Rsubread 1.10.5
Wei Shi
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Rsubread | | Last Changed Rev: 77915 / Revision: 81334 | | Last Changed Date: 2013-06-25 16:58:04 -0700 (Tue, 25 Jun 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Rsubread/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rsubread' version '1.10.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'Rsubread' can be installed ... [12s/13s] OK
* checking installed package size ... NOTE
installed size is 22.3Mb
sub-directories of 1Mb or more:
annot 20.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
createAnnotationFile: no visible global function definition for
'values'
createAnnotationFile: no visible global function definition for
'values<-'
createAnnotationFile: no visible global function definition for
'seqnames'
write.Rsubread: no visible global function definition for 'values'
write.Rsubread: no visible global function definition for 'values<-'
write.Rsubread: no visible global function definition for 'seqnames'
* 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 ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck/Rsubread/libs/Rsubread.so':
Found non-API call to R: 'R_CStackLimit'
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [11s/13s] 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 were 4 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck/00check.log'
for details.
* installing *source* package 'Rsubread' ...
@@@@@ The operating system is Darwin.
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c HelperFunctions.c -o HelperFunctions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c R_wrapper.c -o R_wrapper.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c SNPCalling.c -o SNPCalling.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c aligner.c -o aligner.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c atgcContent.c -o atgcContent.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c detectionCall.c -o detectionCall.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c exon-algorithms.c -o exon-algorithms.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c exon-align.c -o exon-align.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c fullscan.c -o fullscan.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c gene-algorithms.c -o gene-algorithms.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c gene-value-index.c -o gene-value-index.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c hashtable.c -o hashtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c index-builder.c -o index-builder.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c input-files.c -o input-files.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c processExons.c -o processExons.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c propmapped.c -o propmapped.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c qualityScores.c -o qualityScores.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c readSummary.c -o readSummary.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c removeDupReads.c -o removeDupReads.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c sam2bed.c -o sam2bed.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c sambam-file.c -o sambam-file.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o R_wrapper.o SNPCalling.o aligner.o atgcContent.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align.o fullscan.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o sorted-hashtable.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsubread)