Laurent Gatto
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MSnbase |
| Branch: RELEASE_3_9 |
| Last Commit: 4d5899b |
| Last Changed Date: 2019-05-31 07:14:27 -0400 (Fri, 31 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:24:51 -0400 (Wed, 16 Oct 2019).
| Package 1055/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSnbase 2.10.1 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: MSnbase |
| Version: 2.10.1 |
| Command: rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.10.1.tar.gz |
| StartedAt: 2019-10-16 09:43:57 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 09:45:15 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 77.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: MSnbase_2.10.1.zip |
| PackageFileSize: 6.969 MiB |
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### Running command:
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### rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.10.1.tar.gz
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install for i386
* installing *source* package 'MSnbase' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/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 '"MSnSet","SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"SummarizedExperiment","MSnSet"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
** inst
** byte-compile and prepare 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 '"MSnSet","SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"SummarizedExperiment","MSnSet"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
** help
*** installing help indices
converting help for package 'MSnbase'
finding HTML links ... done
Chromatogram-class html
Chromatograms-class html
FeatComp-class html
FeaturesOfInterest-class html
finding level-2 HTML links ... done
MIAPE-class html
MSmap-class html
MSnExp-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpElksDv/R.INSTALL21506a7b1b70/MSnbase/man/MSnExp-class.Rd:251: file link 'isolationWindow' in package 'mzR' does not exist and so has been treated as a topic
MSnProcess-class html
MSnSet-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpElksDv/R.INSTALL21506a7b1b70/MSnbase/man/MSnSet-class.Rd:510: file link 'write.exprs' in package 'MSnbase' does not exist and so has been treated as a topic
MSnSetList-class html
MSnbaseOptions html
MzTab-class html
OnDiskMSnExp-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpElksDv/R.INSTALL21506a7b1b70/MSnbase/man/OnDiskMSnExp-class.Rd:509: file link 'normalize' in package 'MSnbase' does not exist and so has been treated as a topic
ProcessingStep-class html
ReporterIons-class html
Spectra html
Spectrum-class html
Spectrum1-class html
Spectrum2-class html
TMT6 html
addIdentificationData-methods html
aggvar html
averageMSnSet html
bin-methods html
calculateFragments-methods html
chromatogram-MSnExp-method html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpElksDv/R.INSTALL21506a7b1b70/MSnbase/man/chromatogram-MSnExp-method.Rd:70: file link 'Chromatogram' in package 'MSnbase' does not exist and so has been treated as a topic
clean-methods html
combineFeatures html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpElksDv/R.INSTALL21506a7b1b70/MSnbase/man/combineFeatures.Rd:52: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpElksDv/R.INSTALL21506a7b1b70/MSnbase/man/combineFeatures.Rd:159: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
combineSpectra html
combineSpectraMovingWindow html
commonFeatureNames html
compareMSnSets html
compareSpectra-methods html
consensusSpectrum html
defunct html
estimateMzResolution html
estimateMzScattering html
estimateNoise-method html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpElksDv/R.INSTALL21506a7b1b70/MSnbase/man/estimateNoise-method.Rd:45: file link 'estimateNoise' in package 'MALDIquant' does not exist and so has been treated as a topic
exprsToRatios-methods html
extractPrecSpectra-methods html
fData-utils html
factorsAsStrings html
featureCV html
fillUp html
filterIdentificationDataFrame html
formatRt html
get.amino.acids html
get.atomic.mass html
getVariableName html
grepEcols html
hasSpectraOrChromatograms html
iPQF html
iTRAQ4 html
imageNA2 html
impute-methods html
isCentroidedFromFile html
itraqdata html
listOf html
makeCamelCase html
makeNaData html
meanMzInts html
missing-data html
mzRident2dfr html
nFeatures html
nQuants html
naplot html
navMS html
normToReference html
normalise-methods html
npcv html
pSet-class html
pickPeaks-method html
plot-methods html
plot2d-methods html
plotDensity-methods html
plotMzDelta-methods html
plotNA-methods html
plotSpectrumSpectrum-methods html
precSelection html
purityCorrect-methods html
quantify-methods html
readMSData html
readMSnSet html
readMgfData html
readMzIdData html
readMzTabData html
readMzTabData_v0.9 html
readSRMData html
reduce-data.frame-method html
removeNoId-methods html
removePeaks-methods html
removeReporters-methods html
selectFeatureData html
smooth-methods html
trimMz-methods html
updateObject-methods html
writeMSData html
writeMgfData-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_2.10.1.zip
* DONE (MSnbase)