BioC 2.13: CHECK report for MSnbase on zin1
This page was generated on 2014-04-05 09:48:02 -0700 (Sat, 05 Apr 2014).
MSnbase 1.10.4 Laurent Gatto
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/MSnbase | Last Changed Rev: 87955 / Revision: 88450 | Last Changed Date: 2014-03-26 11:52:12 -0700 (Wed, 26 Mar 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
Package: MSnbase |
Version: 1.10.4 |
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.10.4.tar.gz |
StartedAt: 2014-04-05 02:38:50 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 02:42:37 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 227.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSnbase.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/MSnbase.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.10.4’
* 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 ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Unexported object imported by a ‘:::’ call: ‘Biobase:::.showAnnotatedDataFrame’
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘MSnbase-demo.Rnw’, ‘MSnbase-development.Rnw’, ‘MSnbase-io.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [56s/72s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
writeMzTabData 6.332 0.020 18.485
readMgfData 6.084 0.000 6.114
impute-methods 3.505 0.008 5.337
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘test-all.R’ [29s/29s]
[29s/29s] OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘multicore’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
‘/home/biocbuild/bbs-2.13-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
** testing if installed package can be loaded
* DONE (MSnbase)
MSnbase.Rcheck/MSnbase-Ex.timings:
name | user | system | elapsed
|
MSnExp-class | 0.456 | 0.012 | 0.486 |
|
MSnProcess-class | 0.004 | 0.000 | 0.005 |
|
MSnSet-class | 1.028 | 0.000 | 1.031 |
|
NAnnotatedDataFrame-class | 0.168 | 0.000 | 0.168 |
|
ReporterIons-class | 0.016 | 0.004 | 0.023 |
|
TMT6 | 0.012 | 0.004 | 0.017 |
|
chromatogram-methods | 0.060 | 0.008 | 0.125 |
|
clean-methods | 1.492 | 0.016 | 1.511 |
|
combineFeatures | 0.860 | 0.012 | 0.873 |
|
exprsToRatios-methods | 3.608 | 0.000 | 4.609 |
|
extractPrecSpectra-methods | 0.256 | 0.004 | 0.519 |
|
featureCV | 0.420 | 0.000 | 0.837 |
|
fillUp | 0.012 | 0.000 | 0.021 |
|
formatRt | 0.000 | 0.000 | 0.003 |
|
getVariableName | 0.004 | 0.000 | 0.005 |
|
iTRAQ4 | 0.02 | 0.00 | 0.04 |
|
impute-methods | 3.505 | 0.008 | 5.337 |
|
itraqdata | 0.036 | 0.004 | 0.039 |
|
nQuants | 3.764 | 0.004 | 3.792 |
|
normalise-methods | 3.384 | 0.000 | 3.391 |
|
pSet-class | 0.004 | 0.000 | 0.006 |
|
plot-methods | 1.248 | 0.000 | 1.252 |
|
plot2d-methods | 0.952 | 0.004 | 0.956 |
|
plotDensity-methods | 0.868 | 0.004 | 0.875 |
|
plotMzDelta-methods | 2.832 | 0.024 | 2.859 |
|
plotNA-methods | 3.613 | 0.000 | 3.615 |
|
precSelection | 0.044 | 0.000 | 0.044 |
|
purityCorrect-methods | 3.596 | 0.000 | 3.604 |
|
quantify-methods | 3.304 | 0.000 | 3.306 |
|
readIspyData | 0.000 | 0.000 | 0.001 |
|
readMSData | 0.260 | 0.004 | 0.264 |
|
readMSnSet | 0.000 | 0.000 | 0.001 |
|
readMgfData | 6.084 | 0.000 | 6.114 |
|
readMzTabData | 0.236 | 0.000 | 0.346 |
|
removePeaks-methods | 1.705 | 0.000 | 1.708 |
|
removeReporters-methods | 0.772 | 0.000 | 0.775 |
|
trimMz-methods | 0.172 | 0.000 | 0.170 |
|
writeMgfData-methods | 0.020 | 0.000 | 0.019 |
|
writeMzTabData | 6.332 | 0.020 | 18.485 |
|
xic-methods | 0.004 | 0.000 | 0.006 |
|