Mark Dunning
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/beadarray |
| Branch: RELEASE_3_9 |
| Last Commit: 0502079 |
| Last Changed Date: 2019-05-02 11:53:05 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:20:26 -0400 (Wed, 16 Oct 2019).
| Package 121/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| beadarray 2.34.0 Mark Dunning
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: beadarray |
| Version: 2.34.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/beadarray_2.34.0.tar.gz && rm -rf beadarray.buildbin-libdir && mkdir beadarray.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=beadarray.buildbin-libdir beadarray_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL beadarray_2.34.0.zip && rm beadarray_2.34.0.tar.gz beadarray_2.34.0.zip |
| StartedAt: 2019-10-15 19:59:05 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 20:00:21 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 76.1 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/3.9/bioc/src/contrib/beadarray_2.34.0.tar.gz && rm -rf beadarray.buildbin-libdir && mkdir beadarray.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=beadarray.buildbin-libdir beadarray_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL beadarray_2.34.0.zip && rm beadarray_2.34.0.tar.gz beadarray_2.34.0.zip
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install for i386
* installing *source* package 'beadarray' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c BASH.c -o BASH.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c HULK.c -o HULK.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c determiningGridPositions.c -o determiningGridPositions.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:196:29: warning: 'ma' may be used uninitialized in this function [-Wmaybe-uninitialized]
if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
^
findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
^
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:226:20: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized]
beadStatusStruct *status;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
^
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
^
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
^
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.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/beadarray.buildbin-libdir/00LOCK-beadarray/00new/beadarray/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'beadarray'
finding HTML links ... done
BASH html
BASHCompact html
BASHDiffuse html
BASHExtended html
GEO html
GEOtemplate html
HULK html
addFeatureData html
annotationInterface html
backgroundCorrectSingleSection html
beadarray-package html
beadarrayUsersGuide html
boxplot html
calculateDetection html
calculateOutlierStats html
checkRegistration html
class-BeadLevelList html
class-ExpressionSetIllumina html
class-beadLevelData html
class-beadRegistrationData html
class-illuminaChannel html
class-limmaResults html
combine html
controlProbeDetection html
convertBeadLevelList html
createTargetsFile html
deprecatedFunctions html
dim html
expressionQCPipeline html
generateNeighbours html
getBeadData html
identifyControlBeads html
illuminaOutlierMethod html
imageProcessing html
imageplot html
insertBeadData html
insertSectionData html
limmaDE html
makeControlProfile html
makeQCTable html
maplots html
medianNormalise html
metrics html
noOutlierMethod html
normaliseIllumina html
numBeads html
outlierplot html
platformSigs html
plotBeadIntensities html
plotBeadLocations html
plotChipLayout html
plotMAXY html
plotTIFF html
poscontPlot html
processSwathData html
quickSummary html
readBeadSummaryData html
readIdatFiles html
readIllumina html
readLocsFile html
readTIFF html
sampleSheet html
sectionNames html
setWeights html
show html
showArrayMask html
squeezedVarOutlierMethod html
summarize html
transformationFunctions html
weightsOutlierMethod 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 'beadarray' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c BASH.c -o BASH.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c HULK.c -o HULK.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c determiningGridPositions.c -o determiningGridPositions.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:196:29: warning: 'ma' may be used uninitialized in this function [-Wmaybe-uninitialized]
if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
^
findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
^
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:226:20: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized]
beadStatusStruct *status;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
^
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
^
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
^
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.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/beadarray.buildbin-libdir/beadarray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beadarray' as beadarray_2.34.0.zip
* DONE (beadarray)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'beadarray' successfully unpacked and MD5 sums checked