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CHECK report for motifmatchr on veracruz1

This page was generated on 2018-04-12 13:45:05 -0400 (Thu, 12 Apr 2018).

Package 890/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifmatchr 1.0.1
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)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
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###
### 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


Installation output

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)

Tests output

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 

Example timings

motifmatchr.Rcheck/motifmatchr-Ex.timings

nameusersystemelapsed
example_motifs0.0050.0000.006
matchMotifs1.4150.0211.456
motifCounts0.9920.0141.154
motifMatches0.7290.0130.954
motifScores0.4730.0120.612
pwmType0.0080.0000.008