Andrew McDavid
| Snapshot Date: 2024-03-04 14:00:18 -0500 (Mon, 04 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/CellaRepertorium |
| git_branch: devel |
| git_last_commit: f856225 |
| git_last_commit_date: 2023-10-24 11:27:39 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-06 11:37:16 -0500 (Wed, 06 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4682 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4421 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-04 r86048) -- "Unsuffered Consequences" | 4380 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4423 |
| 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 291/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellaRepertorium 1.13.0 (landing page) Andrew McDavid
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the CellaRepertorium package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellaRepertorium.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: CellaRepertorium |
| Version: 1.13.0 |
| Command: rm -rf CellaRepertorium.buildbin-libdir && mkdir CellaRepertorium.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=CellaRepertorium.buildbin-libdir CellaRepertorium_1.13.0.tar.gz |
| StartedAt: 2024-03-05 10:07:40 -0500 (Tue, 05 Mar 2024) |
| EndedAt: 2024-03-05 10:08:42 -0500 (Tue, 05 Mar 2024) |
| EllapsedTime: 62.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CellaRepertorium_1.13.0.zip |
| PackageFileSize: 4.104 MiB |
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### Running command:
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### rm -rf CellaRepertorium.buildbin-libdir && mkdir CellaRepertorium.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=CellaRepertorium.buildbin-libdir CellaRepertorium_1.13.0.tar.gz
###
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* installing *source* package 'CellaRepertorium' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:2:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:160: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
160 | #pragma omp critical
|
cdhit-common.cpp:174: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
174 | #pragma omp critical
|
cdhit-common.cpp:2418: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
2418 | #pragma omp parallel for schedule( dynamic, 1 )
|
cdhit-common.cpp:2435: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
2435 | #pragma omp parallel for schedule( dynamic, 1 )
|
cdhit-common.cpp:2437: warning: ignoring '#pragma omp flush' [-Wunknown-pragmas]
2437 | #pragma omp flush (stop)
|
cdhit-common.cpp:2458: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
2458 | #pragma omp critical
|
cdhit-common.cpp:2467: warning: ignoring '#pragma omp flush' [-Wunknown-pragmas]
2467 | #pragma omp flush (stop)
|
cdhit-common.cpp:2492: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
2492 | #pragma omp parallel for schedule( dynamic, 1 )
|
cdhit-common.cpp:3151: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
3151 | #pragma omp parallel for schedule( dynamic, 1 )
|
In file included from cdhit-common.cpp:37:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:545:13: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
545 | int max_diag = 0;
| ^~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:669:13: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
669 | int max_diag = 0;
| ^~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::SortDivide(Options&, bool)':
cdhit-common.cpp:1774:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
1774 | if (len > max_len) max_len = len;
| ~~~~^~~~~~~~~
cdhit-common.cpp:1775:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
1775 | if (len < min_len) min_len = len;
| ~~~~^~~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::DoClustering(int, const Options&)':
cdhit-common.cpp:2379:16: warning: variable 'mem' set but not used [-Wunused-but-set-variable]
2379 | size_t mem, mega = 1000000;
| ^~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:32:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c progress.cpp -o progress.o
g++ -std=gnu++17 -shared -s -static-libgcc -o CellaRepertorium.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/meat/CellaRepertorium.buildbin-libdir/00LOCK-CellaRepertorium/00new/CellaRepertorium/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* MD5 sums
packaged installation of 'CellaRepertorium' as CellaRepertorium_1.13.0.zip
* DONE (CellaRepertorium)