oligo 1.16.2
Benilton Carvalho
| 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/oligo | | Last Changed Rev: 58369 / Revision: 59457 | | Last Changed Date: 2011-09-25 14:42:45 -0700 (Sun, 25 Sep 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 | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/oligo.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.16.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oligo' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* 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 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 'oligo' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c DABG.c -o DABG.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c LESN.c -o LESN.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_biweight.c -o PLM_biweight.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function 'gzread_one_xys':
ParserGzXYS.c:74:54: warning: unused variable 'token'
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c ParserXYS.c -o ParserXYS.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c SCAB.c -o SCAB.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c baseProfile.c -o baseProfile.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c basecontent.c -o basecontent.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c common_types.c -o common_types.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c do_PLMrma.c -o do_PLMrma.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c idealmismatch.c -o idealmismatch.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c lm_threestep.c -o lm_threestep.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c mas5calls.c -o mas5calls.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c matrix_functions.c -o matrix_functions.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c nthLargestPM.c -o nthLargestPM.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c preprocess.c -o preprocess.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c psi_fns.c -o psi_fns.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rlm_PLM.c -o rlm_PLM.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rlm_threestep.c -o rlm_threestep.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rma2.c -o rma2.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rma_PLM.c -o rma_PLM.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -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'
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c scaling.c -o scaling.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep.c -o threestep.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_PLM.c -o threestep_PLM.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_common.c -o threestep_common.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_summary.c -o threestep_summary.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c transfns.c -o transfns.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.8-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c trimmed.c -o trimmed.o
gcc -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o 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 ParserGzXYS.o ParserXYS.o SCAB.o baseProfile.o basecontent.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o mas5calls.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rma2.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 trimmed.o -lgfortran -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lRblas -lRzlib -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/oligo.Rcheck/oligo/libs/i386
** R
** inst
** preparing package for lazy loading
================================================================================
Welcome to oligoClasses version 1.14.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
Loading package bit1.1-7
package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Loading package ff2.2-3
- getOption("fftempdir")=="E:/biocbld/bbs-2.8-bioc/tmpdir/RtmpcJDJFP"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16095641.6 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==804782080 -- consider a different value for tuning your system
Creating a new generic function for "boxplot" in "oligo"
Creating a new generic function for "summary" in "oligo"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.14.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
================================================================================
Welcome to oligo version 1.16.2
================================================================================
* DONE (oligo)