affyPLM 1.47.0
Ben Bolstad
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyPLM | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD INSTALL affyPLM
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* installing to library ‘/home/biocbuild/bbs-3.3-bioc/R/library’
* installing *source* package ‘affyPLM’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c preprocess.c -o preprocess.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c read_rmaexpress.c -o read_rmaexpress.o
read_rmaexpress.c: In function ‘gzfread_int32’:
read_rmaexpress.c:375:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(int)*n);
^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
read_rmaexpress.c: In function ‘gzfread_float64’:
read_rmaexpress.c:395:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(double)*n);
^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
read_rmaexpress.c: In function ‘gzfread_char’:
read_rmaexpress.c:412:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(char)*n);
^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
read_rmaexpress.c: In function ‘gz_read_rmaexpress_header’:
read_rmaexpress.c:456:15: warning: assignment from incompatible pointer type [enabled by default]
currentFile = gzopen(filename,mode);
^
read_rmaexpress.c: In function ‘gz_read_rmaexpress’:
read_rmaexpress.c:575:15: warning: assignment from incompatible pointer type [enabled by default]
currentFile = gzopen(filename,mode);
^
read_rmaexpress.c: In function ‘isCompressedRMAExpress’:
read_rmaexpress.c:719:15: warning: assignment from incompatible pointer type [enabled by default]
currentFile = gzopen(filename,mode);
^
read_rmaexpress.c:731:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(currentFile);
^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c rlm_PLM.c -o rlm_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c threestep.c -o threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c transfns.c -o transfns.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-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 -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRblas -lz -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/R/library/affyPLM/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘affyPLM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affyPLM)