Rsubread 1.12.6
Wei Shi
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Rsubread | | Last Changed Rev: 84836 / Revision: 88450 | | Last Changed Date: 2013-12-17 21:38:56 -0800 (Tue, 17 Dec 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Rsubread.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsubread’ version ‘1.12.6’
* 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 22.7Mb
sub-directories of 1Mb or more:
annot 20.5Mb
* checking package directory ... OK
* checking ‘build’ 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 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
‘seqnames’
createAnnotationFile: no visible global function definition for
‘strand’
getInBuiltAnnotation: no visible binding for global variable
‘annot.inbuilt’
write.Rsubread: no visible global function definition for ‘values’
write.Rsubread: no visible global function definition for ‘seqnames’
write.Rsubread: no visible global function definition for ‘strand’
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.13-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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘Rsubread.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [17s/18s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 5 notes.
See
‘/Users/biocbuild/bbs-2.13-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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c atgcContent.c -o atgcContent.o
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:73: warning: unused variable ‘data_ready’
atgcContent.c:71: warning: unused variable ‘offset’
atgcContent.c:70: warning: unused variable ‘readlen’
atgcContent.c:68: warning: unused variable ‘z’
atgcContent.c:67: warning: unused variable ‘len’
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:109: warning: unused variable ‘z’
atgcContent.c:108: warning: unused variable ‘len’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c build-sam-index.c -o build-sam-index.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c core-indel.c -o core-indel.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c core-interface-aligner.c -o core-interface-aligner.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c core-junction.c -o core-junction.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c core.c -o core.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c detectionCall.c -o detectionCall.o
detectionCall.c: In function ‘build_ir_data_structure_map’:
detectionCall.c:176: warning: unused variable ‘read_entrezid’
detectionCall.c: In function ‘simplify_SAM_file’:
detectionCall.c:214: warning: unused variable ‘z’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function ‘build_ir_data_structure’:
detectionCallAnnotation.c:117: warning: unused variable ‘read_length’
detectionCallAnnotation.c: In function ‘breakIntegenicRegion’:
detectionCallAnnotation.c:152: warning: unused variable ‘read_length’
detectionCallAnnotation.c:152: warning: unused variable ‘read_entrezid’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c exon-align-indel.c -o exon-align-indel.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c fusion-align.c -o fusion-align.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c interval_merge.c -o interval_merge.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c processExons.c -o processExons.o
processExons.c: In function ‘find_chr’:
processExons.c:237: warning: unused variable ‘pt’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c propmapped.c -o propmapped.o
propmapped.c: In function ‘propmapped’:
propmapped.c:40: warning: unused variable ‘z’
propmapped.c:39: warning: unused variable ‘len’
propmapped.c:68: warning: no return statement in function returning non-void
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c sam2bed.c -o sam2bed.o
sam2bed.c: In function ‘sam2bed’:
sam2bed.c:45: warning: unused variable ‘i’
sam2bed.c:43: warning: unused variable ‘z’
sam2bed.c:42: warning: unused variable ‘len’
sam2bed.c:81: warning: no return statement in function returning non-void
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -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 -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DSUBREAD_VERSION="\"Rsubread 1.12.6\"" -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=core2 -g -O2 -Wall -c sublog.c -o sublog.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 build-sam-index.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o fullscan.o fusion-align.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o interval_merge.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o sorted-hashtable.o sublog.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-2.13-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)