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

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### Running command:
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###   /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.

* 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)

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

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

Summary

Command output