BioC 3.5: CHECK report for MSnbase on veracruz2

Package: MSnbase

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_2.2.0.tar.gz

StartedAt: 2017-10-18 06:29:29 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:47:11 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 1061.5 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_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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  8.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    4.4Mb
* 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 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 13.646  0.462  14.476
MSnSet-class        8.912  0.124   9.340
averageMSnSet       7.307  0.221   7.747
aggvar              5.807  0.088   6.065
quantify-methods    2.266  0.250   6.755
* 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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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	0.380	0.028	0.418
FeaturesOfInterest-class	0.113	0.007	0.122
MSmap-class	0.002	0.000	0.002
MSnExp-class	0.407	0.006	0.422
MSnProcess-class	0.001	0.000	0.002
MSnSet-class	8.912	0.124	9.340
MSnSetList-class	3.930	0.028	4.088
MzTab-class	1.211	0.024	4.191
NAnnotatedDataFrame-class	0.027	0.000	0.027
OnDiskMSnExp-class	13.646	0.462	14.476
ProcessingStep-class	0.006	0.000	0.007
ReporterIons-class	0.020	0.001	0.021
TMT6	0.022	0.001	0.024
addIdentificationData-methods	0.835	0.009	0.864
aggvar	5.807	0.088	6.065
averageMSnSet	7.307	0.221	7.747
bin-methods	0.933	0.019	0.990
calculateFragments-methods	0.779	0.017	0.812
chromatogram-methods	0.104	0.016	0.124
clean-methods	0.885	0.042	0.957
combineFeatures	1.017	0.017	1.058
commonFeatureNames	0.532	0.012	0.554
compareSpectra-methods	0.265	0.009	0.279
estimateNoise-method	0.014	0.001	0.014
exprsToRatios-methods	0.099	0.002	0.102
extractPrecSpectra-methods	0.582	0.005	0.599
featureCV	0.037	0.001	0.040
fillUp	0.018	0.001	0.018
formatRt	0.001	0.000	0.001
get.amino.acids	0.005	0.001	0.006
get.atomic.mass	0.001	0.000	0.001
getVariableName	0.005	0.000	0.004
iPQF	0.528	0.006	0.550
iTRAQ4	0.012	0.000	0.013
imageNA2	4.674	0.071	4.940
impute-methods	0.934	0.018	0.993
itraqdata	0.135	0.003	0.142
listOf	0.004	0.000	0.004
makeNaData	1.251	0.009	1.312
missing-data	3.989	0.049	4.154
nFeatures	0.595	0.030	0.628
nQuants	0.153	0.001	0.156
naplot	0.093	0.010	0.106
navMS	3.753	0.099	3.992
normalise-methods	0.018	0.002	0.019
npcv	0.006	0.000	0.006
pSet-class	0.002	0.001	0.003
pickPeaks-method	0.311	0.008	0.333
plot-methods	1.655	0.013	1.732
plot2d-methods	0.645	0.005	0.697
plotDensity-methods	1.171	0.009	1.213
plotMzDelta-methods	1.228	0.046	1.330
plotNA-methods	0.574	0.005	0.605
plotSpectrumSpectrum-methods	0.898	0.010	0.937
precSelection	0.021	0.001	0.022
purityCorrect-methods	0.105	0.003	0.110
quantify-methods	2.266	0.250	6.755
readMSData	1.045	0.007	1.091
readMSnSet	0.338	0.006	0.353
readMgfData	3.196	0.043	3.359
readMzTabData	2.805	0.035	3.433
readMzTabData_v0.9	0.371	0.003	0.707
removeNoId-methods	1.409	0.010	1.470
removePeaks-methods	1.128	0.017	1.237
removeReporters-methods	0.925	0.009	0.976
selectFeatureData	0.123	0.007	0.131
smooth-methods	0.310	0.009	0.325
trimMz-methods	0.213	0.002	0.217
writeMgfData-methods	0.001	0.001	0.001
xic-methods	0.001	0.000	0.001