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Package 396/514HostnameOS / ArchBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.4.0
Hans-Ulrich Klein
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/R453Plus1Toolbox
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / 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 

Summary

Package: R453Plus1Toolbox
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.4.0.tar.gz
StartedAt: 2012-03-24 03:30:21 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 03:36:00 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 338.3 seconds
RetCode: 0
Status:  OK 
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.4.0'
* 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 'R453Plus1Toolbox' 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
.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'
* 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 ... NOTE
File '/Users/biocbuild/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs/i386/R453Plus1Toolbox.so':
  Found '___stderrp', possibly from 'stderr' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under '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

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  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c readSFF.c -o readSFF.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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'vignette.Rnw' 
** testing if installed package can be loaded

* DONE (R453Plus1Toolbox)

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings:

nameusersystemelapsed
AVASet-class0.1110.0080.193
AVASet0.0310.0020.039
AnnotatedVariants-class0.0040.0000.004
MapperSet-class0.0440.0140.185
MapperSet0.0130.0020.016
SFFContainer-class0.0010.0000.001
SFFRead-class0.0010.0000.002
alignShortReads1.3050.0181.439
annotateVariants0.0020.0000.002
assayDataAmp0.0090.0010.011
avaSetExample0.0290.0030.033
avaSetFiltered0.0600.0090.071
avaSetFiltered_annot0.0040.0020.005
breakpoints0.0050.0010.007
calculateTiTv0.0250.0040.030
captureArray0.0040.0010.005
coverageOnTarget0.5450.0320.579
demultiplexReads0.1240.0020.125
detectBreakpoints0.9590.0200.998
fDataAmp0.0310.0020.033
featureDataAmp0.0300.0010.032
filterChimericReads2.4820.0202.516
genomeSequencerMIDs0.0680.0020.070
getAlignedReads0.2320.0060.239
getVariantPercentages0.0710.0020.074
htmlReport 7.430 0.42810.153
mapperSetExample0.0120.0010.015
mergeBreakpoints11.604 1.54815.083
plotAmpliconCoverage0.0010.0000.000
plotChimericReads6.4870.0166.602
plotVariants0.0020.0010.002
plotVariationFrequency0.0000.0000.001
readSFF000
readsOnTarget0.7960.0100.808
referenceSequences0.0140.0010.016
removeLinker0.0430.0010.043
sequenceCaptureLinkers0.010.000.01
setVariantFilter0.1200.0030.124
transcriptdf0.0020.0010.003