Rsubread 1.20.2
Wei Shi
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rsubread | | Last Changed Rev: 110347 / Revision: 110496 | | Last Changed Date: 2015-11-04 21:07:15 -0800 (Wed, 04 Nov 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rsubread_1.20.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rsubread.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.20.2’
* 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 ... [13s/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 ‘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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘Rsubread/libs/Rsubread.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Objects: ‘SNPCalling.o’, ‘build-sam-index.o’, ‘core-indel.o’,
‘core-interface-aligner.o’, ‘core-interface-subjunc.o’, ‘core.o’,
‘input-files.o’, ‘propmapped.o’, ‘readSummary.o’,
‘sorted-hashtable.o’
Found ‘_srand’, possibly from ‘srand’ (C)
Objects: ‘SNPCalling.o’, ‘core-indel.o’, ‘core.o’, ‘propmapped.o’
File ‘Rsubread/libs/Rsubread.so’:
Found non-API call to R: ‘R_CStackLimit’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 files in ‘vignettes’ ... OK
* checking examples ... [17s/18s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
align 2.941 4.595 7.535
propmapped 2.965 2.716 5.859
* 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
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.2-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 -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC -mtune=core2 -g -O2 -Wall -c core-bigtable.c -o core-bigtable.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 -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC -mtune=core2 -g -O2 -Wall -c core.c -o core.o
core.c: In function ‘do_iteration_two’:
core.c:2491: warning: unused variable ‘current_result’
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 -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC -mtune=core2 -g -O2 -Wall -c long-hashtable.c -o long-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 -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC -mtune=core2 -g -O2 -Wall -c mergeVCF.c -o mergeVCF.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 -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC -mtune=core2 -g -O2 -Wall -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 -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC -mtune=core2 -g -O2 -Wall -c sam2bed.c -o sam2bed.o
sam2bed.c: In function ‘sam2bed’:
sam2bed.c:43: warning: unused variable ‘i’
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 -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -fPIC -mtune=core2 -g -O2 -Wall -c seek-zlib.c -o seek-zlib.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 -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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 -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.20.2\"" -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/Library/Frameworks/R.framework/Resources/lib -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-bigtable.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 long-hashtable.o mergeVCF.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.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-3.2-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)