Alicia Schep
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/motifmatchr |
| Branch: master |
| Last Commit: 9ebc443 |
| Last Changed Date: 2018-10-30 11:54:37 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:48:09 -0400 (Tue, 09 Apr 2019).
| Package 1024/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifmatchr 1.5.0 Alicia Schep
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | [ OK ] | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: motifmatchr |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL motifmatchr |
| StartedAt: 2019-04-08 18:34:44 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 18:36:21 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 97.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL motifmatchr
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘motifmatchr’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c r_interface.cpp -o r_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c MOODS/scanner.cpp -o MOODS/scanner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < cols; ++i){
˜˜^˜˜˜˜˜
MOODS/motif_h.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < m; ++i)
˜˜^˜˜
MOODS/motif_0.cpp:31:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < a; ++j)
˜˜^˜˜
MOODS/motif_0.cpp:38:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 between signed and unsigned integer expressions [-Wsign-compare]
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 between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < window_pos; ++i)
˜˜^˜˜˜˜˜˜˜˜˜˜˜
MOODS/motif_0.cpp:100:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = window_pos+l; i < m; ++i)
˜˜^˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < n; ++i)
˜˜^˜˜
MOODS/moods_tools.cpp:157:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < a; ++j)
˜˜^˜˜
MOODS/moods_tools.cpp:168:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < n; ++i)
˜˜^˜˜
MOODS/moods_tools.cpp:172:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 1; j < a; ++j)
˜˜^˜˜
MOODS/moods_tools.cpp:190:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < a; ++j)
˜˜^˜˜
MOODS/moods_tools.cpp:193:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 1; i < n; ++i)
˜˜^˜˜
MOODS/moods_tools.cpp:195:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 between signed and unsigned integer expressions [-Wsign-compare]
for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MOODS/moods_tools.cpp:328:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < cols; ++i)
˜˜^˜˜˜˜˜
MOODS/moods_tools.cpp:456:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 0; CODE < rows; ++CODE)
˜˜˜˜˜^˜˜˜˜˜
MOODS/moods_tools.cpp:468:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < cols; ++i)
˜˜^˜˜˜˜˜
MOODS/moods_tools.cpp:472:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 1; CODE < rows; ++CODE)
˜˜˜˜˜^˜˜˜˜˜
MOODS/moods_tools.cpp:489:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MOODS/moods_tools.cpp:500:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 1; i < cols; ++i)
˜˜^˜˜˜˜˜
MOODS/moods_tools.cpp:503:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE)
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -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]
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]
CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c MOODS/match_types.cpp -o MOODS/match_types.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o motifmatchr.so ./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 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-motifmatchr/00new/motifmatchr/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (motifmatchr)