DECIPHER 1.3.1
Erik Wright
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DECIPHER | | Last Changed Rev: 66763 / Revision: 66885 | | Last Changed Date: 2012-06-15 14:46:54 -0700 (Fri, 15 Jun 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/DECIPHER.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '1.3.1'
* 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 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 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
FindChimeras: warning in SearchDB(dbConn2, id = group, verbose = FALSE,
limit = maxGroupSize, ... = "nonbases < 20"): partial argument match
of 'id' to 'identifier'
FindChimeras: warning in SearchDB(dbConn2, id = group, verbose = FALSE,
limit = maxGroupSize, ... = "chimera is NULL and nonbases < 20"):
partial argument match of 'id' to 'identifier'
FindChimeras: warning in SearchDB(dbConn1, tblName = tblName, id =
group, replaceChar = "", removeGaps = "all", verbose = FALSE):
partial argument match of 'id' to 'identifier'
FindChimeras: warning in SearchDB(dbConn1, tblName = tblName, id =
group, replaceChar = "", removeGaps = "all", verbose = FALSE, ... =
"chimera is NULL"): partial argument match of 'id' to 'identifier'
FindChimeras: warning in PDict(temp_fragments, algo = "ACtree2", tb.end
= tb.width): partial argument match of 'algo' to 'algorithm'
FindChimeras: warning in PDict(temp_fragments, algo = "ACtree2",
tb.start = tb.width + 1, tb.end = 2 * tb.width): partial argument
match of 'algo' to 'algorithm'
FindChimeras: warning in PDict(fragments[h], algo = "ACtree2", tb.end =
tb.width): partial argument match of 'algo' to 'algorithm'
FindChimeras: warning in SearchDB(dbConn2, id = other, verbose = FALSE,
limit = maxGroupSize, ... = "nonbases < 20"): partial argument match
of 'id' to 'identifier'
FindChimeras: warning in SearchDB(dbConn2, id = other, verbose = FALSE,
limit = maxGroupSize, ... = "nonbases < 20 and chimera is NULL"):
partial argument match of 'id' to 'identifier'
FindChimeras: warning in round(100 * coverage/(end - start + 1), d =
2): partial argument match of 'd' to 'digits'
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 sizes of PDF files under 'inst/doc' ... OK
* 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 was 1 note.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.
* installing *source* package 'DECIPHER' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateDeltaG':
CalculateDeltaG.c:26: warning: 's2' may be used uninitialized in this function
CalculateDeltaG.c:26: warning: 's1' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ClusterML.c -o ClusterML.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:266: warning: ignoring #pragma omp parallel
ClusterNJ.c:276: warning: ignoring #pragma omp critical
ClusterNJ.c:436: warning: ignoring #pragma omp parallel
ClusterNJ.c:448: warning: ignoring #pragma omp parallel
ClusterNJ.c: In function 'reclusterNJ':
ClusterNJ.c:593: warning: 'longestLeaf' may be used uninitialized in this function
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:198: warning: 'utilsPackage' may be used uninitialized in this function
ClusterNJ.c:198: warning: 'percentComplete' may be used uninitialized in this function
ClusterNJ.c:197: warning: 'total' may be used uninitialized in this function
ClusterNJ.c:196: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'minC' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'minR' may be used uninitialized in this function
ClusterNJ.c:509: warning: 'longestLeaf' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:183: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:193: warning: ignoring #pragma omp critical
ClusterUPGMA.c:343: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:355: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:127: warning: 'utilsPackage' may be used uninitialized in this function
ClusterUPGMA.c:127: warning: 'percentComplete' may be used uninitialized in this function
ClusterUPGMA.c:126: warning: 'total' may be used uninitialized in this function
ClusterUPGMA.c:125: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'minC' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'minR' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c CommonGaps.c -o CommonGaps.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ConsensusSequence.c -o ConsensusSequence.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:174: warning: ignoring #pragma omp parallel
DistanceMatrix.c:136: warning: 'utilsPackage' may be used uninitialized in this function
DistanceMatrix.c:136: warning: 'percentComplete' may be used uninitialized in this function
DistanceMatrix.c:134: warning: 'rPercentComplete' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c R_init_decipher.c -o R_init_decipher.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ReplaceChars.c -o ReplaceChars.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DECIPHER.so Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs/i386
** R
** data
** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'DECIPHERing.Rnw'
'FindChimeras.Rnw'
** testing if installed package can be loaded
* DONE (DECIPHER)