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BioC 3.3: CHECK report for MSnbase on linux2.bioconductor.org

This page was generated on 2015-10-27 12:11:55 -0400 (Tue, 27 Oct 2015).

Package 680/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 1.19.2
Laurent Gatto
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase
Last Changed Rev: 109891 / Revision: 109948
Last Changed Date: 2015-10-24 18:09:21 -0400 (Sat, 24 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSnbase
Version: 1.19.2
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.19.2.tar.gz
StartedAt: 2015-10-27 06:08:42 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 06:12:32 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 230.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MSnbase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.19.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MSnbase.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘1.19.2’
* 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 ... [17s/17s] 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 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [57s/59s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
quantify-methods 10.290  1.760   3.769
averageMSnSet     5.854  0.083   5.949
writeMzTabData    1.971  0.020   9.107
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [60s/48s]
 [60s/48s] 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/MSnbase.Rcheck/00check.log’
for details.


MSnbase.Rcheck/00install.out:

* installing *source* package ‘MSnbase’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o imp_neighbour_avg.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/MSnbase.Rcheck/MSnbase/libs
** 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’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
Creating a generic function for ‘split’ 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-class0.2320.0000.233
FeaturesOfInterest-class0.0530.0000.053
MSmap-class0.0010.0000.001
MSnExp-class0.2910.0040.296
MSnProcess-class0.0010.0000.001
MSnSet-class4.1760.0164.191
MSnSetList-class2.6880.0042.694
MzTab-class1.3560.0203.952
NAnnotatedDataFrame-class0.0220.0000.023
ReporterIons-class0.020.000.02
TMT60.0140.0000.015
addIdentificationData-methods0.6570.0000.657
averageMSnSet5.8540.0835.949
bin-methods0.7340.0160.750
calculateFragments-methods0.4840.0040.489
chromatogram-methods0.0320.0080.060
clean-methods0.7790.0120.790
combineFeatures0.5470.0080.555
commonFeatureNames0.3950.0040.400
compareSpectra-methods0.1440.0040.149
exprsToRatios-methods0.0570.0000.057
extractPrecSpectra-methods0.4230.0000.424
featureCV0.0300.0000.029
fillUp0.0040.0000.004
formatRt0.0000.0000.001
get.amino.acids0.0040.0000.003
get.atomic.mass0.0010.0000.000
getVariableName0.0010.0000.001
iPQF0.2190.0000.220
iTRAQ40.0120.0000.011
imageNA21.7690.0001.769
impute-methods0.6160.0040.619
itraqdata0.0480.0000.049
listOf0.0030.0000.004
missing-data1.8210.0081.829
nQuants0.1690.0000.170
normalise-methods0.0160.0000.016
npcv0.0030.0000.002
pSet-class0.0020.0000.002
pickPeaks-method0.1570.0000.158
plot-methods1.2850.0001.286
plot2d-methods0.4050.0000.404
plotDensity-methods0.6840.0000.684
plotMzDelta-methods0.8980.0200.919
plotNA-methods0.4620.0040.467
plotSpectrumSpectrum-methods0.5970.0000.598
precSelection0.010.000.01
purityCorrect-methods0.0180.0000.019
quantify-methods10.290 1.760 3.769
readIspyData0.0010.0000.001
readMSData0.5660.0120.580
readMSnSet0.0010.0000.001
readMgfData2.9790.0403.019
readMzTabData2.1420.0202.501
readMzTabData_v0.90.2240.0000.318
removeNoId-methods1.2330.0001.233
removePeaks-methods1.0430.0001.043
removeReporters-methods0.4460.0040.450
selectFeatureData0.0010.0000.001
smooth-methods0.1380.0040.142
trimMz-methods0.080.000.08
writeMgfData-methods000
writeMzTabData1.9710.0209.107
xic-methods0.0010.0000.000