############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL affyPLM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘affyPLM’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c LESN.c -o LESN.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c SCAB.c -o SCAB.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c common_types.c -o common_types.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o do_PLMrlm.c: In function ‘do_PLM_rlm’: do_PLMrlm.c:620:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 620 | int first_ind; | ^~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o do_PLMrma.c: In function ‘do_PLMrma’: do_PLMrma.c:209:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 209 | int first_ind; | ^~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o do_PLMthreestep.c: In function ‘do_PLMthreestep’: do_PLMthreestep.c:118:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 118 | int first_ind; | ^~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o idealmismatch.c: In function ‘IdealMM_correct_single’: idealmismatch.c:71:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 71 | int first_ind; | ^~~~~~~~~ idealmismatch.c: In function ‘SpecificBiweightCorrect_single’: idealmismatch.c:183:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 183 | int first_ind; | ^~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c preprocess.c -o preprocess.o preprocess.c: In function ‘pp_background’: preprocess.c:158:7: warning: variable ‘which_lesn’ set but not used [-Wunused-but-set-variable] 158 | int which_lesn; | ^~~~~~~~~~ preprocess.c: In function ‘pp_bothstages’: preprocess.c:677:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable] 677 | int rows,cols; | ^~~~ preprocess.c:677:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable] 677 | int rows,cols; | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c psi_fns.c -o psi_fns.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o qnorm_probeset.c: In function ‘qnorm_probeset_c’: qnorm_probeset.c:110:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 110 | int first_ind; | ^~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o rlm_PLM.c: In function ‘R_rlm_PLMset_c’: rlm_PLM.c:1481:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable] 1481 | int rows,cols; | ^~~~ rlm_PLM.c:1481:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable] 1481 | int rows,cols; | ^~~~ rlm_PLM.c: In function ‘rlm_PLMset_nameoutput’: rlm_PLM.c:868:25: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=] 868 | snprintf(tmp_str2,9,"%d",j+2); | ^~ rlm_PLM.c:868:24: note: directive argument in the range [2, 2147483647] 868 | snprintf(tmp_str2,9,"%d",j+2); | ^~~~ In file included from /usr/include/stdio.h:867, from /home/biocbuild/bbs-3.13-bioc/R/include/R.h:56, from preprocess.h:4, from rlm_PLM.c:71: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 9 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o rma_common.c: In function ‘median’: rma_common.c:60:7: warning: unused variable ‘i’ [-Wunused-variable] 60 | int i; | ^ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c scaling.c -o scaling.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep.c -o threestep.o threestep.c: In function ‘threestep_summary’: threestep.c:82:15: warning: variable ‘MM’ set but not used [-Wunused-but-set-variable] 82 | double *PM,*MM; | ^~ threestep.c: In function ‘R_threestep_c’: threestep.c:193:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable] 193 | int rows,cols; | ^~~~ threestep.c:193:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable] 193 | int rows,cols; | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o threestep_summary.c: In function ‘do_3summary’: threestep_summary.c:73:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 73 | int first_ind; | ^~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c transfns.c -o transfns.o gcc -shared -L/home/biocbuild/bbs-3.13-bioc/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/home/biocbuild/bbs-3.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lz -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-affyPLM/00new/affyPLM/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affyPLM)