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Package 404/631HostnameOS / ArchBUILDCHECKBUILD BIN
MSnbase 1.7.16
Laurent Gatto
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase
Last Changed Rev: 72561 / Revision: 72575
Last Changed Date: 2013-01-15 14:27:18 -0800 (Tue, 15 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / 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: MSnbase
Version: 1.7.16
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.7.16.tar.gz
StartedAt: 2013-01-16 04:39:40 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 04:44:51 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 311.1 seconds
RetCode: 0
Status:  OK 
CheckDir: MSnbase.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/MSnbase.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘1.7.16’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMC’
* 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 ‘MSnbase’ can be installed ... 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotMzDelta-methods 23.742  0.628  24.489
writeMzTabData       8.184  0.012  20.336
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’
 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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

MSnbase.Rcheck/00install.out:

* installing *source* package ‘MSnbase’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘scale’ from package ‘base’ in package ‘MSnbase’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘MSnbase-demo.Rnw’ 
   ‘MSnbase-development.Rnw’ 
   ‘MSnbase-io.Rnw’ 
** testing if installed package can be loaded

* DONE (MSnbase)

MSnbase.Rcheck/MSnbase-Ex.timings:

nameusersystemelapsed
MSnExp-class0.5040.0080.515
MSnProcess-class0.0120.0000.013
MSnSet-class1.2560.0201.284
NAnnotatedDataFrame-class0.0400.0000.046
ReporterIons-class0.0360.0000.036
TMT60.0280.0000.030
clean-methods1.8080.0041.825
combineFeatures0.6680.0160.693
exprsToRatios-methods4.4440.0164.489
extractPrecSpectra-methods0.4010.0000.463
featureCV0.5280.0080.539
fillUp0.0160.0000.016
formatRt0.0040.0000.006
getVariableName0.0080.0000.012
iTRAQ40.0320.0000.030
itraqdata0.3000.0040.303
nQuants4.5880.0124.615
normalise-methods4.4040.0164.448
pSet-class0.2960.0000.296
plot-methods1.7720.0001.855
plot2d-methods1.3680.0001.382
plotDensity-methods1.1360.0041.141
plotMzDelta-methods23.742 0.62824.489
plotNA-methods4.9240.0084.935
precSelection0.0680.0000.067
purityCorrect-methods4.1920.0004.198
quantify-methods4.3570.0004.353
readIspyData0.0040.0000.003
readMSData0.4240.0160.442
readMSnSet0.0040.0000.005
readMgfData0.0000.0080.010
readMzTabData0.2520.0080.430
removePeaks-methods1.8840.0401.927
removeReporters-methods0.8680.0080.877
trimMz-methods0.1760.0000.175
writeMgfData-methods0.0080.0000.007
writeMzTabData 8.184 0.01220.336