Aaron Taudt
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/AneuFinder |
| git_branch: RELEASE_3_13 |
| git_last_commit: 1c7aed6 |
| git_last_commit_date: 2021-05-19 12:19:05 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:57 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the AneuFinder package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AneuFinder.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 56/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AneuFinder 1.20.0 (landing page) Aaron Taudt
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: AneuFinder |
| Version: 1.20.0 |
| Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/AneuFinder_1.20.0.tar.gz && rm -rf AneuFinder.buildbin-libdir && mkdir AneuFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AneuFinder.buildbin-libdir AneuFinder_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL AneuFinder_1.20.0.zip && rm AneuFinder_1.20.0.tar.gz AneuFinder_1.20.0.zip |
| StartedAt: 2021-10-14 09:10:19 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 09:12:14 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 114.5 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/AneuFinder_1.20.0.tar.gz && rm -rf AneuFinder.buildbin-libdir && mkdir AneuFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AneuFinder.buildbin-libdir AneuFinder_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL AneuFinder_1.20.0.zip && rm AneuFinder_1.20.0.tar.gz AneuFinder_1.20.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'AneuFinder' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loghmm.cpp -o loghmm.o
loghmm.cpp:320: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
loghmm.cpp:480: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
loghmm.cpp:518: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
loghmm.cpp:583: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
scalehmm.cpp:400: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
scalehmm.cpp:694: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
scalehmm.cpp:732: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
scalehmm.cpp:791: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/AneuFinder.buildbin-libdir/00LOCK-AneuFinder/00new/AneuFinder/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'AneuFinder'
finding HTML links ... done
AneuFinder-package html
Aneufinder html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/AneuFinder.buildbin-libdir/00LOCK-AneuFinder/00new/AneuFinder/help/Aneufinder.html
finding level-2 HTML links ... done
DNAcopy.findCNVs html
HMM.findCNVs html
aneuBiHMM html
aneuHMM html
annotateBreakpoints html
bam2GRanges html
bed2GRanges html
bi.edivisive.findCNVs html
biDNAcopy.findCNVs html
biHMM.findCNVs html
binReads html
binned.data html
binning html
blacklist html
clusterByQuality html
clusterHMMs html
collapseBins html
colors html
compareMethods html
compareModels html
consensusSegments html
correctGC html
edivisive.findCNVs html
estimateComplexity html
export html
filterSegments html
findCNVs html
findCNVs.strandseq html
findHotspots html
fixedWidthBins html
getBreakpoints html
getDistinctColors html
getQC html
getSCEcoordinates html
heatmapAneuploidies html
heatmapGenomewide html
heatmapGenomewideClusters html
hotspotter html
hotspotter.variable html
importBed html
initializeStates html
karyotypeMeasures html
loadFromFiles html
mergeStrandseqFiles html
plot.GRanges html
plot.GRangesList html
plot.aneuBiHMM html
plot.aneuHMM html
plot.character html
plotHeterogeneity html
plotHistogram html
plotKaryogram html
plotProfile html
plot_pca html
print.aneuBiHMM html
print.aneuHMM html
qualityControl html
readConfig html
refineBreakpoints html
simulateReads html
subsetByCNVprofile html
transCoord html
variableWidthBins html
writeConfig html
zinbinom 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 'AneuFinder' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loghmm.cpp -o loghmm.o
loghmm.cpp:320: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
loghmm.cpp:480: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
loghmm.cpp:518: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
loghmm.cpp:583: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
scalehmm.cpp:400: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
scalehmm.cpp:694: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
scalehmm.cpp:732: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
scalehmm.cpp:791: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/AneuFinder.buildbin-libdir/AneuFinder/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AneuFinder' as AneuFinder_1.20.0.zip
* DONE (AneuFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'AneuFinder' successfully unpacked and MD5 sums checked