Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:48:10 -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 check --install=check:motifmatchr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings motifmatchr_1.5.0.tar.gz |
StartedAt: 2019-04-09 02:09:33 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 02:14:42 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 308.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: motifmatchr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:motifmatchr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings motifmatchr_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/motifmatchr.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘motifmatchr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘motifmatchr’ version ‘1.5.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘motifmatchr’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.9-bioc/meat/motifmatchr.Rcheck/00check.log’ for details.
motifmatchr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL motifmatchr ### ############################################################################## ############################################################################## * 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)
motifmatchr.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(motifmatchr) > > test_check("motifmatchr") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 50 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 20.303 0.626 20.945
motifmatchr.Rcheck/motifmatchr-Ex.timings
name | user | system | elapsed | |
example_motifs | 0.004 | 0.000 | 0.004 | |
matchMotifs | 0.616 | 0.008 | 0.624 | |
motifCounts | 0.777 | 0.032 | 0.809 | |
motifMatches | 0.531 | 0.008 | 0.539 | |
motifScores | 0.521 | 0.008 | 0.529 | |
pwmType | 0.009 | 0.000 | 0.009 | |