BioC 3.6: CHECK report for MSnbase on malbec1

Package: MSnbase

Version: 2.3.9

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_2.3.9.tar.gz

StartedAt: 2017-08-16 00:56:55 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:07:22 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 627.1 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_2.3.9.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MSnbase.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.3.9’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    6.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Laurent Gatto <lg390@cam.ac.uk> [aut, cre]
  Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre]
  Sebastian Gibb <mail@sebastiangibb.de> [aut, cre]
* 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’
  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 ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
OnDiskMSnExp-class         11.112  0.156  11.418
chromatogram-MSnExp-method  7.640  0.276   8.723
MSnSet-class                6.624  0.008   6.647
averageMSnSet               5.856  0.028   6.241
MzTab-class                 2.064  0.052   5.957
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

* installing *source* package ‘MSnbase’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: ‘_new_Spectrum1’ defined but not used [-Wunused-function]
 static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: ‘_new_Spectrum2’ defined but not used [-Wunused-function]
 static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘compar_double_dd_for_stable_asc_order’:
utils.c:92:15: warning: unused variable ‘ret’ [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function ‘compar_double_dd_for_stable_desc_order’:
utils.c:107:15: warning: unused variable ‘ret’ [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function ‘compar_double_asc_order’:
utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: In function ‘compar_double_desc_order’:
utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: At top level:
utils.c:121:12: warning: ‘compar_double_asc_order’ defined but not used [-Wunused-function]
 static int compar_double_asc_order(const void *p1, const void *p2)
            ^
utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function]
 static int compar_double_desc_order(const void *p1, const void *p2)
            ^
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/MSnbase.Rcheck/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** preparing package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnbase)

name	user	system	elapsed
Chromatogram-class	0.072	0.000	0.072
Chromatograms-class	0.224	0.000	0.223
FeatComp-class	0.280	0.012	0.323
FeaturesOfInterest-class	0.068	0.000	0.070
MSmap-class	0.004	0.000	0.001
MSnExp-class	0.400	0.004	0.405
MSnProcess-class	0.004	0.000	0.001
MSnSet-class	6.624	0.008	6.647
MSnSetList-class	2.784	0.004	2.787
MzTab-class	2.064	0.052	5.957
NAnnotatedDataFrame-class	0.008	0.000	0.009
OnDiskMSnExp-class	11.112	0.156	11.418
ProcessingStep-class	0.004	0.000	0.005
ReporterIons-class	0.016	0.000	0.016
TMT6	0.016	0.000	0.015
addIdentificationData-methods	0.424	0.004	0.430
aggvar	3.908	0.012	3.931
averageMSnSet	5.856	0.028	6.241
bin-methods	0.324	0.008	0.333
calculateFragments-methods	0.812	0.000	0.813
chromatogram-MSnExp-method	7.640	0.276	8.723
clean-methods	0.264	0.012	0.277
combineFeatures	0.860	0.012	0.876
commonFeatureNames	0.408	0.000	0.407
compareSpectra-methods	0.200	0.000	0.197
estimateNoise-method	0.008	0.000	0.009
exprsToRatios-methods	0.080	0.000	0.079
extractPrecSpectra-methods	0.628	0.040	0.666
factorsAsStrings	0.012	0.000	0.010
featureCV	0.028	0.000	0.027
fillUp	0.012	0.000	0.012
formatRt	0	0	0
get.amino.acids	0.004	0.000	0.003
get.atomic.mass	0	0	0
getVariableName	0.000	0.004	0.003
iPQF	0.392	0.000	0.390
iTRAQ4	0.008	0.000	0.009
imageNA2	2.836	0.008	2.844
impute-methods	0.716	0.008	0.871
itraqdata	0.092	0.004	0.092
listOf	0.004	0.000	0.003
makeCamelCase	0.000	0.000	0.001
makeNaData	0.808	0.000	0.807
missing-data	2.592	0.004	2.600
mzRident2dfr	0.044	0.000	0.043
nFeatures	0.544	0.004	0.546
nQuants	0.100	0.004	0.105
naplot	0.064	0.000	0.066
navMS	1.032	0.012	1.185
normToReference	0.14	0.00	0.14
normalise-methods	0.012	0.000	0.014
npcv	0.004	0.000	0.004
pSet-class	0.000	0.000	0.001
pickPeaks-method	0.224	0.000	0.227
plot-methods	1.232	0.000	1.233
plot2d-methods	0.608	0.000	0.609
plotDensity-methods	0.908	0.000	0.906
plotMzDelta-methods	1.112	0.008	1.119
plotNA-methods	0.416	0.000	0.419
plotSpectrumSpectrum-methods	0.812	0.000	0.815
precSelection	0.012	0.000	0.015
purityCorrect-methods	0.072	0.000	0.075
quantify-methods	1.228	0.108	1.936
readMSData	1.108	0.000	1.109
readMSnSet	0.300	0.000	0.311
readMgfData	2.404	0.004	2.411
readMzIdData	1.092	0.128	1.309
readMzTabData	2.044	0.016	2.948
readMzTabData_v0.9	0.396	0.008	0.855
reduce-data.frame-method	0.028	0.000	0.029
removeNoId-methods	0.768	0.000	0.765
removePeaks-methods	0.764	0.000	0.764
removeReporters-methods	0.696	0.000	0.698
selectFeatureData	0.156	0.000	0.165
smooth-methods	0.204	0.000	0.202
trimMz-methods	0.172	0.000	0.174
writeMgfData-methods	0.000	0.000	0.001