BioC 3.5: CHECK report for MSnbase on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_2.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘2.2.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    4.3Mb
* 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 11.840  0.300  12.346
MSnSet-class        6.364  0.040   6.420
averageMSnSet       5.948  0.064   7.431
navMS               3.688  0.040   5.807
MzTab-class         2.324  0.108   6.489
quantify-methods    1.932  0.212   5.054
* 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-3.5-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

* installing *source* package ‘MSnbase’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-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-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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
FeatComp-class	0.304	0.004	0.378
FeaturesOfInterest-class	0.084	0.000	0.084
MSmap-class	0.000	0.000	0.001
MSnExp-class	0.376	0.008	0.384
MSnProcess-class	0.004	0.000	0.001
MSnSet-class	6.364	0.040	6.420
MSnSetList-class	2.972	0.000	2.970
MzTab-class	2.324	0.108	6.489
NAnnotatedDataFrame-class	0.032	0.000	0.031
OnDiskMSnExp-class	11.840	0.300	12.346
ProcessingStep-class	0.004	0.000	0.006
ReporterIons-class	0.012	0.000	0.015
TMT6	0.012	0.000	0.014
addIdentificationData-methods	0.772	0.000	0.771
aggvar	3.896	0.000	3.906
averageMSnSet	5.948	0.064	7.431
bin-methods	1.028	0.008	1.038
calculateFragments-methods	0.716	0.008	0.724
chromatogram-methods	0.060	0.020	0.104
clean-methods	0.964	0.032	0.999
combineFeatures	1.100	0.000	1.102
commonFeatureNames	0.404	0.000	0.403
compareSpectra-methods	0.216	0.004	0.218
estimateNoise-method	0.012	0.000	0.011
exprsToRatios-methods	0.080	0.000	0.081
extractPrecSpectra-methods	0.552	0.000	0.552
featureCV	0.028	0.000	0.026
fillUp	0.012	0.000	0.012
formatRt	0.004	0.000	0.001
get.amino.acids	0.004	0.000	0.002
get.atomic.mass	0.000	0.000	0.001
getVariableName	0.004	0.000	0.003
iPQF	0.392	0.000	0.390
iTRAQ4	0.008	0.000	0.009
imageNA2	2.836	0.008	2.845
impute-methods	0.880	0.004	1.205
itraqdata	0.112	0.000	0.109
listOf	0.004	0.000	0.004
makeNaData	0.804	0.000	0.804
missing-data	3.196	0.012	3.208
nFeatures	0.560	0.020	0.579
nQuants	0.132	0.000	0.130
naplot	0.064	0.008	0.070
navMS	3.688	0.040	5.807
normalise-methods	0.016	0.000	0.014
npcv	0.004	0.000	0.004
pSet-class	0.004	0.000	0.003
pickPeaks-method	0.216	0.000	0.218
plot-methods	1.268	0.000	1.270
plot2d-methods	0.736	0.000	0.738
plotDensity-methods	1.144	0.004	1.149
plotMzDelta-methods	1.156	0.004	1.160
plotNA-methods	0.440	0.000	0.438
plotSpectrumSpectrum-methods	0.800	0.004	0.806
precSelection	0.016	0.000	0.016
purityCorrect-methods	0.076	0.000	0.076
quantify-methods	1.932	0.212	5.054
readMSData	1.104	0.000	1.107
readMSnSet	0.268	0.008	0.292
readMgfData	2.552	0.004	2.557
readMzTabData	2.164	0.020	3.034
readMzTabData_v0.9	0.540	0.004	1.093
removeNoId-methods	1.232	0.000	1.232
removePeaks-methods	0.716	0.000	0.718
removeReporters-methods	0.656	0.000	0.654
selectFeatureData	0.152	0.008	0.174
smooth-methods	0.208	0.000	0.210
trimMz-methods	0.176	0.000	0.177
writeMgfData-methods	0.000	0.000	0.001
xic-methods	0	0	0

BioC 3.5: CHECK report for MSnbase on malbec2

Summary

Command output