BioC 3.1: CHECK report for MSnbase on morelia

Package: MSnbase

Version: 1.16.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.16.2.tar.gz

StartedAt: 2015-10-08 04:33:13 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 04:37:36 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 262.8 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.16.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/MSnbase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [21s/21s] 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 ... [54s/53s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
quantify-methods 6.340  2.453   5.063
averageMSnSet    6.123  0.337   8.855
writeMzTabData   2.884  0.144   9.022
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [68s/52s]
 [68s/52s] 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

* installing *source* package ‘MSnbase’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MSnbase.so RcppExports.o imp_neighbour_avg.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.217	0.012	0.333
FeaturesOfInterest-class	0.072	0.004	0.077
MSmap-class	0.002	0.000	0.002
MSnExp-class	0.340	0.010	0.449
MSnProcess-class	0.001	0.000	0.001
MSnSet-class	0.311	0.014	0.325
NAnnotatedDataFrame-class	0.027	0.000	0.027
ReporterIons-class	0.023	0.001	0.023
TMT6	0.021	0.001	0.021
addIdentificationData-methods	0.527	0.003	0.530
averageMSnSet	6.123	0.337	8.855
bin-methods	0.534	0.016	0.551
calculateFragments-methods	0.488	0.068	0.555
chromatogram-methods	0.073	0.013	0.203
clean-methods	0.855	0.035	0.891
combineFeatures	0.505	0.063	0.568
compareSpectra-methods	0.145	0.019	0.164
exprsToRatios-methods	0.100	0.008	0.108
extractPrecSpectra-methods	0.444	0.035	0.480
featureCV	0.054	0.006	0.061
fillUp	0.008	0.003	0.010
formatRt	0.001	0.000	0.002
get.amino.acids	0.007	0.004	0.010
get.atomic.mass	0	0	0
getVariableName	0.002	0.001	0.003
iTRAQ4	0.016	0.005	0.020
imageNA2	2.009	0.119	2.170
impute-methods	0.723	0.028	0.978
itraqdata	0.032	0.002	0.033
listOf	0.003	0.000	0.003
missing-data	2.268	0.049	2.324
nQuants	0.292	0.003	0.294
normalise-methods	0.022	0.001	0.023
npcv	0.003	0.000	0.003
pSet-class	0.003	0.001	0.003
pickPeaks-method	0.223	0.009	0.232
plot-methods	0.982	0.008	1.037
plot2d-methods	0.485	0.002	0.487
plotDensity-methods	0.734	0.033	0.770
plotMzDelta-methods	1.095	0.071	1.167
plotNA-methods	0.402	0.003	0.409
plotSpectrumSpectrum-methods	0.698	0.076	0.775
precSelection	0.011	0.001	0.012
purityCorrect-methods	0.016	0.001	0.017
quantify-methods	6.340	2.453	5.063
readIspyData	0	0	0
readMSData	0.442	0.020	0.462
readMSnSet	0.001	0.000	0.000
readMgfData	4.052	0.255	4.313
readMzTabData	0.241	0.002	0.547
removeNoId-methods	0.869	0.004	0.873
removePeaks-methods	0.887	0.011	0.898
removeReporters-methods	0.619	0.023	0.642
smooth-methods	0.218	0.004	0.222
trimMz-methods	0.109	0.001	0.110
writeMgfData-methods	0.001	0.000	0.002
writeMzTabData	2.884	0.144	9.022
xic-methods	0.001	0.000	0.001