BioC 3.2: CHECK report for MSnbase on zin1

Package: MSnbase

Version: 1.17.14

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.17.14.tar.gz

StartedAt: 2015-08-24 01:59:44 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:03:39 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 235.2 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.17.14.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MSnbase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.17.14’
* 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 ... [19s/19s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [56s/62s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
quantify-methods 7.152  1.154   3.792
averageMSnSet    5.963  0.103   6.268
MSnSet-class     5.911  0.029   5.935
writeMzTabData   2.090  0.008   8.832
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [53s/47s]
 [54s/47s] 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-3.2-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

* installing *source* package ‘MSnbase’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o imp_neighbour_avg.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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 ‘lengths’ from package ‘base’ 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	0.224	0.004	0.264
FeaturesOfInterest-class	0.059	0.004	0.063
MSmap-class	0.001	0.000	0.001
MSnExp-class	0.473	0.007	0.494
MSnProcess-class	0.002	0.000	0.002
MSnSet-class	5.911	0.029	5.935
MSnSetList-class	3.700	0.008	3.705
MzTab-class	1.282	0.000	4.502
NAnnotatedDataFrame-class	0.018	0.000	0.018
ReporterIons-class	0.016	0.000	0.019
TMT6	0.011	0.000	0.015
addIdentificationData-methods	0.533	0.000	0.545
averageMSnSet	5.963	0.103	6.268
bin-methods	0.630	0.008	0.637
calculateFragments-methods	0.527	0.004	0.531
chromatogram-methods	0.047	0.004	0.086
clean-methods	0.805	0.020	0.824
combineFeatures	0.689	0.000	0.688
commonFeatureNames	0.513	0.004	0.516
compareSpectra-methods	0.123	0.004	0.127
exprsToRatios-methods	0.067	0.000	0.067
extractPrecSpectra-methods	0.450	0.004	0.450
featureCV	0.041	0.000	0.044
fillUp	0.007	0.000	0.006
formatRt	0.001	0.000	0.001
get.amino.acids	0.005	0.000	0.005
get.atomic.mass	0.000	0.000	0.001
getVariableName	0.002	0.000	0.002
iPQF	0.067	0.000	0.066
iTRAQ4	0.017	0.000	0.017
imageNA2	1.910	0.004	1.916
impute-methods	0.616	0.012	0.766
itraqdata	0.038	0.000	0.038
listOf	0.003	0.000	0.003
missing-data	1.895	0.012	1.906
nQuants	0.2	0.0	0.2
normalise-methods	0.018	0.000	0.018
npcv	0.002	0.000	0.002
pSet-class	0.002	0.000	0.002
pickPeaks-method	0.162	0.000	0.162
plot-methods	0.879	0.004	0.882
plot2d-methods	0.550	0.004	0.556
plotDensity-methods	0.559	0.004	0.562
plotMzDelta-methods	1.400	0.024	1.422
plotNA-methods	0.521	0.008	0.529
plotSpectrumSpectrum-methods	0.662	0.000	0.662
precSelection	0.013	0.000	0.012
purityCorrect-methods	0.023	0.000	0.023
quantify-methods	7.152	1.154	3.792
readIspyData	0	0	0
readMSData	0.437	0.000	0.437
readMSnSet	0.001	0.000	0.000
readMgfData	2.455	0.020	2.481
readMzTabData	2.619	0.012	2.964
readMzTabData_v0.9	0.190	0.000	0.357
removeNoId-methods	1.067	0.000	1.077
removePeaks-methods	1.117	0.000	1.133
removeReporters-methods	0.603	0.000	0.607
smooth-methods	0.176	0.000	0.175
trimMz-methods	0.102	0.000	0.102
writeMgfData-methods	0.001	0.000	0.001
writeMzTabData	2.090	0.008	8.832
xic-methods	0.001	0.000	0.000