BioC 3.5: CHECK report for MSnbase on toluca2

Package: MSnbase

Version: 2.1.18

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_2.1.18.tar.gz

StartedAt: 2017-04-23 07:05:46 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:25:12 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 1165.4 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_2.1.18.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘2.1.18’
* 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  8.2Mb
  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 sizes of PDF files under ‘inst/doc’ ... 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 14.299  0.412  14.835
MSnSet-class        9.467  0.140   9.950
averageMSnSet       8.140  0.173   9.124
aggvar              6.746  0.069   6.888
quantify-methods    2.432  0.264   7.100
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

* installing *source* package ‘MSnbase’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: unused function '_new_Spectrum1' [-Wunused-function]
static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
            ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: unused function '_new_Spectrum2' [-Wunused-function]
static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
            ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c utils.c -o utils.o
utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable]
  int i1, i2, ret;
              ^
utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable]
  int i1, i2, ret;
              ^
utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable]
  double d1, d2, ret;
                 ^
utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable]
  double d1, d2, ret;
                 ^
utils.c:121:12: warning: unused function 'compar_double_asc_order' [-Wunused-function]
static int compar_double_asc_order(const void *p1, const void *p2)
           ^
utils.c:131:12: warning: unused function 'compar_double_desc_order' [-Wunused-function]
static int compar_double_desc_order(const void *p1, const void *p2)
           ^
6 warnings generated.
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 Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.427	0.029	0.527
FeaturesOfInterest-class	0.128	0.005	0.151
MSmap-class	0.002	0.000	0.002
MSnExp-class	0.481	0.005	0.544
MSnProcess-class	0.002	0.000	0.002
MSnSet-class	9.467	0.140	9.950
MSnSetList-class	4.637	0.016	4.695
MzTab-class	1.399	0.025	3.636
NAnnotatedDataFrame-class	0.032	0.001	0.032
OnDiskMSnExp-class	14.299	0.412	14.835
ProcessingStep-class	0.007	0.000	0.008
ReporterIons-class	0.025	0.001	0.026
TMT6	0.024	0.001	0.025
addIdentificationData-methods	0.871	0.008	0.883
aggvar	6.746	0.069	6.888
averageMSnSet	8.140	0.173	9.124
bin-methods	0.953	0.015	1.042
calculateFragments-methods	0.827	0.016	0.869
chromatogram-methods	0.115	0.019	0.138
clean-methods	1.000	0.048	1.068
combineFeatures	1.164	0.011	1.190
commonFeatureNames	0.575	0.017	0.614
compareSpectra-methods	0.299	0.008	0.320
estimateNoise-method	0.015	0.001	0.015
exprsToRatios-methods	0.122	0.001	0.124
extractPrecSpectra-methods	0.530	0.003	0.540
featureCV	0.042	0.002	0.043
fillUp	0.021	0.000	0.021
formatRt	0.001	0.000	0.001
get.amino.acids	0.005	0.000	0.005
get.atomic.mass	0.000	0.001	0.001
getVariableName	0.005	0.000	0.005
iPQF	0.695	0.003	0.704
iTRAQ4	0.012	0.001	0.012
imageNA2	3.949	0.140	4.105
impute-methods	0.977	0.015	1.015
itraqdata	0.131	0.004	0.136
listOf	0.005	0.001	0.005
makeNaData	1.526	0.009	1.792
missing-data	4.214	0.081	4.452
nFeatures	0.637	0.037	0.818
nQuants	0.165	0.002	0.191
naplot	0.081	0.003	0.105
navMS	3.582	0.083	4.076
normalise-methods	0.021	0.001	0.038
npcv	0.007	0.001	0.007
pSet-class	0.003	0.000	0.003
pickPeaks-method	0.367	0.007	0.378
plot-methods	1.927	0.009	2.055
plot2d-methods	0.927	0.005	0.938
plotDensity-methods	1.413	0.004	1.462
plotMzDelta-methods	1.370	0.044	1.419
plotNA-methods	0.620	0.003	0.625
plotSpectrumSpectrum-methods	0.914	0.007	0.932
precSelection	0.027	0.001	0.029
purityCorrect-methods	0.132	0.002	0.139
quantify-methods	2.432	0.264	7.100
readMSData	1.015	0.004	1.031
readMSnSet	0.412	0.008	0.421
readMgfData	3.803	0.046	3.932
readMzTabData	2.954	0.025	3.786
readMzTabData_v0.9	0.444	0.004	0.780
removeNoId-methods	1.272	0.006	1.290
removePeaks-methods	1.130	0.011	1.147
removeReporters-methods	0.990	0.006	1.002
selectFeatureData	0.137	0.011	0.151
smooth-methods	0.341	0.010	0.354
trimMz-methods	0.207	0.001	0.208
writeMgfData-methods	0.001	0.000	0.002
xic-methods	0	0	0