| Back to "Blame Jeroen" build/check report for BioC 3.11 |
This page was generated on 2020-04-15 03:20:15 -0400 (Wed, 15 Apr 2020).
| These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html) |
| TO THE DEVELOPERS/MAINTAINERS OF THE MSnbase PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 55/89 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| MSnbase 2.13.6 Laurent Gatto
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | ERROR | skipped | skipped |
| Package: MSnbase |
| Version: 2.13.6 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/MSnbase_2.13.6.tar.gz && rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.13.6.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL MSnbase_2.13.6.zip && rm MSnbase_2.13.6.tar.gz MSnbase_2.13.6.zip |
| StartedAt: 2020-04-14 18:16:07 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 18:17:44 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 96.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/MSnbase_2.13.6.tar.gz && rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnbase.buildbin-libdir MSnbase_2.13.6.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL MSnbase_2.13.6.zip && rm MSnbase_2.13.6.tar.gz MSnbase_2.13.6.zip
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install for i386
* installing *source* package 'MSnbase' ...
** using staged installation
** libs
/mingw32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
^~~~~~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
^~~~~~~~~~~~~~
/mingw32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~
At top level:
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)
^~~~~~~~~~~~~~~~~~~~~~~~
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)
^~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/g++ -std=gnu++11 -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/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/libs/i386
** R
** data
*** moving datasets to lazyload DB
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 '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
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatogram-class.Rd:142: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatogram-class.Rd:146: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatogram-class.Rd:156: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Chromatograms-class html
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatograms-class.Rd:145: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/Chromatograms-class.Rd:150: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/MSnExp-class.Rd:252: 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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/MSnSet-class.Rd:504: 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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/chromatogram-MSnExp-method.Rd:76: 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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/combineFeatures.Rd:44: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/combineFeatures.Rd:151: 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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpMRkbmP/R.INSTALLc90181318ec/MSnbase/man/estimateNoise-method.Rd:45: file link 'estimateNoise' in package 'MALDIquant' does not exist and so has been treated as a topic
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
writeMzTabData 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
/mingw64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
^~~~~~~~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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,
^~~~~~~~~~~~~~
/mingw64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~
At top level:
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)
^~~~~~~~~~~~~~~~~~~~~~~~
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)
^~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/g++ -std=gnu++11 -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/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/MSnbase.buildbin-libdir/MSnbase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_2.13.6.zip
* DONE (MSnbase)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'MSnbase' successfully unpacked and MD5 sums checked