DECIPHER 1.4.0
Erik Wright
| 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/DECIPHER | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/DECIPHER.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 ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘1.4.0’
* 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 whether package ‘DECIPHER’ 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 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
CreateChimeras: no visible binding for global variable ‘s1’
CreateChimeras: no visible binding for global variable ‘d’
CreateChimeras: no visible binding for global variable ‘myName’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TileSeqs 149.71 0.24 153.349
* 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 was 1 note.
See
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
* installing *source* package ‘DECIPHER’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function ‘calculateDeltaG’:
CalculateDeltaG.c:26:10: warning: ‘s2’ may be used uninitialized in this function [-Wuninitialized]
CalculateDeltaG.c:206:15: warning: ‘s1’ 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 -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c ClusterML.c -o ClusterML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function ‘clusterNJ._omp_fn.0’:
ClusterNJ.c:280:12: warning: ‘minC’ may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:62: note: ‘minC’ was declared here
ClusterNJ.c:279:12: warning: ‘minR’ may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:56: note: ‘minR’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function ‘clusterUPGMA._omp_fn.0’:
ClusterUPGMA.c:197:12: warning: ‘minC’ may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:62: note: ‘minC’ was declared here
ClusterUPGMA.c:196:12: warning: ‘minR’ may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: note: ‘minR’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c CommonGaps.c -o CommonGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c MultiMatch.c -o MultiMatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/stats/include" -fopenmp -fpic -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o DECIPHER.so Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o MultiMatch.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -fopenmp -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs
** R
** data
** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘DECIPHERing.Rnw’
‘DesignPrimers.Rnw’
‘FindChimeras.Rnw’
** testing if installed package can be loaded
* DONE (DECIPHER)