DECIPHER 1.5.1
Erik Wright
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DECIPHER | | Last Changed Rev: 74767 / Revision: 74774 | | Last Changed Date: 2013-03-24 11:50:20 -0700 (Sun, 24 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.5.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... [20s/21s] OK
* checking installed package size ... OK
* 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
DB2FASTA: warning in writeXStringSet(myDNAStringSet, file = file,
append = append): partial argument match of 'file' to 'filepath'
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 ... [169s/175s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
TileSeqs 152.654 0.092 158.158
* 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
‘/home/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
* installing *source* package ‘DECIPHER’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -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-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c ClusterML.c -o ClusterML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function ‘clusterNJ’:
ClusterNJ.c:266:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:276:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterNJ.c:436:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:448:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:195:41: warning: ‘minCol’ may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:33: warning: ‘minRow’ 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 -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function ‘clusterUPGMA’:
ClusterUPGMA.c:183:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:193:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterUPGMA.c:343:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:355:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:124:41: warning: ‘minCol’ may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:33: warning: ‘minRow’ 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 -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c CommonGaps.c -o CommonGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘distMatrix’:
DistanceMatrix.c:174:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function ‘intMatch’:
MultiMatch.c:189:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
MultiMatch.c: In function ‘firstMatchUpper’:
MultiMatch.c:215:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/stats/include" -fpic -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c: In function ‘terminalMismatch’:
TerminalMismatch.c:46:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -std=gnu99 -shared -L/usr/local/lib -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 -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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)