affyPLM 1.20.0
Ben Bolstad
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/affyPLM | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/affyPLM.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.20.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affyPLM' can be installed ... 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 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 name space can be loaded with stated dependencies ... 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 ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 ... OK
* checking examples ... OK
* checking tests ...
Running 'C_code_tests.R'
Running 'PLM_tests.R'
Running 'preprocess_tests.R'
Running 'threestepPLM_tests.R'
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package 'affyPLM' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60: warning: unused variable 'i'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -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 -L/home/biocbuild/bbs-2.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.4-bioc/R/lib -lRblas -lz -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: Biostrings
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
cbind,
duplicated,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rank,
rbind,
rep.int,
sapply,
sort,
table,
unique
** help
*** installing help indices
>>> Building/Updating help pages for package 'affyPLM'
Formats: text html latex example
Note: removing empty section \usage in file 'MAplot.Rd'
MAplot text html latex
Note: removing empty section \examples in file 'PLMset-class.Rd'
PLMset-class text html latex
PLMset2exprSet text html latex example
ReadRMAExpress text html latex
affyPLM-internal text html latex
bg.correct.LESN text html latex example
fitPLM text html latex example
normalize.exprSet text html latex example
normalize.quantiles.probeset text html latex
normalize.scaling text html latex example
preprocess text html latex example
Note: removing empty section \examples in file 'pseudo.Rd'
pseudo text html latex
rmaPLM text html latex example
threestep text html latex example
threestepPLM text html latex example
** building package indices ...
* DONE (affyPLM)