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 ‘/home/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.10.5’
* 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 ... [13s/14s] OK
* checking installed package size ... NOTE
installed size is 22.9Mb
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 ‘/home/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 installed files from ‘inst/doc’ ... OK
* checking examples ... [11s/11s] 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
‘/home/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck/00check.log’
for details.
* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Linux.
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o
SNPCalling.c: In function ‘process_snp_votes’:
SNPCalling.c:171:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
SNPCalling.c:172:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
SNPCalling.c:173:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
SNPCalling.c:174:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c aligner.c -o aligner.o
aligner.c: In function ‘run_search’:
aligner.c:930:9: warning: variable ‘total_results’ set but not used [-Wunused-but-set-variable]
aligner.c:709:9: warning: variable ‘t0’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c atgcContent.c -o atgcContent.o
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:73:7: warning: unused variable ‘data_ready’ [-Wunused-variable]
atgcContent.c:71:7: warning: unused variable ‘offset’ [-Wunused-variable]
atgcContent.c:70:7: warning: unused variable ‘readlen’ [-Wunused-variable]
atgcContent.c:68:11: warning: unused variable ‘z’ [-Wunused-variable]
atgcContent.c:67:10: warning: unused variable ‘len’ [-Wunused-variable]
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:109:11: warning: unused variable ‘z’ [-Wunused-variable]
atgcContent.c:108:10: warning: unused variable ‘len’ [-Wunused-variable]
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:85:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:151:2: warning: ‘readlen’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c detectionCall.c -o detectionCall.o
detectionCall.c: In function ‘build_ir_data_structure_map’:
detectionCall.c:175:32: warning: unused variable ‘read_entrezid’ [-Wunused-variable]
detectionCall.c: In function ‘simplify_SAM_file’:
detectionCall.c:213:9: warning: unused variable ‘z’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function ‘build_ir_data_structure’:
detectionCallAnnotation.c:115:32: warning: unused variable ‘read_length’ [-Wunused-variable]
detectionCallAnnotation.c: In function ‘breakIntegenicRegion’:
detectionCallAnnotation.c:150:47: warning: unused variable ‘read_length’ [-Wunused-variable]
detectionCallAnnotation.c:150:10: warning: unused variable ‘read_entrezid’ [-Wunused-variable]
detectionCallAnnotation.c: In function ‘calculateIRGCContent’:
detectionCallAnnotation.c:281:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
detectionCallAnnotation.c: In function ‘calculateExonGCContent’:
detectionCallAnnotation.c:194:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c exon-align.c -o exon-align.o
exon-align.c: In function ‘junction_tree_b_explorer’:
exon-align.c:906:6: warning: variable ‘digged’ set but not used [-Wunused-but-set-variable]
exon-align.c: In function ‘junction_tree_f_explorer’:
exon-align.c:1054:6: warning: variable ‘digged’ set but not used [-Wunused-but-set-variable]
exon-align.c: In function ‘explorer_junc_exonbed’:
exon-align.c:1452:9: warning: variable ‘last_indel’ set but not used [-Wunused-but-set-variable]
exon-align.c:1268:84: warning: variable ‘total_total_matched_bases’ set but not used [-Wunused-but-set-variable]
exon-align.c: In function ‘run_exon_search’:
exon-align.c:3588:6: warning: unused variable ‘good_match’ [-Wunused-variable]
exon-align.c:3586:9: warning: variable ‘t0’ set but not used [-Wunused-but-set-variable]
exon-align.c: In function ‘run_exon_search_index_tolerable’:
exon-align.c:4045:6: warning: variable ‘last_table’ set but not used [-Wunused-but-set-variable]
exon-align.c: In function ‘main_junction’:
exon-align.c:4667:7: warning: variable ‘is_successful’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c fullscan.c -o fullscan.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function ‘show_cigar’:
gene-algorithms.c:634:6: warning: variable ‘last_end’ set but not used [-Wunused-but-set-variable]
gene-algorithms.c:633:9: warning: variable ‘is_error’ set but not used [-Wunused-but-set-variable]
gene-algorithms.c: In function ‘search_DP_branch’:
gene-algorithms.c:1735:6: warning: variable ‘table_mask2_j_1’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o
gene-value-index.c: In function ‘gvindex_load’:
gene-value-index.c:141:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c index-builder.c -o index-builder.o
index-builder.c: In function ‘scan_gene_index’:
index-builder.c:454:19: warning: variable ‘table_no’ set but not used [-Wunused-but-set-variable]
index-builder.c: In function ‘main_buildindex’:
index-builder.c:1001:9: warning: ignoring return value of ‘mkstemp’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c input-files.c -o input-files.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c processExons.c -o processExons.o
processExons.c: In function ‘find_chr’:
processExons.c:235:10: warning: unused variable ‘pt’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c propmapped.c -o propmapped.o
propmapped.c: In function ‘propmapped’:
propmapped.c:40:11: warning: unused variable ‘z’ [-Wunused-variable]
propmapped.c:39:10: warning: unused variable ‘len’ [-Wunused-variable]
propmapped.c:68:1: warning: control reaches end of non-void function [-Wreturn-type]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c qualityScores.c -o qualityScores.o
qualityScores.c: In function ‘retrieve_scores’:
qualityScores.c:36:7: warning: unused variable ‘data_ready’ [-Wunused-variable]
qualityScores.c:31:11: warning: unused variable ‘z’ [-Wunused-variable]
qualityScores.c:30:10: warning: unused variable ‘len’ [-Wunused-variable]
qualityScores.c:76:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c readSummary.c -o readSummary.o
readSummary.c: In function ‘process_line_buffer’:
readSummary.c:708:22: warning: variable ‘second_chr_chr’ set but not used [-Wunused-but-set-variable]
readSummary.c:708:8: warning: variable ‘last_chr_chr’ set but not used [-Wunused-but-set-variable]
readSummary.c: In function ‘readSummary’:
readSummary.c:1331:9: warning: variable ‘curchr_name’ set but not used [-Wunused-but-set-variable]
readSummary.c:1330:15: warning: variable ‘curpos’ set but not used [-Wunused-but-set-variable]
readSummary.c:1330:7: warning: variable ‘curchr’ set but not used [-Wunused-but-set-variable]
readSummary.c: In function ‘load_feature_info’:
readSummary.c:210:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
readSummary.c:256:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
readSummary.c:264:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o
removeDupReads.c: In function ‘parse_base_blocks’:
removeDupReads.c:87:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
removeDupReads.c:96:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c sam2bed.c -o sam2bed.o
sam2bed.c: In function ‘sam2bed’:
sam2bed.c:45:7: warning: unused variable ‘i’ [-Wunused-variable]
sam2bed.c:43:11: warning: unused variable ‘z’ [-Wunused-variable]
sam2bed.c:42:10: warning: unused variable ‘len’ [-Wunused-variable]
sam2bed.c:40:10: warning: variable ‘tok’ set but not used [-Wunused-but-set-variable]
sam2bed.c:81:1: warning: control reaches end of non-void function [-Wreturn-type]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c sambam-file.c -o sambam-file.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o
sorted-hashtable.c: In function ‘load_int32’:
sorted-hashtable.c:877:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
sorted-hashtable.c: In function ‘load_int64’:
sorted-hashtable.c:886:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
sorted-hashtable.c: In function ‘gehash_load’:
sorted-hashtable.c:897:9: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -shared -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 -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/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)