affyPLM 1.28.5
Ben Bolstad
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/affyPLM | | Last Changed Rev: 54886 / Revision: 59457 | | Last Changed Date: 2011-04-15 12:41:43 -0700 (Fri, 15 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ WARNINGS ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/affyPLM.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.28.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affyPLM' can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
doc 8.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: MAplot.Rd:11-13: Dropping empty section \usage
prepare_Rd: PLMset-class.Rd:171-172: Dropping empty section \examples
prepare_Rd: pseudo.Rd:37-39: Dropping empty section \examples
* 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 examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: MASS
* 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' ... WARNING
Package vignette(s) without corresponding PDF:
AffyExtensions.Rnw
MAplots.Rnw
QualityAssess.Rnw
ThreeStep.Rnw
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
'D:/biocbld/bbs-2.8-bioc/meat/affyPLM.Rcheck/00check.log'
for details
* installing *source* package 'affyPLM' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c LESN.c -o LESN.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c PLM_avg_log.c -o PLM_avg_log.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c PLM_biweight.c -o PLM_biweight.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c PLM_log_avg.c -o PLM_log_avg.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c PLM_medianPM.c -o PLM_medianPM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c PLM_median_logPM.c -o PLM_median_logPM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c PLM_medianpolish.c -o PLM_medianpolish.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c SCAB.c -o SCAB.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c chipbackground.c -o chipbackground.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c common_types.c -o common_types.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c do_PLMrlm.c -o do_PLMrlm.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c do_PLMrma.c -o do_PLMrma.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c do_PLMthreestep.c -o do_PLMthreestep.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c idealmismatch.c -o idealmismatch.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c lm_threestep.c -o lm_threestep.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c matrix_functions.c -o matrix_functions.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c nthLargestPM.c -o nthLargestPM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c preprocess.c -o preprocess.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c psi_fns.c -o psi_fns.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c qnorm_probeset.c -o qnorm_probeset.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c read_rmaexpress.c -o read_rmaexpress.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c rlm_PLM.c -o rlm_PLM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c rlm_threestep.c -o rlm_threestep.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c rma_PLM.c -o rma_PLM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60:7: warning: unused variable 'i'
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c scaling.c -o scaling.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c threestep.c -o threestep.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c threestep_PLM.c -o threestep_PLM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c threestep_common.c -o threestep_common.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c threestep_summary.c -o threestep_summary.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c threestep_summary_methods.c -o threestep_summary_methods.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"D:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O2 -Wall -std=gnu99 -c transfns.c -o transfns.o
x86_64-w64-mingw32-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 -lgfortran -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lRblas -lRzlib -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/affyPLM.Rcheck/affyPLM/libs/x64
** R
** inst
** preparing package for lazy loading
Creating a new generic function for "summary" in "affyPLM"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (affyPLM)