affyPLM 1.34.0
Ben Bolstad
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/affyPLM | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/affyPLM.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'affyPLM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
show,PLMset: warning in ls(env = cdf.env): partial argument match of
'env' to 'envir'
* checking Rd files ... NOTE
prepare_Rd: MAplot.Rd:11-13: Dropping empty section \usage
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
threestep 30.421 1.388 32.260
fitPLM 16.986 1.289 18.573
PLMset2exprSet 12.760 0.426 13.529
preprocess 5.554 0.613 6.229
bg.correct.LESN 5.386 0.485 6.072
normalize.scaling 4.574 0.526 5.317
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'C_code_tests.R'
Running 'PLM_tests.R'
Running 'preprocess_tests.R'
Running 'threestepPLM_tests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/affyPLM.Rcheck/00check.log'
for details.
* installing *source* package 'affyPLM' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c LESN.c -o LESN.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c PLM_avg_log.c -o PLM_avg_log.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c PLM_biweight.c -o PLM_biweight.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c PLM_log_avg.c -o PLM_log_avg.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c PLM_medianPM.c -o PLM_medianPM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c SCAB.c -o SCAB.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c chipbackground.c -o chipbackground.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c common_types.c -o common_types.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c do_PLMrlm.c -o do_PLMrlm.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c do_PLMrma.c -o do_PLMrma.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c idealmismatch.c -o idealmismatch.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c lm_threestep.c -o lm_threestep.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c matrix_functions.c -o matrix_functions.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c nthLargestPM.c -o nthLargestPM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c preprocess.c -o preprocess.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c psi_fns.c -o psi_fns.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c qnorm_probeset.c -o qnorm_probeset.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c read_rmaexpress.c -o read_rmaexpress.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c rlm_PLM.c -o rlm_PLM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c rlm_threestep.c -o rlm_threestep.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c rma_PLM.c -o rma_PLM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60: warning: unused variable 'i'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c scaling.c -o scaling.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c threestep.c -o threestep.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c threestep_PLM.c -o threestep_PLM.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c threestep_common.c -o threestep_common.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c threestep_summary.c -o threestep_summary.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c transfns.c -o transfns.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/affyPLM.Rcheck/affyPLM/libs/i386
** 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
'AffyExtensions.Rnw'
'MAplots.Rnw'
'QualityAssess.Rnw'
'ThreeStep.Rnw'
** testing if installed package can be loaded
* DONE (affyPLM)