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Package 506/658HostnameOS / ArchBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.9.5
Hans-Ulrich Klein
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/R453Plus1Toolbox
Last Changed Rev: 74154 / Revision: 74774
Last Changed Date: 2013-03-11 07:20:54 -0700 (Mon, 11 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 

Summary

Package: R453Plus1Toolbox
Version: 1.9.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.9.5.tar.gz
StartedAt: 2013-03-25 04:13:25 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:20:06 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 400.7 seconds
RetCode: 0
Status:  OK 
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.9.5'
* 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 'R453Plus1Toolbox' can be installed ... [30s/31s] 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
.getEnsemblInfo: no visible binding for global variable 'cds_length'
.getEnsemblInfo: no visible binding for global variable
  'ensembl_transcript_id'
.getMutations: no visible binding for global variable 'PatternStart'
.getMutations: no visible binding for global variable 'PatternEnd'
.htmlReport: no visible binding for global variable 'VarFreqForward'
.htmlReport: no visible binding for global variable 'VarFreqReverse'
.plotVariants: no visible binding for global variable 'mutation'
qualityReportSFF: no visible binding for '<<-' assignment to 'tmp'
* 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 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 ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mergeBreakpoints  10.916  1.125  12.105
htmlReport         6.944  0.442   7.686
plotChimericReads  6.401  0.027   6.430
* 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-2.12-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.

R453Plus1Toolbox.Rcheck/00install.out:

* installing *source* package 'R453Plus1Toolbox' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c readSFF.c -o readSFF.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c writeSFF.c -o writeSFF.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 R453Plus1Toolbox.so readSFF.o writeSFF.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'boxplot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
   'vignette.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'boxplot' when loading 'graphics'
* DONE (R453Plus1Toolbox)

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings:

nameusersystemelapsed
AVASet-class0.6080.0410.649
AVASet0.2070.0220.234
AnnotatedVariants-class0.0130.0100.024
MapperSet-class0.0490.0210.070
MapperSet0.0190.0060.025
SFFContainer-class0.0150.0120.028
SFFRead-class0.2590.0100.269
alignShortReads1.1450.0131.174
annotateVariants0.0140.0110.025
assayDataAmp0.2690.0070.277
ava2vcf0.3120.0250.338
avaSetExample0.0370.0100.047
avaSetFiltered0.0630.0180.082
avaSetFiltered_annot0.0040.0040.009
breakpoints0.0060.0040.010
calculateTiTv0.0240.0070.032
captureArray0.0040.0050.009
coverageOnTarget0.4190.0310.449
demultiplexReads0.0990.0090.108
detectBreakpoints0.5590.0290.599
fDataAmp0.0270.0070.036
featureDataAmp0.0250.0070.032
filterChimericReads2.2760.0352.314
genomeSequencerMIDs0.0500.0060.056
getAlignedReads0.1540.0110.166
getVariantPercentages0.0650.0180.083
htmlReport6.9440.4427.686
mapperSetExample0.0170.0070.023
mergeBreakpoints10.916 1.12512.105
mutationInfo0.0050.0050.010
plotAmpliconCoverage0.0030.0060.009
plotChimericReads6.4010.0276.430
plotVariants0.0150.0200.035
plotVariationFrequency0.0020.0050.007
qualityReportSFF0.0050.0130.018
readSFF0.1260.0080.134
readsOnTarget1.1790.0321.212
referenceSequences0.0160.0070.023
regions0.0070.0050.012
removeLinker0.0450.0090.054
sequenceCaptureLinkers0.0100.0040.014
setVariantFilter0.1010.0130.114
variants0.0060.0050.011
writeSFF0.0330.0080.042