Rsubread 1.8.2
Wei Shi
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/Rsubread | | Last Changed Rev: 74263 / Revision: 74773 | | Last Changed Date: 2013-03-12 22:27:02 -0700 (Tue, 12 Mar 2013) |
| lamb1 | Linux (openSUSE 12.1) / 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 Leopard (10.5.8) / i386 | N O T S U P P O R T E D |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Rsubread.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.8.2’
* 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 whether package ‘Rsubread’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 90.5Mb
sub-directories of 1Mb or more:
annot 89.0Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Rsubread.Rcheck/Rsubread/libs/Rsubread.so’:
Found ‘exit’, possibly from ‘exit’ (C)
Objects: ‘gene-algorithms.o’, ‘propmapped.o’, ‘readSummary.o’,
‘sam2bed.o’
Found ‘printf’, possibly from ‘printf’ (C)
Objects: ‘SNPCalling.o’, ‘aligner.o’, ‘detectionCallAnnotation.o’,
‘exon-align.o’, ‘fullscan.o’, ‘gene-algorithms.o’,
‘index-builder.o’, ‘input-files.o’, ‘processExons.o’,
‘propmapped.o’, ‘readSummary.o’, ‘removeDupReads.o’,
‘sorted-hashtable.o’
Found ‘putchar’, possibly from ‘putchar’ (C)
Objects: ‘aligner.o’, ‘exon-align.o’, ‘gene-algorithms.o’,
‘index-builder.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Objects: ‘SNPCalling.o’, ‘aligner.o’, ‘detectionCallAnnotation.o’,
‘exon-align.o’, ‘fullscan.o’, ‘gene-algorithms.o’,
‘gene-value-index.o’, ‘index-builder.o’, ‘input-files.o’,
‘processExons.o’, ‘propmapped.o’, ‘readSummary.o’,
‘removeDupReads.o’, ‘sam2bed.o’, ‘sorted-hashtable.o’
Found ‘stdout’, possibly from ‘stdout’ (C)
Objects: ‘SNPCalling.o’, ‘aligner.o’, ‘exon-align.o’,
‘gene-algorithms.o’, ‘index-builder.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... 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
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Rsubread.Rcheck/00check.log’
for details.
* installing *source* package ‘Rsubread’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:903:9: warning: variable ‘total_results’ set but not used [-Wunused-but-set-variable]
aligner.c: At top level:
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:54:7: warning: unused variable ‘data_ready’ [-Wunused-variable]
atgcContent.c:52:7: warning: unused variable ‘offset’ [-Wunused-variable]
atgcContent.c:51:7: warning: unused variable ‘readlen’ [-Wunused-variable]
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:126:2: warning: ‘readlen’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:156:32: warning: unused variable ‘read_entrezid’ [-Wunused-variable]
detectionCall.c: In function ‘simplify_SAM_file’:
detectionCall.c:194:9: warning: unused variable ‘z’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:96:32: warning: unused variable ‘read_length’ [-Wunused-variable]
detectionCallAnnotation.c: In function ‘breakIntegenicRegion’:
detectionCallAnnotation.c:131:47: warning: unused variable ‘read_length’ [-Wunused-variable]
detectionCallAnnotation.c:131:10: warning: unused variable ‘read_entrezid’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:885:6: warning: variable ‘digged’ set but not used [-Wunused-but-set-variable]
exon-align.c: In function ‘junction_tree_f_explorer’:
exon-align.c:1033:6: warning: variable ‘digged’ set but not used [-Wunused-but-set-variable]
exon-align.c: In function ‘explorer_junc_exonbed’:
exon-align.c:1420:9: warning: variable ‘last_indel’ set but not used [-Wunused-but-set-variable]
exon-align.c:1236:84: warning: variable ‘total_total_matched_bases’ set but not used [-Wunused-but-set-variable]
exon-align.c: In function ‘run_exon_search_index_tolerable’:
exon-align.c:3979:6: warning: variable ‘last_table’ set but not used [-Wunused-but-set-variable]
exon-align.c: In function ‘main_junction’:
exon-align.c:4564:7: warning: variable ‘is_successful’ set but not used [-Wunused-but-set-variable]
exon-align.c: At top level:
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c fullscan.c -o fullscan.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:613:6: warning: variable ‘last_end’ set but not used [-Wunused-but-set-variable]
gene-algorithms.c:612:9: warning: variable ‘is_error’ set but not used [-Wunused-but-set-variable]
gene-algorithms.c: In function ‘search_DP_branch’:
gene-algorithms.c:1578:6: warning: variable ‘table_mask2_j_1’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:120:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
gene-value-index.c: At top level:
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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-2.11-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:425:7: warning: variable ‘read_names’ set but not used [-Wunused-but-set-variable]
index-builder.c:418:19: warning: variable ‘table_no’ set but not used [-Wunused-but-set-variable]
index-builder.c: At top level:
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c input-files.c -o input-files.o
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:216:10: warning: unused variable ‘pt’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:44:1: warning: control reaches end of non-void function [-Wreturn-type]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:17:7: warning: unused variable ‘data_ready’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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 ‘readSummary’:
readSummary.c:109:5: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
readSummary.c:183:3: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat]
readSummary.c:183:3: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat]
readSummary.c:195:1: warning: control reaches end of non-void function [-Wreturn-type]
readSummary.c:154:37: warning: ‘fragment_length’ may be used uninitialized in this function [-Wuninitialized]
readSummary.c:149:21: warning: ‘mate_pos’ may be used uninitialized in this function [-Wuninitialized]
readSummary.c:127:124: warning: ‘read_length’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -fpic -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:19:10: warning: variable ‘tok’ set but not used [-Wunused-but-set-variable]
sam2bed.c:46:1: warning: control reaches end of non-void function [-Wreturn-type]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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:872:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
sorted-hashtable.c: In function ‘load_int64’:
sorted-hashtable.c:881:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
sorted-hashtable.c: In function ‘gehash_load’:
sorted-hashtable.c:892:9: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
sorted-hashtable.c: At top level:
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gene-algorithms.h:25:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined [enabled by default]
gene-algorithms.h:24:13: warning: inline function ‘add_gene_vote’ declared but never defined [enabled by default]
gcc -std=gnu99 -shared -L/usr/local/lib64 -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 -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/Rsubread.Rcheck/Rsubread/libs
** 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)