affyPLM 1.29.2
Ben Bolstad
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyPLM | | Last Changed Rev: 56151 / Revision: 56603 | | Last Changed Date: 2011-06-13 15:14:15 -0700 (Mon, 13 Jun 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | ERROR | skipped | skipped |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/affyPLM.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyPLM/DESCRIPTION’ ... OK
* this is package ‘affyPLM’ version ‘1.29.2’
* 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 installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
doc 6.1Mb
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package ‘affyPLM’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-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:60:7: warning: unused variable ‘i’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-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-2.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.9-bioc/R/lib -lRblas -lz -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/affyPLM.Rcheck/affyPLM/libs
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Creating a generic function for "summary" from package "base" in package “affyPLM”
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘AffyExtensions.Rnw’
‘MAplots.Rnw’
‘QualityAssess.Rnw’
‘ThreeStep.Rnw’
** testing if installed package can be loaded
* DONE (affyPLM)