Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.0: CHECK report for MSnbase on perceval

This page was generated on 2015-04-10 09:55:41 -0700 (Fri, 10 Apr 2015).

Package 583/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 1.14.2
Laurent Gatto
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MSnbase
Last Changed Rev: 100966 / Revision: 102249
Last Changed Date: 2015-03-21 00:54:49 -0700 (Sat, 21 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: MSnbase
Version: 1.14.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.14.2.tar.gz
StartedAt: 2015-04-10 04:10:20 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:17:50 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 449.8 seconds
RetCode: 0
Status:  OK 
CheckDir: MSnbase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnbase_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MSnbase.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘1.14.2’
* 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 ‘MSnbase’ can be installed ... [29s/42s] 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
'library' or 'require' call to ‘rols’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’
  ‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’
  ‘MALDIquant:::.savitzkyGolay’ ‘MALDIquant:::.which.closest’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeMTD: no visible global function definition for ‘olsQuery’
makeMTD: no visible global function definition for ‘term’
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [171s/117s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
writeMzTabData         12.755  5.593  16.382
quantify-methods        9.353  5.580   6.579
compareSpectra-methods 13.364  0.157  13.609
averageMSnSet          12.405  0.425  13.874
normalise-methods       6.632  4.699   2.529
purityCorrect-methods   6.068  4.754   2.995
plotNA-methods          6.152  4.618   3.295
nQuants                 5.774  4.172   3.167
impute-methods          5.536  4.193   3.363
readMgfData             7.859  0.119   8.018
featureCV               3.937  2.665   0.689
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat.R’ [80s/46s]
 [80s/46s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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 new generic function for ‘smooth’ in package ‘MSnbase’
Creating a generic function for ‘t’ from package ‘base’ in package ‘MSnbase’
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:

nameusersystemelapsed
FeatComp-class0.2920.0310.874
FeaturesOfInterest-class0.4290.0070.451
MSmap-class0.0020.0000.002
MSnExp-class0.5750.0160.608
MSnProcess-class0.0020.0000.002
MSnSet-class1.0760.7711.113
NAnnotatedDataFrame-class0.0300.0000.031
ReporterIons-class0.0370.0010.039
TMT60.0170.0000.017
addIdentificationData-methods1.1150.0641.223
averageMSnSet12.405 0.42513.874
bin-methods1.5590.0131.572
calculateFragments-methods0.8250.0120.837
chromatogram-methods0.0760.0360.256
clean-methods1.2590.0551.689
combineFeatures1.6581.1461.634
compareSpectra-methods13.364 0.15713.609
exprsToRatios-methods2.3481.5882.354
extractPrecSpectra-methods0.9100.1561.065
featureCV3.9372.6650.689
fillUp0.0100.0030.012
formatRt0.0010.0010.002
get.amino.acids0.0070.0030.010
get.atomic.mass0.0000.0000.001
getVariableName0.0020.0000.003
iTRAQ40.0250.0040.029
impute-methods5.5364.1933.363
itraqdata0.0320.0070.039
listOf0.0060.0010.007
nQuants5.7744.1723.167
normalise-methods6.6324.6992.529
npcv0.0040.0020.006
pSet-class0.0040.0020.006
pickPeaks-method0.3350.0440.378
plot-methods1.2200.0621.327
plot2d-methods0.8500.0500.942
plotDensity-methods0.8910.0101.065
plotMzDelta-methods3.9630.1784.153
plotNA-methods6.1524.6183.295
plotSpectrumSpectrum-methods0.9430.1421.102
precSelection0.0220.0010.024
purityCorrect-methods6.0684.7542.995
quantify-methods9.3535.5806.579
readIspyData0.0000.0010.001
readMSData1.0020.0121.015
readMSnSet0.0010.0000.001
readMgfData7.8590.1198.018
readMzTabData0.3330.0040.499
removeNoId-methods1.9600.0111.972
removePeaks-methods1.3910.0221.413
removeReporters-methods0.7960.0150.811
smooth-methods0.2810.0090.291
trimMz-methods0.1100.0040.112
writeMgfData-methods0.0020.0000.001
writeMzTabData12.755 5.59316.382
xic-methods0.0010.0000.001