BioC 2.12: CHECK report for R453Plus1Toolbox on petty
This page was generated on 2013-10-09 09:39:54 -0700 (Wed, 09 Oct 2013).
R453Plus1Toolbox 1.10.0 Hans-Ulrich Klein
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/R453Plus1Toolbox | Last Changed Rev: 75263 / Revision: 81334 | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 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 Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
Summary
Package: R453Plus1Toolbox |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.10.0.tar.gz |
StartedAt: 2013-10-08 23:34:53 -0700 (Tue, 08 Oct 2013) |
EndedAt: 2013-10-08 23:44:41 -0700 (Tue, 08 Oct 2013) |
EllapsedTime: 588.1 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 version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.10.0'
* 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 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 ... [49s/52s] 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 ... [70s/80s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mergeBreakpoints 14.760 1.136 21.484
htmlReport 9.427 0.461 13.147
plotChimericReads 9.211 0.028 9.340
* 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c readSFF.c -o readSFF.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c writeSFF.c -o writeSFF.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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
** 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
** testing if installed package can be loaded
Warning: replacing previous import 'boxplot' when loading 'graphics'
* DONE (R453Plus1Toolbox)
R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings:
name | user | system | elapsed
|
AVASet-class | 1.088 | 0.035 | 1.138 |
|
AVASet | 0.356 | 0.011 | 0.375 |
|
AnnotatedVariants-class | 0.019 | 0.003 | 0.023 |
|
MapperSet-class | 0.070 | 0.014 | 0.089 |
|
MapperSet | 0.022 | 0.004 | 0.026 |
|
SFFContainer-class | 0.022 | 0.008 | 0.031 |
|
SFFRead-class | 0.016 | 0.006 | 0.022 |
|
alignShortReads | 2.235 | 0.013 | 2.375 |
|
annotateVariants | 0.508 | 0.015 | 0.534 |
|
assayDataAmp | 0.012 | 0.007 | 0.020 |
|
ava2vcf | 0.498 | 0.038 | 0.550 |
|
avaSetExample | 0.037 | 0.010 | 0.049 |
|
avaSetFiltered | 0.068 | 0.017 | 0.086 |
|
avaSetFiltered_annot | 0.006 | 0.004 | 0.011 |
|
breakpoints | 0.008 | 0.004 | 0.012 |
|
calculateTiTv | 0.026 | 0.007 | 0.035 |
|
captureArray | 0.005 | 0.005 | 0.011 |
|
coverageOnTarget | 0.720 | 0.044 | 0.827 |
|
demultiplexReads | 0.165 | 0.011 | 0.208 |
|
detectBreakpoints | 0.980 | 0.031 | 1.039 |
|
fDataAmp | 0.045 | 0.008 | 0.052 |
|
featureDataAmp | 0.042 | 0.008 | 0.051 |
|
filterChimericReads | 3.558 | 0.051 | 3.703 |
|
genomeSequencerMIDs | 0.071 | 0.006 | 0.086 |
|
getAlignedReads | 0.231 | 0.016 | 0.258 |
|
getVariantPercentages | 0.103 | 0.014 | 0.128 |
|
htmlReport | 9.427 | 0.461 | 13.147 |
|
mapperSetExample | 0.016 | 0.004 | 0.043 |
|
mergeBreakpoints | 14.760 | 1.136 | 21.484 |
|
mutationInfo | 0.007 | 0.004 | 0.012 |
|
plotAmpliconCoverage | 0.003 | 0.006 | 0.010 |
|
plotChimericReads | 9.211 | 0.028 | 9.340 |
|
plotVariants | 0.019 | 0.024 | 0.043 |
|
plotVariationFrequency | 0.002 | 0.003 | 0.005 |
|
qualityReportSFF | 0.003 | 0.005 | 0.008 |
|
readSFF | 0.237 | 0.010 | 0.247 |
|
readsOnTarget | 1.329 | 0.049 | 1.385 |
|
referenceSequences | 0.020 | 0.006 | 0.026 |
|
regions | 0.008 | 0.006 | 0.014 |
|
removeLinker | 0.075 | 0.016 | 0.091 |
|
sequenceCaptureLinkers | 0.022 | 0.004 | 0.027 |
|
setVariantFilter | 0.169 | 0.016 | 0.186 |
|
variants | 0.018 | 0.013 | 0.030 |
|
writeSFF | 0.051 | 0.006 | 0.057 |
|