oligo 1.20.0
Benilton Carvalho
| Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/oligo | | Last Changed Rev: 64678 / Revision: 64719 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| puck5 | Linux (Ubuntu 12.04) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/oligo.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMPI'
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 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 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 compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'doRUnit.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 was 1 note.
See
'/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/oligo.Rcheck/00check.log'
for details.
* installing *source* package 'oligo' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c DABG.c -o DABG.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c ParserGzXYS.c -o ParserGzXYS.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function 'R_read_xys_header':
ParserXYS.c:320:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
ParserXYS.c: In function 'xys_header_field':
ParserXYS.c:145:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c baseProfile.c -o baseProfile.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c basecontent.c -o basecontent.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c trimmed.c -o trimmed.o
gcc -std=gnu99 -shared -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -lm -lquadmath -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lRlapack -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lRblas -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/oligo.Rcheck/oligo/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'V1Overview.Rnw'
'V2NExpression.Rnw'
'V3AffySnpGenotype.Rnw'
'V4Experimental.Rnw'
'V5ExonGene.Rnw'
** testing if installed package can be loaded
* DONE (oligo)