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Package 394/609HostnameOS / ArchBUILDCHECKBUILD BIN
MSnbase 1.6.2
Laurent Gatto
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/MSnbase
Last Changed Rev: 72541 / Revision: 74773
Last Changed Date: 2013-01-15 10:43:56 -0800 (Tue, 15 Jan 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: MSnbase
Version: 1.6.2
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.6.2.tar.gz
StartedAt: 2013-03-25 03:14:04 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 03:19:02 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 297.4 seconds
RetCode: 0
Status:  OK 
CheckDir: MSnbase.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/MSnbase.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.6.2’
* 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 whether package ‘MSnbase’ 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 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 20.401   0.36  20.877
* 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-2.11-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
** 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-class0.8040.0240.854
MSnProcess-class0.0000.0000.001
MSnSet-class1.3240.0241.374
NAnnotatedDataFrame-class0.0240.0000.025
ReporterIons-class0.0160.0000.015
TMT60.0120.0000.016
clean-methods1.4600.0121.493
combineFeatures1.0760.0081.110
extractPrecSpectra-methods0.3800.0080.388
fillUp0.0040.0000.008
formatRt000
getVariableName0.0040.0000.002
iTRAQ40.0160.0000.015
itraqdata0.0680.0000.067
nQuants4.2240.0164.463
normalise-methods4.3370.0044.391
pSet-class0.0000.0000.001
plot-methods1.7720.0001.821
plot2d-methods1.4360.0162.042
plotDensity-methods1.1200.0121.133
plotMzDelta-methods20.401 0.36020.877
plotNA-methods4.4930.0084.566
precSelection0.0680.0000.064
purityCorrect-methods4.0600.0164.225
quantify-methods4.3120.0124.369
readIspyData000
readMSData0.4000.0120.422
readMSnSet000
readMgfData000
readMzTabData0.0040.0000.000
removePeaks-methods1.6240.0001.642
removeReporters-methods1.1680.0241.194
trimMz-methods0.1680.0040.220
writeMgfData-methods0.0000.0000.001
writeMzTabData0.0000.0000.001