| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 147/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beadarray 2.55.0 (landing page) Mark Dunning
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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To the developers/maintainers of the beadarray package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/beadarray.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: beadarray |
| Version: 2.55.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL beadarray |
| StartedAt: 2024-06-09 16:12:32 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 16:13:24 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 51.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL beadarray
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'beadarray' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BASH.c -o BASH.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HULK.c -o HULK.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c determiningGridPositions.c -o determiningGridPositions.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:196:35: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized]
196 | if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
| ~~~^~~~~~~~~~~~
findAllOutliers.c:155:16: note: 'm' was declared here
155 | double m, ma;
| ^
findAllOutliers.c:189:15: warning: 'ma' may be used uninitialized [-Wmaybe-uninitialized]
189 | if(ma==0) {
| ^
findAllOutliers.c:155:19: note: 'ma' was declared here
155 | double m, ma;
| ^~
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:246:20: warning: 'status' may be used uninitialized [-Wmaybe-uninitialized]
246 | free(status->validInds);
| ~~~~~~^~~~~~~~~~~
findAllOutliers.c:226:27: note: 'status' was declared here
226 | beadStatusStruct *status;
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
88 | #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
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imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
135 | #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
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imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
244 | #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
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imageProcessing.c:251: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
251 | #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
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gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-beadarray/00new/beadarray/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (beadarray)