Ben Bolstad
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/affyPLM |
| Branch: RELEASE_3_7 |
| Last Commit: 13dfc55 |
| Last Changed Date: 2018-04-30 10:34:58 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:31:57 -0400 (Wed, 17 Oct 2018).
| Package 28/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| affyPLM 1.56.0 Ben Bolstad
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: affyPLM |
| Version: 1.56.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/affyPLM_1.56.0.tar.gz && rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyPLM.buildbin-libdir affyPLM_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL affyPLM_1.56.0.zip && rm affyPLM_1.56.0.tar.gz affyPLM_1.56.0.zip |
| StartedAt: 2018-10-16 19:53:19 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 19:54:45 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 86.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/affyPLM_1.56.0.tar.gz && rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyPLM.buildbin-libdir affyPLM_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL affyPLM_1.56.0.zip && rm affyPLM_1.56.0.tar.gz affyPLM_1.56.0.zip
###
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install for i386
* installing *source* package 'affyPLM' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c LESN.c -o LESN.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_avg_log.c -o PLM_avg_log.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_biweight.c -o PLM_biweight.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_log_avg.c -o PLM_log_avg.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_medianPM.c -o PLM_medianPM.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_median_logPM.c -o PLM_median_logPM.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_medianpolish.c -o PLM_medianpolish.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_modelmatrix.c -o PLM_modelmatrix.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SCAB.c -o SCAB.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c common_types.c -o common_types.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
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]
int first_ind;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c lm_threestep.c -o lm_threestep.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c matrix_functions.c -o matrix_functions.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c nthLargestPM.c -o nthLargestPM.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
int which_lesn;
^
preprocess.c: In function 'pp_bothstages':
preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c psi_fns.c -o psi_fns.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_rmaexpress.c -o read_rmaexpress.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
int rows,cols;
^
rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rlm_threestep.c -o rlm_threestep.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rma_PLM.c -o rma_PLM.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
int i;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c scaling.c -o scaling.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
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]
int rows,cols;
^
threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c threestep_PLM.c -o threestep_PLM.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c threestep_common.c -o threestep_common.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c threestep_summary_methods.c -o threestep_summary_methods.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c transfns.c -o transfns.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o affyPLM.dll tmp.def 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 -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'affyPLM'
finding HTML links ... done
MAplot html
PLMset-class html
PLMset2exprSet html
ReadRMAExpress html
affyPLM-internal html
bg.correct.LESN html
fitPLM html
normalize.exprSet html
normalize.quantiles.probeset html
normalize.scaling html
preprocess html
pseudo html
rmaPLM html
threestep html
threestepPLM html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'affyPLM' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c LESN.c -o LESN.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_avg_log.c -o PLM_avg_log.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_biweight.c -o PLM_biweight.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_log_avg.c -o PLM_log_avg.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_medianPM.c -o PLM_medianPM.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_median_logPM.c -o PLM_median_logPM.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_medianpolish.c -o PLM_medianpolish.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_modelmatrix.c -o PLM_modelmatrix.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SCAB.c -o SCAB.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c common_types.c -o common_types.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
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]
int first_ind;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c lm_threestep.c -o lm_threestep.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c matrix_functions.c -o matrix_functions.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c nthLargestPM.c -o nthLargestPM.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
int which_lesn;
^
preprocess.c: In function 'pp_bothstages':
preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c psi_fns.c -o psi_fns.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_rmaexpress.c -o read_rmaexpress.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
int rows,cols;
^
rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rlm_threestep.c -o rlm_threestep.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rma_PLM.c -o rma_PLM.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
int i;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c scaling.c -o scaling.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
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]
int rows,cols;
^
threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c threestep_PLM.c -o threestep_PLM.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c threestep_common.c -o threestep_common.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]
int first_ind;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c threestep_summary_methods.c -o threestep_summary_methods.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c transfns.c -o transfns.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o affyPLM.dll tmp.def 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 -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyPLM' as affyPLM_1.56.0.zip
* DONE (affyPLM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'affyPLM' successfully unpacked and MD5 sums checked
In R CMD INSTALL