Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:39 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1241/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
motifmatchr 1.21.0 (landing page) Alicia Schep
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: motifmatchr |
Version: 1.21.0 |
Command: rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=motifmatchr.buildbin-libdir motifmatchr_1.21.0.tar.gz |
StartedAt: 2022-12-29 05:25:26 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 05:26:33 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 67.0 seconds |
RetCode: 0 |
Status: OK |
PackageFile: motifmatchr_1.21.0.zip |
PackageFileSize: 505.6 KiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=motifmatchr.buildbin-libdir motifmatchr_1.21.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'motifmatchr' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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 std::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-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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 std::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 std::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-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-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-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc-rtools43/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_1.21.0.zip * DONE (motifmatchr)