Rsubread 1.1.0
Wei Shi
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsubread | | Last Changed Rev: 54802 / Revision: 55359 | | Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | N O T S U P P O R T E D |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | N O T S U P P O R T E D |
| pelham | 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-2.9-bioc/meat/Rsubread.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.1.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘Rsubread’ can be installed ... OK
* checking installed package size ... OK
* 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 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
* installing *source* package ‘Rsubread’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c aligner.c -o aligner.o
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -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’
atgcContent.c:52:7: warning: unused variable ‘offset’
atgcContent.c:51:7: warning: unused variable ‘readlen’
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:90:7: warning: ‘readlen’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c exon-align.c -o exon-align.o
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c index-builder.c -o index-builder.o
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c input-files.c -o input-files.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -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’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c sam2bed.c -o sam2bed.o
sam2bed.c: In function ‘sam2bed’:
sam2bed.c:46:1: warning: control reaches end of non-void function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gene-algorithms.h:27:13: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26:13: warning: inline function ‘add_gene_vote’ declared but never defined
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c unmapped.c -o unmapped.o
unmapped.c: In function ‘unmapped’:
unmapped.c:38:1: warning: control reaches end of non-void function
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rsubread.so R_wrapper.o aligner.o atgcContent.o exon-algorithms.o exon-align.o gene-algorithms.o gene-value-index.o index-builder.o input-files.o qualityScores.o sam2bed.o sorted-hashtable.o unmapped.o -lpthread -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/Rsubread.Rcheck/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘Rsubread.Rnw’
** testing if installed package can be loaded
* DONE (Rsubread)