BioC 3.1: CHECK report for MSnbase on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MSnbase_1.16.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.16.2’
* 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 ... [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 ... NOTE
curveStats,Spectrum : .local: no visible global function definition for
  ‘curveStats_Spectrum’
exprsToRatios,matrix : .local: no visible global function definition
  for ‘conames<-’
impute,MSnSet : .local: no visible global function definition for
  ‘prelim.norm’
impute,MSnSet : .local: no visible global function definition for
  ‘em.norm’
impute,MSnSet : .local: no visible global function definition for
  ‘rngseed’
impute,MSnSet : .local: no visible global function definition for
  ‘imp.norm’
plot3D,MSmap : .local: no visible global function definition for
  ‘plot3d’
plot3D,MSmap : .local: no visible binding for global variable ‘ms’
plotMzDelta,mzRramp : .local: no visible binding for global variable
  ‘ms’
* 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 ... [42s/44s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
quantify-methods 6.678  0.909   3.511
averageMSnSet    5.642  0.067   5.838
writeMzTabData   2.409  0.028   8.528
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [48s/43s]
 [48s/43s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

* installing *source* package ‘MSnbase’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o imp_neighbour_avg.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/MSnbase.Rcheck/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (MSnbase)

name	user	system	elapsed
FeatComp-class	0.183	0.008	0.230
FeaturesOfInterest-class	0.052	0.004	0.056
MSmap-class	0.001	0.000	0.001
MSnExp-class	0.299	0.004	0.322
MSnProcess-class	0.002	0.000	0.002
MSnSet-class	0.243	0.016	0.259
NAnnotatedDataFrame-class	0.019	0.000	0.019
ReporterIons-class	0.017	0.000	0.017
TMT6	0.013	0.000	0.013
addIdentificationData-methods	0.505	0.000	0.504
averageMSnSet	5.642	0.067	5.838
bin-methods	0.61	0.00	0.61
calculateFragments-methods	0.460	0.008	0.468
chromatogram-methods	0.038	0.008	0.116
clean-methods	0.805	0.028	0.832
combineFeatures	0.375	0.000	0.375
compareSpectra-methods	0.124	0.000	0.126
exprsToRatios-methods	0.071	0.000	0.071
extractPrecSpectra-methods	0.429	0.000	0.428
featureCV	0.040	0.000	0.039
fillUp	0.005	0.000	0.006
formatRt	0.001	0.000	0.001
get.amino.acids	0.004	0.000	0.005
get.atomic.mass	0	0	0
getVariableName	0.000	0.000	0.001
iTRAQ4	0.015	0.000	0.014
imageNA2	1.871	0.016	1.901
impute-methods	0.602	0.008	0.752
itraqdata	0.038	0.000	0.038
listOf	0.003	0.000	0.003
missing-data	2.156	0.012	2.170
nQuants	0.22	0.00	0.22
normalise-methods	0.02	0.00	0.02
npcv	0.003	0.000	0.003
pSet-class	0.002	0.000	0.002
pickPeaks-method	0.177	0.004	0.182
plot-methods	1.006	0.000	1.007
plot2d-methods	0.501	0.000	0.504
plotDensity-methods	0.539	0.004	0.552
plotMzDelta-methods	1.397	0.020	1.415
plotNA-methods	0.334	0.004	0.338
plotSpectrumSpectrum-methods	0.642	0.000	0.642
precSelection	0.014	0.000	0.013
purityCorrect-methods	0.017	0.004	0.022
quantify-methods	6.678	0.909	3.511
readIspyData	0	0	0
readMSData	0.416	0.000	0.416
readMSnSet	0.000	0.000	0.001
readMgfData	3.567	0.008	3.574
readMzTabData	0.191	0.001	0.465
removeNoId-methods	0.937	0.008	0.944
removePeaks-methods	1.039	0.008	1.050
removeReporters-methods	0.583	0.004	0.596
smooth-methods	0.196	0.000	0.199
trimMz-methods	0.117	0.000	0.119
writeMgfData-methods	0.001	0.000	0.001
writeMzTabData	2.409	0.028	8.528
xic-methods	0.001	0.000	0.000

BioC 3.1: CHECK report for MSnbase on zin2

Summary

Command output