Alicia Schep
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/motifmatchr |
| Branch: RELEASE_3_6 |
| Last Commit: 5014590 |
| Last Changed Date: 2017-10-31 23:18:56 -0400 (Tue, 31 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:45:05 -0400 (Thu, 12 Apr 2018).
| Package 890/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifmatchr 1.0.1 Alicia Schep
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: motifmatchr |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifmatchr_1.0.1.tar.gz |
| StartedAt: 2018-04-12 06:40:22 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 06:45:29 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 306.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: motifmatchr.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifmatchr_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/motifmatchr.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.1’ * 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 ... OK * checking installed files from ‘inst/doc’ ... OK * 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: OK
motifmatchr.Rcheck/00install.out
* installing *source* package ‘motifmatchr’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c r_interface.cpp -o r_interface.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/scanner.cpp -o MOODS/scanner.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp:256:25: warning: '&' within '^' [-Wbitwise-op-parentheses]
CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
MOODS/motif_h.cpp:256:25: note: place parentheses around the '&' expression to silence this warning
CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
^
( )
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/motif_0.cpp -o MOODS/motif_0.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
bool done = 0;
^
MOODS/moods_scan.cpp:252:33: warning: '&' within '|' [-Wbitwise-op-parentheses]
CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
MOODS/moods_scan.cpp:252:33: note: place parentheses around the '&' expression to silence this warning
CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
^
( )
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MOODS/match_types.cpp -o MOODS/match_types.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/motifmatchr.Rcheck/motifmatchr/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifmatchr)
motifmatchr.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
18.638 0.469 23.249
motifmatchr.Rcheck/motifmatchr-Ex.timings
| name | user | system | elapsed | |
| example_motifs | 0.005 | 0.000 | 0.006 | |
| matchMotifs | 1.415 | 0.021 | 1.456 | |
| motifCounts | 0.992 | 0.014 | 1.154 | |
| motifMatches | 0.729 | 0.013 | 0.954 | |
| motifScores | 0.473 | 0.012 | 0.612 | |
| pwmType | 0.008 | 0.000 | 0.008 | |