BioC 3.4: CHECK report for MSnbase on morelia

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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_2.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/MSnbase.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.0.2’
* 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 ... 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 13.635  0.423  14.621
averageMSnSet       7.715  0.139   8.174
MSnSet-class        6.815  0.167   7.359
quantify-methods    2.130  0.257   8.262
MzTab-class         1.664  0.034   5.796
* 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: 2 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
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/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
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/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’
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	0.249	0.022	0.392
FeaturesOfInterest-class	0.075	0.008	0.084
MSmap-class	0.002	0.001	0.002
MSnExp-class	0.494	0.006	0.576
MSnProcess-class	0.002	0.000	0.003
MSnSet-class	6.815	0.167	7.359
MSnSetList-class	4.259	0.025	4.293
MzTab-class	1.664	0.034	5.796
NAnnotatedDataFrame-class	0.028	0.000	0.030
OnDiskMSnExp-class	13.635	0.423	14.621
ProcessingStep-class	0.008	0.001	0.007
ReporterIons-class	0.020	0.000	0.021
TMT6	0.015	0.001	0.016
addIdentificationData-methods	0.598	0.007	0.605
averageMSnSet	7.715	0.139	8.174
bin-methods	0.802	0.025	0.827
calculateFragments-methods	0.628	0.023	0.651
chromatogram-methods	0.071	0.015	0.167
clean-methods	1.175	0.058	1.237
combineFeatures	1.184	0.016	1.200
commonFeatureNames	0.612	0.019	0.633
compareSpectra-methods	0.310	0.019	0.329
estimateNoise-method	0.034	0.000	0.035
exprsToRatios-methods	0.081	0.001	0.082
extractPrecSpectra-methods	0.517	0.003	0.520
featureCV	0.056	0.001	0.057
fillUp	0.011	0.001	0.011
formatRt	0.001	0.000	0.002
get.amino.acids	0.006	0.001	0.007
get.atomic.mass	0.001	0.000	0.001
getVariableName	0.002	0.000	0.002
iPQF	0.509	0.006	0.518
iTRAQ4	0.020	0.001	0.021
imageNA2	4.709	0.167	4.889
impute-methods	0.804	0.020	1.167
itraqdata	0.075	0.006	0.081
listOf	0.007	0.000	0.007
makeNaData	1.560	0.011	1.572
missing-data	4.051	0.090	4.158
nQuants	0.230	0.001	0.232
naplot	0.095	0.005	0.101
normalise-methods	0.025	0.001	0.027
npcv	0.004	0.000	0.004
pSet-class	0.003	0.001	0.003
pickPeaks-method	0.419	0.004	0.423
plot-methods	2.260	0.015	2.280
plot2d-methods	0.990	0.004	0.998
plotDensity-methods	1.000	0.003	1.004
plotMzDelta-methods	1.387	0.051	1.439
plotNA-methods	0.611	0.004	0.617
plotSpectrumSpectrum-methods	0.943	0.011	0.954
precSelection	0.016	0.001	0.016
purityCorrect-methods	0.029	0.002	0.032
quantify-methods	2.130	0.257	8.262
readMSData	0.947	0.006	0.954
readMSnSet	0.429	0.012	0.572
readMgfData	3.686	0.034	3.817
readMzTabData	3.255	0.022	4.424
readMzTabData_v0.9	0.218	0.002	0.623
removeNoId-methods	1.208	0.004	1.213
removePeaks-methods	1.497	0.032	1.530
removeReporters-methods	0.831	0.005	0.837
selectFeatureData	0.139	0.007	0.160
smooth-methods	0.296	0.011	0.307
trimMz-methods	0.193	0.002	0.194
writeMgfData-methods	0.002	0.000	0.001
xic-methods	0.001	0.000	0.001

BioC 3.4: CHECK report for MSnbase on morelia

Summary

Command output