Alicia Schep
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/motifmatchr |
| git_branch: RELEASE_3_16 |
| git_last_commit: 3a72a09 |
| git_last_commit_date: 2022-11-01 11:15:47 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:41 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the motifmatchr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifmatchr.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1257/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifmatchr 1.20.0 (landing page) Alicia Schep
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: motifmatchr |
| Version: 1.20.0 |
| Command: rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=motifmatchr.buildbin-libdir motifmatchr_1.20.0.tar.gz |
| StartedAt: 2023-04-11 08:20:52 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 08:22:09 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 76.3 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: motifmatchr_1.20.0.zip |
| PackageFileSize: 495.3 KiB |
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### Running command:
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### rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=motifmatchr.buildbin-libdir motifmatchr_1.20.0.tar.gz
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* installing *source* package 'motifmatchr' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_interface.cpp -o r_interface.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MOODS/scanner.cpp -o MOODS/scanner.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp: In member function 'std::vector<double> MOODS::scan::MotifH::expected_scores(const std::vector<double>&)':
MOODS/motif_h.cpp:26:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
26 | for (int i = 0; i < cols; ++i){
| ~~^~~~~~
MOODS/motif_h.cpp:27:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
27 | for (int j = 0; j < rows; ++j){
| ~~^~~~~~
MOODS/motif_h.cpp: In member function 'virtual std::pair<bool, double> MOODS::scan::MotifH::check_hit(const string&, const std::vector<unsigned char>&, std::size_t, double)':
MOODS/motif_h.cpp:256:25: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses]
256 | CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
| ~~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MOODS/motif_0.cpp -o MOODS/motif_0.o
MOODS/motif_0.cpp: In function 'std::vector<double> MOODS::scan::expected_differences(const score_matrix&, const std::vector<double>&)':
MOODS/motif_0.cpp:28:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long long unsigned int'} [-Wsign-compare]
28 | for (int i = 0; i < m; ++i)
| ~~^~~
MOODS/motif_0.cpp:31:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long long unsigned int'} [-Wsign-compare]
31 | for (int j = 0; j < a; ++j)
| ~~^~~
MOODS/motif_0.cpp:38:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long long unsigned int'} [-Wsign-compare]
38 | for (int j = 0; j < a; ++j)
| ~~^~~
MOODS/motif_0.cpp: In function 'unsigned int MOODS::scan::window_position(const std::vector<double>&, unsigned int, unsigned int)':
MOODS/motif_0.cpp:64:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
64 | for (int i = 0; i < m - l; ++i)
| ~~^~~~~~~
MOODS/motif_0.cpp: In function 'std::vector<unsigned int> MOODS::scan::compute_lookahead_order(const std::vector<double>&, unsigned int, unsigned int, unsigned int)':
MOODS/motif_0.cpp:96:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
96 | for (int i = 0; i < window_pos; ++i)
| ~~^~~~~~~~~~~~
MOODS/motif_0.cpp:100:38: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
100 | for (int i = window_pos+l; i < m; ++i)
| ~~^~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&)':
MOODS/moods_tools.cpp:155:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
155 | for (size_t i = 0; i < n; ++i)
| ~~^~~
MOODS/moods_tools.cpp:157:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
157 | for (size_t j = 0; j < a; ++j)
| ~~^~~
MOODS/moods_tools.cpp:168:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
168 | for (size_t i = 0; i < n; ++i)
| ~~^~~
MOODS/moods_tools.cpp:172:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
172 | for (size_t j = 1; j < a; ++j)
| ~~^~~
MOODS/moods_tools.cpp:190:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
190 | for (size_t j = 0; j < a; ++j)
| ~~^~~
MOODS/moods_tools.cpp:193:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
193 | for (size_t i = 1; i < n; ++i)
| ~~^~~
MOODS/moods_tools.cpp:195:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
195 | for (size_t j = 0; j < a; ++j)
| ~~^~~
MOODS/moods_tools.cpp: In function 'score_matrix MOODS::tools::log_odds(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<double>&, double, std::size_t)':
MOODS/moods_tools.cpp:320:38: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
320 | for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){
| ~~~~~~^~~~~~~~~~~~~~~~~~
MOODS/moods_tools.cpp:328:46: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
328 | for (size_t SCODE = 0; SCODE < 1 << (SHIFT * (q - r - 1)); ++SCODE){
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&, std::size_t)':
MOODS/moods_tools.cpp:454:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
454 | for (size_t i = 0; i < cols; ++i)
| ~~^~~~~~
MOODS/moods_tools.cpp:456:36: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
456 | for (size_t CODE = 0; CODE < rows; ++CODE)
| ~~~~~^~~~~~
MOODS/moods_tools.cpp:468:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
468 | for (size_t i = 0; i < cols; ++i)
| ~~^~~~~~
MOODS/moods_tools.cpp:472:36: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
472 | for (size_t CODE = 1; CODE < rows; ++CODE)
| ~~~~~^~~~~~
MOODS/moods_tools.cpp:489:32: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
489 | for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){
| ~~~~~^~~~~~~~~~~~~~~~~~~~
MOODS/moods_tools.cpp:500:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
500 | for (size_t i = 1; i < cols; ++i)
| ~~^~~~~~
MOODS/moods_tools.cpp:503:36: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
503 | for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE)
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp: In function 'std::vector<std::vector<MOODS::match> > MOODS::scan::scan_best_hits_dna(const string&, const std::vector<std::vector<std::vector<double> > >&, std::size_t, int, unsigned int, std::size_t, std::size_t)':
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
97 | bool done = 0;
| ^~~~
MOODS/moods_scan.cpp: In function 'std::vector<MOODS::match> MOODS::scan::naive_scan_dna(const string&, score_matrix, double, std::size_t)':
MOODS/moods_scan.cpp:252:33: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
252 | CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
| ~~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MOODS/match_types.cpp -o MOODS/match_types.o
g++ -shared -s -static-libgcc -o motifmatchr.dll tmp.def ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/motifmatchr.buildbin-libdir/00LOCK-motifmatchr/00new/motifmatchr/libs/x64
** R
** data
** 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
* MD5 sums
packaged installation of 'motifmatchr' as motifmatchr_1.20.0.zip
* DONE (motifmatchr)