BioC 3.5: CHECK report for MSnbase on tokay2

Package: MSnbase

Version: 2.2.0

Command: rm -rf MSnbase.buildbin-libdir MSnbase.Rcheck && mkdir MSnbase.buildbin-libdir MSnbase.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_2.2.0.tar.gz >MSnbase.Rcheck\00install.out 2>&1 && cp MSnbase.Rcheck\00install.out MSnbase-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_2.2.0.tar.gz

StartedAt: 2017-10-18 01:33:49 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:06:59 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 1989.5 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   rm -rf MSnbase.buildbin-libdir MSnbase.Rcheck && mkdir MSnbase.buildbin-libdir MSnbase.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_2.2.0.tar.gz >MSnbase.Rcheck\00install.out 2>&1 && cp MSnbase.Rcheck\00install.out MSnbase-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'MSnbase' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    4.4Mb
    libs   1.5Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/i386/MSnbase.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
OnDiskMSnExp-class 12.92   0.71   17.10
readMzTabData      12.05   0.00   12.17
MzTab-class         7.71   0.02    8.42
MSnSet-class        7.45   0.01    8.02
averageMSnSet       6.43   0.22    9.10
navMS               3.31   0.09   14.73
quantify-methods    1.92   0.05    9.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
OnDiskMSnExp-class 13.42   0.39   13.80
readMzTabData       8.67   0.10    8.81
MSnSet-class        7.75   0.04    7.80
averageMSnSet       7.20   0.17    8.31
MzTab-class         5.30   0.03    5.55
quantify-methods    3.01   0.00   10.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: '_new_Spectrum1' defined but not used [-Wunused-function]
 static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: '_new_Spectrum2' defined but not used [-Wunused-function]
 static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function 'compar_double_dd_for_stable_asc_order':
utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function 'compar_double_dd_for_stable_desc_order':
utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function 'compar_double_asc_order':
utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: In function 'compar_double_desc_order':
utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: At top level:
utils.c:121:12: warning: 'compar_double_asc_order' defined but not used [-Wunused-function]
 static int compar_double_asc_order(const void *p1, const void *p2)
            ^
utils.c:131:12: warning: 'compar_double_desc_order' defined but not used [-Wunused-function]
 static int compar_double_desc_order(const void *p1, const void *p2)
            ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/i386
** 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

install for x64

* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: '_new_Spectrum1' defined but not used [-Wunused-function]
 static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: '_new_Spectrum2' defined but not used [-Wunused-function]
 static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function 'compar_double_dd_for_stable_asc_order':
utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function 'compar_double_dd_for_stable_desc_order':
utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable]
   int i1, i2, ret;
               ^
utils.c: In function 'compar_double_asc_order':
utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: In function 'compar_double_desc_order':
utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable]
   double d1, d2, ret;
                  ^
utils.c: At top level:
utils.c:121:12: warning: 'compar_double_asc_order' defined but not used [-Wunused-function]
 static int compar_double_asc_order(const void *p1, const void *p2)
            ^
utils.c:131:12: warning: 'compar_double_desc_order' defined but not used [-Wunused-function]
 static int compar_double_desc_order(const void *p1, const void *p2)
            ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_2.2.0.zip
* DONE (MSnbase)

name	user	system	elapsed
FeatComp-class	0.51	0.04	4.51
FeaturesOfInterest-class	0.10	0.02	0.11
MSmap-class	0	0	0
MSnExp-class	0.41	0.00	0.40
MSnProcess-class	0	0	0
MSnSet-class	7.45	0.01	8.02
MSnSetList-class	2.35	0.02	2.36
MzTab-class	7.71	0.02	8.42
NAnnotatedDataFrame-class	0.04	0.00	0.03
OnDiskMSnExp-class	12.92	0.71	17.10
ProcessingStep-class	0.01	0.00	0.01
ReporterIons-class	0.02	0.00	0.02
TMT6	0.01	0.00	0.01
addIdentificationData-methods	0.61	0.00	0.61
aggvar	3.96	0.02	4.03
averageMSnSet	6.43	0.22	9.10
bin-methods	0.45	0.06	0.52
calculateFragments-methods	0.66	0.00	0.66
chromatogram-methods	0.12	0.12	1.26
clean-methods	0.73	0.03	0.77
combineFeatures	1.07	0.03	1.09
commonFeatureNames	0.37	0.00	0.38
compareSpectra-methods	0.22	0.00	0.22
estimateNoise-method	0.02	0.00	0.01
exprsToRatios-methods	0.06	0.00	0.06
extractPrecSpectra-methods	0.45	0.02	0.47
featureCV	0.03	0.00	0.03
fillUp	0.02	0.00	0.02
formatRt	0	0	0
get.amino.acids	0	0	0
get.atomic.mass	0	0	0
getVariableName	0.00	0.02	0.01
iPQF	0.39	0.00	0.40
iTRAQ4	0.02	0.00	0.01
imageNA2	3.29	0.06	3.36
impute-methods	0.99	0.00	1.63
itraqdata	0.18	0.00	0.18
listOf	0	0	0
makeNaData	0.86	0.00	0.86
missing-data	2.57	0.03	2.60
nFeatures	0.63	0.03	0.66
nQuants	0.09	0.00	0.09
naplot	0.08	0.00	0.08
navMS	3.31	0.09	14.73
normalise-methods	0.02	0.00	0.02
npcv	0	0	0
pSet-class	0	0	0
pickPeaks-method	0.2	0.0	0.2
plot-methods	2.06	0.02	2.08
plot2d-methods	0.63	0.00	0.66
plotDensity-methods	0.84	0.00	0.84
plotMzDelta-methods	1.30	0.03	1.33
plotNA-methods	0.39	0.00	0.39
plotSpectrumSpectrum-methods	0.62	0.00	0.62
precSelection	0.02	0.00	0.02
purityCorrect-methods	0.06	0.00	0.06
quantify-methods	1.92	0.05	9.53
readMSData	0.91	0.00	0.91
readMSnSet	0.53	0.00	0.75
readMgfData	3.00	0.05	3.05
readMzTabData	12.05	0.00	12.17
readMzTabData_v0.9	0.39	0.00	0.44
removeNoId-methods	1.03	0.00	1.03
removePeaks-methods	0.75	0.02	0.77
removeReporters-methods	0.59	0.00	0.59
selectFeatureData	0.24	0.00	0.27
smooth-methods	0.33	0.01	0.34
trimMz-methods	0.26	0.00	0.27
writeMgfData-methods	0	0	0
xic-methods	0	0	0

name	user	system	elapsed
FeatComp-class	0.58	0.02	0.59
FeaturesOfInterest-class	0.11	0.00	0.11
MSmap-class	0	0	0
MSnExp-class	0.45	0.00	0.45
MSnProcess-class	0	0	0
MSnSet-class	7.75	0.04	7.80
MSnSetList-class	3.45	0.00	3.45
MzTab-class	5.30	0.03	5.55
NAnnotatedDataFrame-class	0.03	0.00	0.03
OnDiskMSnExp-class	13.42	0.39	13.80
ProcessingStep-class	0.02	0.00	0.01
ReporterIons-class	0.01	0.00	0.02
TMT6	0.02	0.00	0.01
addIdentificationData-methods	0.87	0.02	0.89
aggvar	4.27	0.00	4.27
averageMSnSet	7.20	0.17	8.31
bin-methods	0.67	0.03	0.70
calculateFragments-methods	0.94	0.00	0.94
chromatogram-methods	0.06	0.11	0.17
clean-methods	0.80	0.02	0.81
combineFeatures	0.86	0.01	0.88
commonFeatureNames	0.45	0.00	0.45
compareSpectra-methods	0.89	0.00	0.89
estimateNoise-method	0	0	0
exprsToRatios-methods	0.09	0.00	0.09
extractPrecSpectra-methods	0.64	0.00	0.64
featureCV	0.03	0.00	0.03
fillUp	0.02	0.00	0.02
formatRt	0	0	0
get.amino.acids	0	0	0
get.atomic.mass	0	0	0
getVariableName	0	0	0
iPQF	0.42	0.00	0.43
iTRAQ4	0.02	0.00	0.01
imageNA2	3.36	0.02	3.38
impute-methods	0.97	0.02	1.42
itraqdata	0.12	0.01	0.14
listOf	0	0	0
makeNaData	0.97	0.00	0.97
missing-data	3.24	0.05	3.28
nFeatures	0.56	0.01	0.58
nQuants	0.12	0.00	0.12
naplot	0.1	0.0	0.1
navMS	4.00	0.05	4.04
normalise-methods	0.01	0.02	0.03
npcv	0	0	0
pSet-class	0	0	0
pickPeaks-method	0.23	0.03	0.27
plot-methods	1.49	0.00	1.48
plot2d-methods	0.67	0.00	0.67
plotDensity-methods	0.98	0.00	0.99
plotMzDelta-methods	1.30	0.04	1.34
plotNA-methods	1.02	0.02	1.03
plotSpectrumSpectrum-methods	0.90	0.00	0.91
precSelection	0.02	0.00	0.01
purityCorrect-methods	0.08	0.02	0.10
quantify-methods	3.01	0.00	10.95
readMSData	1.36	0.00	1.36
readMSnSet	0.28	0.01	0.30
readMgfData	2.59	0.03	2.63
readMzTabData	8.67	0.10	8.81
readMzTabData_v0.9	0.39	0.00	0.42
removeNoId-methods	1.52	0.00	1.52
removePeaks-methods	1.08	0.00	1.07
removeReporters-methods	0.79	0.01	0.80
selectFeatureData	0.10	0.00	0.11
smooth-methods	0.29	0.00	0.28
trimMz-methods	0.2	0.0	0.2
writeMgfData-methods	0	0	0
xic-methods	0	0	0