BioC 3.2: CHECK report for MSnbase on linux1.bioconductor.org

Package: MSnbase

Version: 1.18.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.18.0.tar.gz

StartedAt: 2015-10-27 06:05:42 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:09:55 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 253.5 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_1.18.0.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 ‘1.18.0’
* 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 ... [18s/18s] 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 ... [66s/72s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
quantify-methods 10.870  1.836   3.969
averageMSnSet     6.336  0.103   6.444
MSnSet-class      5.831  0.056   5.896
writeMzTabData    3.320  0.008  13.881
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [61s/50s]
 [61s/50s] 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 ‘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	0.414	0.004	0.418
FeaturesOfInterest-class	0.069	0.004	0.072
MSmap-class	0.002	0.000	0.002
MSnExp-class	0.301	0.004	0.306
MSnProcess-class	0.001	0.000	0.002
MSnSet-class	5.831	0.056	5.896
MSnSetList-class	3.838	0.008	3.846
MzTab-class	1.160	0.001	4.312
NAnnotatedDataFrame-class	0.022	0.000	0.022
ReporterIons-class	0.02	0.00	0.02
TMT6	0.015	0.000	0.015
addIdentificationData-methods	0.624	0.004	0.628
averageMSnSet	6.336	0.103	6.444
bin-methods	0.817	0.016	0.835
calculateFragments-methods	0.558	0.004	0.563
chromatogram-methods	0.031	0.008	0.070
clean-methods	1.045	0.024	1.070
combineFeatures	0.937	0.004	0.944
commonFeatureNames	0.681	0.004	0.686
compareSpectra-methods	0.169	0.000	0.169
exprsToRatios-methods	0.089	0.000	0.090
extractPrecSpectra-methods	0.573	0.004	0.578
featureCV	0.048	0.000	0.049
fillUp	0.005	0.000	0.004
formatRt	0.001	0.000	0.001
get.amino.acids	0.003	0.000	0.003
get.atomic.mass	0	0	0
getVariableName	0.001	0.000	0.001
iPQF	0.310	0.004	0.311
iTRAQ4	0.018	0.000	0.020
imageNA2	3.079	0.016	3.099
impute-methods	0.717	0.008	0.728
itraqdata	0.028	0.004	0.033
listOf	0.003	0.000	0.003
missing-data	1.558	0.000	1.558
nQuants	0.157	0.000	0.157
normalise-methods	0.015	0.000	0.015
npcv	0.001	0.000	0.002
pSet-class	0.002	0.000	0.002
pickPeaks-method	0.15	0.00	0.15
plot-methods	0.768	0.000	0.769
plot2d-methods	0.492	0.000	0.493
plotDensity-methods	0.659	0.004	0.667
plotMzDelta-methods	1.782	0.020	1.802
plotNA-methods	0.439	0.016	0.455
plotSpectrumSpectrum-methods	0.769	0.004	0.775
precSelection	0.018	0.000	0.018
purityCorrect-methods	0.029	0.004	0.033
quantify-methods	10.870	1.836	3.969
readIspyData	0.000	0.000	0.001
readMSData	0.468	0.000	0.468
readMSnSet	0.001	0.000	0.000
readMgfData	2.382	0.016	2.399
readMzTabData	3.829	0.032	4.190
readMzTabData_v0.9	0.265	0.004	0.479
removeNoId-methods	1.299	0.000	1.299
removePeaks-methods	0.969	0.000	0.970
removeReporters-methods	0.428	0.004	0.435
smooth-methods	0.135	0.000	0.135
trimMz-methods	0.089	0.000	0.089
writeMgfData-methods	0.001	0.000	0.000
writeMzTabData	3.320	0.008	13.881
xic-methods	0.001	0.000	0.001