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).
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 ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
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
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###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.19.2.tar.gz
###
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* 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:
name | user | system | elapsed
|
FeatComp-class | 0.232 | 0.000 | 0.233 |
|
FeaturesOfInterest-class | 0.053 | 0.000 | 0.053 |
|
MSmap-class | 0.001 | 0.000 | 0.001 |
|
MSnExp-class | 0.291 | 0.004 | 0.296 |
|
MSnProcess-class | 0.001 | 0.000 | 0.001 |
|
MSnSet-class | 4.176 | 0.016 | 4.191 |
|
MSnSetList-class | 2.688 | 0.004 | 2.694 |
|
MzTab-class | 1.356 | 0.020 | 3.952 |
|
NAnnotatedDataFrame-class | 0.022 | 0.000 | 0.023 |
|
ReporterIons-class | 0.02 | 0.00 | 0.02 |
|
TMT6 | 0.014 | 0.000 | 0.015 |
|
addIdentificationData-methods | 0.657 | 0.000 | 0.657 |
|
averageMSnSet | 5.854 | 0.083 | 5.949 |
|
bin-methods | 0.734 | 0.016 | 0.750 |
|
calculateFragments-methods | 0.484 | 0.004 | 0.489 |
|
chromatogram-methods | 0.032 | 0.008 | 0.060 |
|
clean-methods | 0.779 | 0.012 | 0.790 |
|
combineFeatures | 0.547 | 0.008 | 0.555 |
|
commonFeatureNames | 0.395 | 0.004 | 0.400 |
|
compareSpectra-methods | 0.144 | 0.004 | 0.149 |
|
exprsToRatios-methods | 0.057 | 0.000 | 0.057 |
|
extractPrecSpectra-methods | 0.423 | 0.000 | 0.424 |
|
featureCV | 0.030 | 0.000 | 0.029 |
|
fillUp | 0.004 | 0.000 | 0.004 |
|
formatRt | 0.000 | 0.000 | 0.001 |
|
get.amino.acids | 0.004 | 0.000 | 0.003 |
|
get.atomic.mass | 0.001 | 0.000 | 0.000 |
|
getVariableName | 0.001 | 0.000 | 0.001 |
|
iPQF | 0.219 | 0.000 | 0.220 |
|
iTRAQ4 | 0.012 | 0.000 | 0.011 |
|
imageNA2 | 1.769 | 0.000 | 1.769 |
|
impute-methods | 0.616 | 0.004 | 0.619 |
|
itraqdata | 0.048 | 0.000 | 0.049 |
|
listOf | 0.003 | 0.000 | 0.004 |
|
missing-data | 1.821 | 0.008 | 1.829 |
|
nQuants | 0.169 | 0.000 | 0.170 |
|
normalise-methods | 0.016 | 0.000 | 0.016 |
|
npcv | 0.003 | 0.000 | 0.002 |
|
pSet-class | 0.002 | 0.000 | 0.002 |
|
pickPeaks-method | 0.157 | 0.000 | 0.158 |
|
plot-methods | 1.285 | 0.000 | 1.286 |
|
plot2d-methods | 0.405 | 0.000 | 0.404 |
|
plotDensity-methods | 0.684 | 0.000 | 0.684 |
|
plotMzDelta-methods | 0.898 | 0.020 | 0.919 |
|
plotNA-methods | 0.462 | 0.004 | 0.467 |
|
plotSpectrumSpectrum-methods | 0.597 | 0.000 | 0.598 |
|
precSelection | 0.01 | 0.00 | 0.01 |
|
purityCorrect-methods | 0.018 | 0.000 | 0.019 |
|
quantify-methods | 10.290 | 1.760 | 3.769 |
|
readIspyData | 0.001 | 0.000 | 0.001 |
|
readMSData | 0.566 | 0.012 | 0.580 |
|
readMSnSet | 0.001 | 0.000 | 0.001 |
|
readMgfData | 2.979 | 0.040 | 3.019 |
|
readMzTabData | 2.142 | 0.020 | 2.501 |
|
readMzTabData_v0.9 | 0.224 | 0.000 | 0.318 |
|
removeNoId-methods | 1.233 | 0.000 | 1.233 |
|
removePeaks-methods | 1.043 | 0.000 | 1.043 |
|
removeReporters-methods | 0.446 | 0.004 | 0.450 |
|
selectFeatureData | 0.001 | 0.000 | 0.001 |
|
smooth-methods | 0.138 | 0.004 | 0.142 |
|
trimMz-methods | 0.08 | 0.00 | 0.08 |
|
writeMgfData-methods | 0 | 0 | 0 |
|
writeMzTabData | 1.971 | 0.020 | 9.107 |
|
xic-methods | 0.001 | 0.000 | 0.000 |
|