BioC 3.4: CHECK report for MSnbase on morelia

Package: MSnbase

Version: 1.99.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.99.1.tar.gz

StartedAt: 2016-09-20 09:38:41 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:50:09 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 688.8 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.99.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/MSnbase.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.99.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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  6.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.4Mb
* 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 ... 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 7.365  0.242   8.150
averageMSnSet      5.119  0.111   5.811
quantify-methods   1.784  0.189   5.343
MzTab-class        1.272  0.026   5.680
* 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-3.4-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/3.3/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/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Spectrum1_class.c -o Spectrum1_class.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/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Spectrum2_class.c -o Spectrum2_class.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/3.3/Resources/library/Rcpp/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/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-3.4-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’
Creating a generic function for ‘t’ from package ‘base’ in package ‘MSnbase’
Creating a generic function for ‘scale’ from package ‘base’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
Creating a generic function for ‘split’ from package ‘base’ in package ‘MSnbase’
Creating a generic function for ‘all.equal’ from package ‘base’ in package ‘MSnbase’
** 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’
Creating a generic function for ‘t’ from package ‘base’ in package ‘MSnbase’
Creating a generic function for ‘scale’ from package ‘base’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
Creating a generic function for ‘split’ from package ‘base’ in package ‘MSnbase’
Creating a generic function for ‘all.equal’ from package ‘base’ in package ‘MSnbase’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnbase)

name	user	system	elapsed
FeatComp-class	0.211	0.014	0.262
FeaturesOfInterest-class	0.047	0.004	0.051
MSmap-class	0.001	0.000	0.001
MSnExp-class	0.375	0.004	0.402
MSnProcess-class	0.002	0.001	0.002
MSnSet-class	4.817	0.105	4.967
MSnSetList-class	3.647	0.019	3.668
MzTab-class	1.272	0.026	5.680
NAnnotatedDataFrame-class	0.012	0.000	0.012
OnDiskMSnExp-class	7.365	0.242	8.150
ProcessingStep-class	0.006	0.000	0.005
ReporterIons-class	0.011	0.000	0.012
TMT6	0.008	0.001	0.008
addIdentificationData-methods	0.424	0.004	0.428
averageMSnSet	5.119	0.111	5.811
bin-methods	0.589	0.015	0.604
calculateFragments-methods	0.407	0.012	0.418
chromatogram-methods	0.072	0.014	0.175
clean-methods	0.812	0.021	0.833
combineFeatures	0.753	0.006	0.758
commonFeatureNames	0.409	0.016	0.427
compareSpectra-methods	0.163	0.004	0.167
estimateNoise-method	0.003	0.000	0.003
exprsToRatios-methods	0.051	0.001	0.053
extractPrecSpectra-methods	0.335	0.002	0.337
featureCV	0.028	0.000	0.028
fillUp	0.004	0.001	0.005
formatRt	0.001	0.000	0.001
get.amino.acids	0.003	0.000	0.004
get.atomic.mass	0.001	0.000	0.001
getVariableName	0.002	0.000	0.002
iPQF	0.409	0.002	0.412
iTRAQ4	0.020	0.001	0.021
imageNA2	3.068	0.106	3.184
impute-methods	0.657	0.018	0.890
itraqdata	0.058	0.005	0.064
listOf	0.005	0.001	0.005
makeNaData	0.970	0.006	0.976
missing-data	2.622	0.055	2.689
nQuants	0.210	0.002	0.212
naplot	0.058	0.002	0.063
normalise-methods	0.015	0.001	0.016
npcv	0.002	0.001	0.002
pSet-class	0.001	0.000	0.002
pickPeaks-method	0.219	0.003	0.222
plot-methods	1.070	0.010	1.084
plot2d-methods	1.029	0.005	1.232
plotDensity-methods	0.563	0.002	0.989
plotMzDelta-methods	0.876	0.032	0.910
plotNA-methods	0.466	0.003	0.470
plotSpectrumSpectrum-methods	0.642	0.007	0.656
precSelection	0.010	0.001	0.010
purityCorrect-methods	0.033	0.002	0.035
quantify-methods	1.784	0.189	5.343
readMSData	0.794	0.004	0.799
readMSnSet	0.252	0.006	0.324
readMgfData	2.669	0.031	2.704
readMzTabData	2.428	0.016	3.309
readMzTabData_v0.9	0.506	0.004	0.915
removeNoId-methods	0.771	0.003	0.774
removePeaks-methods	0.765	0.011	0.776
removeReporters-methods	0.780	0.002	0.782
selectFeatureData	0.089	0.006	0.118
smooth-methods	0.255	0.007	0.262
trimMz-methods	0.158	0.002	0.160
writeMgfData-methods	0.001	0.001	0.001
xic-methods	0.000	0.000	0.001