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CHECK report for M3D on merida2

This page was generated on 2019-04-09 13:30:08 -0400 (Tue, 09 Apr 2019).

Package 882/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3D 1.17.0
Tom Mayo
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/M3D
Branch: master
Last Commit: 7516302
Last Changed Date: 2018-10-30 11:54:33 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: M3D
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3D_1.17.0.tar.gz
StartedAt: 2019-04-09 01:53:16 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:57:49 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 272.9 seconds
RetCode: 0
Status:  OK 
CheckDir: M3D.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3D_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/M3D.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3D/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘M3D’ version ‘1.17.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘M3D’ 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 ... NOTE
M3D_Wrapper: no visible global function definition for ‘txtProgressBar’
M3D_Wrapper: no visible global function definition for
  ‘setTxtProgressBar’
M3D_Wrapper_lite: no visible global function definition for
  ‘txtProgressBar’
M3D_Wrapper_lite: no visible global function definition for
  ‘setTxtProgressBar’
plotCoverageSampleProfiles: no visible global function definition for
  ‘plot’
plotCoverageSampleProfiles: no visible global function definition for
  ‘lines’
plotCoverageSampleProfiles: no visible global function definition for
  ‘points’
plotCoverageSampleProfiles: no visible global function definition for
  ‘title’
plotMethProfile: no visible global function definition for ‘plot’
plotMethProfile: no visible global function definition for ‘lines’
plotMethProfile: no visible global function definition for ‘points’
plotMethProfile: no visible global function definition for ‘title’
plotMethSampleProfiles: no visible global function definition for
  ‘plot’
plotMethSampleProfiles: no visible global function definition for
  ‘lines’
plotMethSampleProfiles: no visible global function definition for
  ‘points’
plotMethSampleProfiles: no visible global function definition for
  ‘title’
pvals: no visible global function definition for ‘p.adjust’
pvals_lite: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  lines p.adjust plot points setTxtProgressBar title txtProgressBar
Consider adding
  importFrom("graphics", "lines", "plot", "points", "title")
  importFrom("stats", "p.adjust")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/M3D.Rcheck/00check.log’
for details.



Installation output

M3D.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL M3D
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘M3D’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/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"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp_fns.cpp -o cpp_fns.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 M3D.so RcppExports.o cpp_fns.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/M3D/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (M3D)

Tests output

M3D.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(M3D)
> 
> test_check("M3D")

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══ testthat results  ═══════════════════════════════════════════════════════════
OK: 20 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 14.698   0.794  15.574 

Example timings

M3D.Rcheck/M3D-Ex.timings

nameusersystemelapsed
M3D_Wrapper0.4440.0220.475
M3D_Wrapper_lite0.4080.0150.425
determineGroupComps0.4570.0170.475
findComps1.0580.0281.095
median_freq000
plotCoverageSampleProfiles0.3120.0070.322
plotMethProfile0.3130.0070.326
plotMethSampleProfiles0.3060.0070.319
pvals0.6200.0400.666
pvals_lite0.5860.0320.627
readBedFiles000
readBedRaw000