Rsubread 1.18.0
Wei Shi
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/Rsubread | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rsubread_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Rsubread.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.18.0’
* 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/11s] OK
* checking installed package size ... NOTE
installed size is 22.2Mb
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’, ‘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 ... [10s/10s] 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
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/Rsubread.Rcheck/00check.log’
for details.
* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Darwin.
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c HelperFunctions.c -o HelperFunctions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c R_wrapper.c -o R_wrapper.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c SNPCalling.c -o SNPCalling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c aligner.c -o aligner.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c atgcContent.c -o atgcContent.o
atgcContent.c:68:11: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
atgcContent.c:73:7: warning: unused variable 'data_ready' [-Wunused-variable]
int data_ready=1;
^
atgcContent.c:71:7: warning: unused variable 'offset' [-Wunused-variable]
int offset;
^
atgcContent.c:67:10: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
atgcContent.c:70:7: warning: unused variable 'readlen' [-Wunused-variable]
int readlen;
^
atgcContent.c:108:10: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
atgcContent.c:109:11: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c build-sam-index.c -o build-sam-index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c core-indel.c -o core-indel.o
core-indel.c:1488:28: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
if(head_indel_left_edge>=0 && abs(head_indel_movement)<=global_context -> config.max_indel_length)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^ ˜
core-indel.c:1867:5: warning: variable 'all_reads' is uninitialized when used here [-Wuninitialized]
all_reads += 0xff&(next_moves>>(8*test_next));
^˜˜˜˜˜˜˜˜
core-indel.c:1860:17: note: initialize the variable 'all_reads' to silence this warning
int all_reads;
^
= 0
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c core-junction.c -o core-junction.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c core.c -o core.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c detectionCall.c -o detectionCall.o
detectionCall.c:176:28: warning: unused variable 'read_entrezid' [-Wunused-variable]
int read_start, read_end, read_entrezid, read_n, read_gc, read_at;
^
detectionCall.c:214:9: warning: unused variable 'z' [-Wunused-variable]
size_t z;
^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c:117:28: warning: unused variable 'read_length' [-Wunused-variable]
int read_start, read_end, read_length;
^
detectionCallAnnotation.c:152:43: warning: unused variable 'read_length' [-Wunused-variable]
int read_entrezid, read_start, read_end, read_length;
^
detectionCallAnnotation.c:152:6: warning: unused variable 'read_entrezid' [-Wunused-variable]
int read_entrezid, read_start, read_end, read_length;
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c exon-algorithms.c -o exon-algorithms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c exon-align-indel.c -o exon-align-indel.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c exon-align.c -o exon-align.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c fullscan.c -o fullscan.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c fusion-align.c -o fusion-align.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c gene-algorithms.c -o gene-algorithms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c gene-value-index.c -o gene-value-index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c hashtable.c -o hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c index-builder.c -o index-builder.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c input-files.c -o input-files.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c interval_merge.c -o interval_merge.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c mergeVCF.c -o mergeVCF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c processExons.c -o processExons.o
processExons.c:237:10: warning: unused variable 'pt' [-Wunused-variable]
char *pt = strcpy(gene_array[gene_pos].chr_array[current_chr_index].id,chr_id);
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c propmapped.c -o propmapped.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c qualityScores.c -o qualityScores.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c readSummary.c -o readSummary.o
readSummary.c:534:30: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(ret_features[xk1].start<0 || ret_features[xk1].start>0x7fffffff)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
readSummary.c:541:28: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(ret_features[xk1].end<0 || ret_features[xk1].end>0x7fffffff)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c removeDupReads.c -o removeDupReads.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c sam2bed.c -o sam2bed.o
sam2bed.c:43:7: warning: unused variable 'i' [-Wunused-variable]
int i, readlen, chr_start, chr_end, flag, mqs;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c sambam-file.c -o sambam-file.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.18.0\"" -fPIC -Wall -mtune=core2 -g -O2 -c sublog.c -o sublog.o
clang -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 -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 mergeVCF.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
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-3.1-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)