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CHECK report for M3D on tokay1

This page was generated on 2018-04-12 13:24:44 -0400 (Thu, 12 Apr 2018).

Package 767/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3D 1.12.0
Tom Mayo
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/M3D
Branch: RELEASE_3_6
Last Commit: be02c7b
Last Changed Date: 2017-10-30 12:40:21 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: M3D
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings M3D_1.12.0.tar.gz
StartedAt: 2018-04-12 01:04:54 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:09:00 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 245.9 seconds
RetCode: 0
Status:  OK  
CheckDir: M3D.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings M3D_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'M3D/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'M3D' version '1.12.0'
* 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 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 loading without being on the library search path ... 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 ... 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck/00check.log'
for details.



Installation output

M3D.Rcheck/00install.out

* installing *source* package 'M3D' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c cpp_fns.cpp -o cpp_fns.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o M3D.dll tmp.def RcppExports.o cpp_fns.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
C:\Rtools\mingw_32\bin\nm.exe: C:/Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck/00_pkg_src/M3D/src/RcppExports.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: C:/Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck/00_pkg_src/M3D/src/cpp_fns.o: File format not recognized
Warning messages:
1: running command '"C:\Rtools\mingw_32\bin\nm.exe" -Pg "C:/Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck/00_pkg_src/M3D/src/RcppExports.o"' had status 1 
2: running command '"C:\Rtools\mingw_32\bin\nm.exe" -Pg "C:/Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck/00_pkg_src/M3D/src/cpp_fns.o"' had status 1 
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck/M3D/libs/x64
** 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 (M3D)
In R CMD INSTALL

Tests output

M3D.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-w64-mingw32/x64 (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 
  10.60    0.32   10.93 

Example timings

M3D.Rcheck/M3D-Ex.timings

nameusersystemelapsed
M3D_Wrapper0.550.000.54
M3D_Wrapper_lite0.710.000.72
determineGroupComps0.270.020.28
findComps0.30.00.3
median_freq000
plotCoverageSampleProfiles0.190.010.20
plotMethProfile0.670.000.67
plotMethSampleProfiles0.190.000.18
pvals0.420.020.44
pvals_lite0.380.030.41
readBedFiles000
readBedRaw000