 seconds starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/bin:/gnu/store/3b41as1rgymz766iv8pk7p34dma6blhi-pkg-config-0.29.2/bin:/gnu/store/x5nk7jclncdrrsjhpmjjfl2z9p36bxyw-tar-1.35/bin:/gnu/store/vcmbby8alqahhhd5qnidpf5pbvr102jl-gzip-1.14/bin:/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/bin:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/bin:/gnu/store/d7q1jypzi0hjx0gf2034yzljvapy7fvy-diffutils-3.12/bin:/gnu/store/3yky2jh15qsknnxnzplhj4by14sqmfig-patch-2.7.6/bin:/gnu/store/nfs39m8hsbx905q5kgjiw1irfrllkk00-findutils-4.10.0/bin:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/bin:/gnu/store/d4bzgx28m0640plahv0x3h5hxlh1npnj-zstd-1.5.6/bin:/gnu/store/5a3p82yj9nrj6rhk11f7b2sb84wirc2k-sed-4.9/bin:/gnu/store/1lkl6hik16bbhpjjsl825fivp2dsr9vi-grep-3.11/bin:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/bin:/gnu/store/pai3hvsiihllqi03b2198qi5qq9a28ga-coreutils-9.1/bin:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/bin:/gnu/store/k66i68s5l93n1lgxp29vn2292nsywp1v-bash-minimal-5.2.37/bin:/gnu/store/pazcfyngzb35khc8ad33dmsb22ibnl80-ld-wrapper-0/bin:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/bin:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/bin:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/bin:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/sbin' environment variable `R_LIBS_SITE' set to `/gnu/store/lkjb1szfgf6v21fvz6q5gqg29j0wy52m-r-affydata-1.58.0/site-library/:/gnu/store/skd84naha9a59xdwj1xakik4fhnqcyvc-r-hgu95av2cdf-2.18.0/site-library/:/gnu/store/f8api7j1mq7m24lfysiwvdii51alai4i-r-kernsmooth-2.23-26/site-library/:/gnu/store/ir1ic8a5hm72xl9443i3j42kwl1xgfpy-r-mass-7.3-65/site-library/:/gnu/store/s4my8lpcgqn1z7gdcphv62i4r86kgb87-r-affy-1.88.0/site-library/:/gnu/store/xjw20radl1iq2i3vpsbp0q5gljb4wx0c-r-biobase-2.70.0/site-library/:/gnu/store/sdj5l6nsmryiny677np532xgrglcdnyv-r-biocgenerics-0.56.0/site-library/:/gnu/store/5sr46cp63pp0fbfii6ghxc00dyilr5b9-r-gcrma-2.82.0/site-library/:/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/:/gnu/store/dy9maqhz2j30sxlqyfzmcdip5b8affic-r-annotationdbi-1.72.0/site-library/:/gnu/store/kr3jnx6i4hqjsis78y5k6yxcmv4dk0mg-r-biocmanager-1.30.27/site-library/:/gnu/store/cpa7hm7azzw51sqmd4wk29kd2w17xc5p-r-affyio-1.80.0/site-library/:/gnu/store/w00jbinxgx5v7z5613wny9fgq018is2n-r-generics-0.1.4/site-library/:/gnu/store/7kh1ffj8f7ny25zl8g0rjn7j753syqs2-r-xvector-0.50.0/site-library/:/gnu/store/svk0zr906zgz6js1908kv5rmsw7rwlv5-r-biostrings-2.78.0/site-library/:/gnu/store/y3aaf0ma5d5l71ql3wl6dsn3c4y107aa-r-s4vectors-0.48.0/site-library/:/gnu/store/8ihihn4kaw5m4smkw05fl2xpgw6a7gya-r-rsqlite-2.4.4/site-library/:/gnu/store/wf6j3xivhbl8ly9inrwj0ra7zqwjmdcx-r-keggrest-1.50.0/site-library/:/gnu/store/2q4bwl05zivrhr4n8vfia9pya2nsl9cn-r-iranges-2.44.0/site-library/:/gnu/store/0mb31xzvcryg597day75ka5f2wffc6xg-r-dbi-1.2.3/site-library/:/gnu/store/vgqm5vzr9hrbbxyky2f0icnvb0yxng23-r-seqinfo-1.0.0/site-library/:/gnu/store/k47c8nw7vi5m46v1kg7sjrvljji05svm-r-crayon-1.5.3/site-library/:/gnu/store/q83z93pn0nzi4agvdk6jdaihw1vdi773-r-rlang-1.1.6/site-library/:/gnu/store/lci33l959c09zsvizx8qlp0is9cbqk3n-r-plogr-0.2.0/site-library/:/gnu/store/n7lrqyp0svg4ym01sa5cnh4al7y24z3y-r-pkgconfig-2.0.3/site-library/:/gnu/store/pc957f56k611yjzbzn882g2zx1kf219j-r-memoise-2.0.1/site-library/:/gnu/store/7fg0wz6990m8bkyr9si3d7wfd0dhbqmg-r-cpp11-0.5.2/site-library/:/gnu/store/wdrbr9psr4gh43h4fnh672cpll5wgyaq-r-blob-1.2.4/site-library/:/gnu/store/qm2j3b1kbsx0dwiahnn3vgvniakgrs8w-r-bit64-4.6.0-1/site-library/:/gnu/store/m16jwklcpybccdrgnl6aqd5smdnkyx20-r-png-0.1-8/site-library/:/gnu/store/7p4mw408c5lxyrh8d0mlk5hm3q0jzisg-r-httr-1.4.7/site-library/:/gnu/store/6sxg655grm5wgf4zzdaiq0073b2aisbl-r-cachem-1.1.0/site-library/:/gnu/store/0bksakw9zj510isa7rp33hd72fh0g8nk-r-vctrs-0.6.5/site-library/:/gnu/store/kayf9ksnfkpmvp24ghm015xa6ihym1bm-r-bit-4.6.0/site-library/:/gnu/store/vlkp9qwd7k1jnzz34848h655m8ckx5f3-r-r6-2.6.1/site-library/:/gnu/store/2wlxc14l1bjgikbym0qs5vxf8lm07rxi-r-openssl-2.3.4/site-library/:/gnu/store/hpjmzyj8kad6ajvdxyhvrfw3ap7y48vp-r-mime-0.13/site-library/:/gnu/store/v775nkpib6sbz3q59yshrby71c5ykcp8-r-jsonlite-2.0.0/site-library/:/gnu/store/g9bxak7xss794pds4qfpafyfcn0cf53g-r-curl-7.0.0/site-library/:/gnu/store/rrawyx478p0bblrvfwgb5aqcg21nh29j-r-fastmap-1.2.0/site-library/:/gnu/store/2jm7igf1lhycvxmng0cf6ay06vh0f2ap-r-lifecycle-1.0.4/site-library/:/gnu/store/7k1d6dvd3634glwvargf1aa80brnyipr-r-glue-1.8.0/site-library/:/gnu/store/3vl9ljw22y3w64wf4vgm3z0a6kgr3x0v-r-cli-3.6.5/site-library/:/gnu/store/9gjbar7i1gw3jnmj775rik6dx6bqd1ax-r-askpass-1.2.1/site-library/:/gnu/store/7nwjxzbxpchxf4495z6s61jwq2a4j54w-r-sys-3.4.3/site-library/' environment variable `PKG_CONFIG_PATH' set to `/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/pkgconfig:/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/lib/pkgconfig:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/lib/pkgconfig:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/lib/pkgconfig' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include/c++:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include' environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include' environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include/c++:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include' environment variable `LIBRARY_PATH' set to `/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib:/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/lib:/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/lib:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/lib:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/lib:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/lib:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/lib:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/lib:/gnu/store/q1s19kv8bdq9ssfdgznzgkmfmj90vdfd-glibc-2.41-static/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/lib/locale' environment variable `TZDIR' unset phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'C.UTF-8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' affyPLM/CHANGELOG affyPLM/DESCRIPTION affyPLM/MD5 affyPLM/NAMESPACE affyPLM/R/ affyPLM/R/LESN.R affyPLM/R/PLMSet2exprSet.R affyPLM/R/PLMset.R affyPLM/R/ReadRMAExpress.R affyPLM/R/bg.correct.gcrma.R affyPLM/R/fitPLM.R affyPLM/R/init_fns.R affyPLM/R/internalfunctions.R affyPLM/R/normalize.exprSet.R affyPLM/R/normalize.scaling.R affyPLM/R/preprocess.R affyPLM/R/quantile_extensions.R affyPLM/R/rmaPLM.R affyPLM/R/threestep.R affyPLM/R/threestepPLM.R affyPLM/build/ affyPLM/build/vignette.rds affyPLM/inst/ affyPLM/inst/CITATION affyPLM/inst/doc/ affyPLM/inst/doc/AffyExtensions.R affyPLM/inst/doc/AffyExtensions.Rnw affyPLM/inst/doc/AffyExtensions.pdf affyPLM/inst/doc/MAplots.R affyPLM/inst/doc/MAplots.Rnw affyPLM/inst/doc/MAplots.pdf affyPLM/inst/doc/QualityAssess.R affyPLM/inst/doc/QualityAssess.Rnw affyPLM/inst/doc/QualityAssess.pdf affyPLM/inst/doc/ThreeStep.R affyPLM/inst/doc/ThreeStep.Rnw affyPLM/inst/doc/ThreeStep.pdf affyPLM/man/ affyPLM/man/MAplot.Rd affyPLM/man/PLMset-class.Rd affyPLM/man/PLMset2exprSet.Rd affyPLM/man/ReadRMAExpress.Rd affyPLM/man/affyPLM-internal.Rd affyPLM/man/bg.correct.LESN.Rd affyPLM/man/fitPLM.Rd affyPLM/man/normalize.exprSet.Rd affyPLM/man/normalize.quantiles.probeset.Rd affyPLM/man/normalize.scaling.Rd affyPLM/man/preprocess.Rd affyPLM/man/pseudo.Rd affyPLM/man/rmaPLM.Rd affyPLM/man/threestep.Rd affyPLM/man/threestepPLM.Rd affyPLM/src/ affyPLM/src/LESN.c affyPLM/src/LESN.h affyPLM/src/Makevars affyPLM/src/Makevars.win affyPLM/src/PLM_avg_log.c affyPLM/src/PLM_avg_log.h affyPLM/src/PLM_biweight.c affyPLM/src/PLM_biweight.h affyPLM/src/PLM_log_avg.c affyPLM/src/PLM_log_avg.h affyPLM/src/PLM_medianPM.c affyPLM/src/PLM_medianPM.h affyPLM/src/PLM_median_logPM.c affyPLM/src/PLM_median_logPM.h affyPLM/src/PLM_medianpolish.c affyPLM/src/PLM_medianpolish.h affyPLM/src/PLM_modelmatrix.c affyPLM/src/PLM_modelmatrix.h affyPLM/src/SCAB.c affyPLM/src/chipbackground.c affyPLM/src/common_types.c affyPLM/src/common_types.h affyPLM/src/do_PLMrlm.c affyPLM/src/do_PLMrlm.h affyPLM/src/do_PLMrma.c affyPLM/src/do_PLMrma.h affyPLM/src/do_PLMthreestep.c affyPLM/src/do_PLMthreestep.h affyPLM/src/dqrls.h affyPLM/src/idealmismatch.c affyPLM/src/idealmismatch.h affyPLM/src/lm_threestep.c affyPLM/src/lm_threestep.h affyPLM/src/matrix_functions.c affyPLM/src/matrix_functions.h affyPLM/src/nthLargestPM.c affyPLM/src/nthLargestPM.h affyPLM/src/preprocess.c affyPLM/src/preprocess.h affyPLM/src/psi_fns.c affyPLM/src/psi_fns.h affyPLM/src/qnorm_probeset.c affyPLM/src/qnorm_probeset.h affyPLM/src/read_rmaexpress.c affyPLM/src/rlm_PLM.c affyPLM/src/rlm_threestep.c affyPLM/src/rlm_threestep.h affyPLM/src/rmaPLM_pseudo.c affyPLM/src/rmaPLM_pseudo.h affyPLM/src/rma_PLM.c affyPLM/src/rma_common.c affyPLM/src/rma_common.h affyPLM/src/scaling.c affyPLM/src/scaling.h affyPLM/src/threestep.c affyPLM/src/threestep_PLM.c affyPLM/src/threestep_common.c affyPLM/src/threestep_common.h affyPLM/src/threestep_summary.c affyPLM/src/threestep_summary.h affyPLM/src/threestep_summary_methods.c affyPLM/src/threestep_summary_methods.h affyPLM/src/threestep_summary_methods_param.h affyPLM/src/transfns.c affyPLM/src/transfns.h affyPLM/tests/ affyPLM/tests/C_code_tests.R affyPLM/tests/PLM_tests.R affyPLM/tests/preprocess_tests.R affyPLM/tests/threestepPLM_tests.R affyPLM/vignettes/ affyPLM/vignettes/00Index.dcf affyPLM/vignettes/AffyExtensions.Rnw affyPLM/vignettes/AffyExtensions.bib affyPLM/vignettes/MAplots.Rnw affyPLM/vignettes/QualityAssess.Rnw affyPLM/vignettes/ThreeStep.Rnw affyPLM/vignettes/negresid.png affyPLM/vignettes/posresid.png affyPLM/vignettes/resid.png affyPLM/vignettes/weights.png phase `unpack' succeeded after 0.1 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' * installing *source* package ‘affyPLM’ ... ** this is package ‘affyPLM’ version ‘1.86.0’ ** package ‘affyPLM’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 14.3.0’ gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c LESN.c -o LESN.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c PLM_avg_log.c -o PLM_avg_log.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c PLM_biweight.c -o PLM_biweight.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c PLM_log_avg.c -o PLM_log_avg.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c PLM_medianPM.c -o PLM_medianPM.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c PLM_median_logPM.c -o PLM_median_logPM.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c PLM_medianpolish.c -o PLM_medianpolish.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c SCAB.c -o SCAB.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c chipbackground.c -o chipbackground.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c common_types.c -o common_types.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c do_PLMrlm.c -o do_PLMrlm.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c do_PLMrma.c -o do_PLMrma.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c do_PLMthreestep.c -o do_PLMthreestep.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c idealmismatch.c -o idealmismatch.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c lm_threestep.c -o lm_threestep.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c matrix_functions.c -o matrix_functions.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c nthLargestPM.c -o nthLargestPM.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c preprocess.c -o preprocess.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c psi_fns.c -o psi_fns.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c qnorm_probeset.c -o qnorm_probeset.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c read_rmaexpress.c -o read_rmaexpress.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c rlm_PLM.c -o rlm_PLM.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c rlm_threestep.c -o rlm_threestep.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c rma_PLM.c -o rma_PLM.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c rma_common.c -o rma_common.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c scaling.c -o scaling.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c threestep.c -o threestep.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c threestep_PLM.c -o threestep_PLM.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c threestep_common.c -o threestep_common.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c threestep_summary.c -o threestep_summary.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c threestep_summary_methods.c -o threestep_summary_methods.o gcc -std=gnu23 -I"/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/include" -DNDEBUG -I'/gnu/store/pdgck862qcvyr5b00lpagbc5ph08k3i8-r-preprocesscore-1.72.0/site-library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -c transfns.c -o transfns.o gcc -std=gnu23 -shared -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -L/usr/local/lib -o affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -lRlapack -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -lRblas -L/gnu/store/qysmiprwgpnly3fjjzbydm29fi85ijrf-gfortran-14.3.0-lib/lib/gcc/x86_64-unknown-linux-gnu/14.3.0 -L/gnu/store/qysmiprwgpnly3fjjzbydm29fi85ijrf-gfortran-14.3.0-lib/lib -lgfortran -lm -lquadmath -lz -L/gnu/store/271j3n302pz5dnrbs9ymp4hp295z22mq-r-minimal-4.5.2/lib/R/lib -lR installing to /gnu/store/7d4rb3q0yf51zrwgnyrhk0zi0bfb4mhg-r-affyplm-1.86.0/site-library/00LOCK-affyPLM/00new/affyPLM/libs ** R ** inst ** tests ** 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 (affyPLM) phase `install' succeeded after 24.2 seconds starting phase `check' Running specific tests for package ‘affyPLM’ Running ‘C_code_tests.R’ Running ‘PLM_tests.R’ Running ‘preprocess_tests.R’ Running ‘threestepPLM_tests.R’ Running vignettes for package ‘affyPLM’ Running ‘AffyExtensions.Rnw’ Running ‘MAplots.Rnw’ Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Running ‘QualityAssess.Rnw’ Running ‘ThreeStep.Rnw’ Warning messages: 1: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu95av2cdf’ 2: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu95av2cdf’ phase `check' succeeded after 209.1 seconds starting phase `patch-shebangs' phase `patch-shebangs' succeeded after 0.0 seconds starting phase `strip' phase `strip' succeeded after 0.0 seconds starting phase `validate-runpath' phase `validate-runpath' succeeded after 0.0 seconds starting phase `validate-documentation-location' phase `validate-documentation-location' succeeded after 0.0 seconds starting phase `delete-info-dir-file' phase `delete-info-dir-file' succeeded after 0.0 seconds starting phase `patch-dot-desktop-files' phase `patch-dot-desktop-files' succeeded after 0.0 seconds starting phase `make-dynamic-linker-cache' phase `make-dynamic-linker-cache' succeeded after 0.0 seconds starting phase `install-license-files' installing 0 license files from '.' phase `install-license-files' succeeded after 0.0 seconds starting phase `reset-gzip-timestamps' phase `reset-gzip-timestamps' succeeded after 0.0 seconds starting phase `compress-documentation' phase `compress-documentation' succeeded after 0.0 seconds