Rsubread 1.9.3
Wei Shi
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsubread | | Last Changed Rev: 74594 / Revision: 74774 | | Last Changed Date: 2013-03-19 20:53:18 -0700 (Tue, 19 Mar 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 Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Rsubread/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rsubread' version '1.9.3'
* 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 ... [10s/16s] OK
* checking installed package size ... NOTE
installed size is 90.1Mb
sub-directories of 1Mb or more:
annot 89.0Mb
* 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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [9s/9s] 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 3 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck/00check.log'
for details.
* installing *source* package 'Rsubread' ...
@@@@@ The operation system is supposed to be Darwin.
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c R_wrapper.c -o R_wrapper.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c SNPCalling.c -o SNPCalling.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c aligner.c -o aligner.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c atgcContent.c -o atgcContent.o
atgcContent.c: In function 'retrieve_sequence':
atgcContent.c:54: warning: unused variable 'data_ready'
atgcContent.c:52: warning: unused variable 'offset'
atgcContent.c:51: warning: unused variable 'readlen'
atgcContent.c:49: warning: unused variable 'z'
atgcContent.c:48: warning: unused variable 'len'
atgcContent.c: In function 'atgcContent':
atgcContent.c:90: warning: unused variable 'z'
atgcContent.c:89: warning: unused variable 'len'
atgcContent.c:92: warning: 'readlen' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c detectionCall.c -o detectionCall.o
detectionCall.c: In function 'build_ir_data_structure_map':
detectionCall.c:156: warning: unused variable 'read_entrezid'
detectionCall.c: In function 'simplify_SAM_file':
detectionCall.c:194: warning: unused variable 'z'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function 'build_ir_data_structure':
detectionCallAnnotation.c:96: warning: unused variable 'read_length'
detectionCallAnnotation.c: In function 'breakIntegenicRegion':
detectionCallAnnotation.c:131: warning: unused variable 'read_length'
detectionCallAnnotation.c:131: warning: unused variable 'read_entrezid'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c exon-algorithms.c -o exon-algorithms.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c exon-align.c -o exon-align.o
exon-align.c: In function 'get_grouped_position':
exon-align.c:786: warning: pointer of type 'void *' used in arithmetic
exon-align.c:786: warning: pointer of type 'void *' used in subtraction
exon-align.c:793: warning: pointer of type 'void *' used in arithmetic
exon-align.c:793: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'junction_tree_b_explorer':
exon-align.c:835: warning: pointer of type 'void *' used in arithmetic
exon-align.c:835: warning: pointer of type 'void *' used in arithmetic
exon-align.c:835: warning: pointer of type 'void *' used in subtraction
exon-align.c:853: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'junction_tree_f_explorer':
exon-align.c:975: warning: pointer of type 'void *' used in arithmetic
exon-align.c:975: warning: pointer of type 'void *' used in arithmetic
exon-align.c:975: warning: pointer of type 'void *' used in subtraction
exon-align.c:999: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'merge_pos_table':
exon-align.c:1644: warning: pointer of type 'void *' used in subtraction
exon-align.c:1646: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1647: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1647: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'merge_connection_table':
exon-align.c:1668: warning: pointer of type 'void *' used in subtraction
exon-align.c:1670: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1706: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'remove_neighbours':
exon-align.c:1810: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1830: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1831: warning: pointer of type 'void *' used in arithmetic
exon-align.c: In function 'put_connection_table':
exon-align.c:1984: warning: pointer of type 'void *' used in arithmetic
exon-align.c:1990: warning: pointer of type 'void *' used in arithmetic
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c fullscan.c -o fullscan.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function 'find_and_explain_indel':
gene-algorithms.c:917: warning: overflow in implicit constant conversion
gene-algorithms.c: In function 'explain_indel_in_middle':
gene-algorithms.c:1068: warning: overflow in implicit constant conversion
gene-algorithms.c:1095: warning: overflow in implicit constant conversion
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c gene-value-index.c -o gene-value-index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c hashtable.c -o hashtable.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c index-builder.c -o index-builder.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c input-files.c -o input-files.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c processExons.c -o processExons.o
processExons.c: In function 'find_chr':
processExons.c:216: warning: unused variable 'pt'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c propmapped.c -o propmapped.o
propmapped.c: In function 'propmapped':
propmapped.c:21: warning: unused variable 'z'
propmapped.c:20: warning: unused variable 'len'
propmapped.c:49: warning: control reaches end of non-void function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c qualityScores.c -o qualityScores.o
qualityScores.c: In function 'retrieve_scores':
qualityScores.c:17: warning: unused variable 'data_ready'
qualityScores.c:12: warning: unused variable 'z'
qualityScores.c:11: warning: unused variable 'len'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c readSummary.c -o readSummary.o
readSummary.c: In function 'readSummary':
readSummary.c:116: warning: suggest explicit braces to avoid ambiguous 'else'
readSummary.c:193: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
readSummary.c:193: warning: format '%d' expects type 'int', but argument 6 has type 'long int'
readSummary.c:26: warning: unused variable 'z'
readSummary.c:25: warning: unused variable 'len'
readSummary.c:205: warning: control reaches end of non-void function
readSummary.c:18: warning: 'read_length' may be used uninitialized in this function
readSummary.c:44: warning: 'fragment_length' may be used uninitialized in this function
readSummary.c:44: warning: 'mate_pos' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c removeDupReads.c -o removeDupReads.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c sam2bed.c -o sam2bed.o
sam2bed.c: In function 'sam2bed':
sam2bed.c:23: warning: unused variable 'z'
sam2bed.c:22: warning: unused variable 'len'
sam2bed.c:52: warning: control reaches end of non-void function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -g -O2 -Wall -pedantic -c sorted-hashtable.c -o sorted-hashtable.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rsubread.so 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 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/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'Rsubread.Rnw'
** testing if installed package can be loaded
* DONE (Rsubread)