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BioC 3.5: CHECK report for M3D on tokay2

This page was generated on 2017-10-18 14:23:47 -0400 (Wed, 18 Oct 2017).

Package 735/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3D 1.10.0
Tom Mayo
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/M3D
Branch: RELEASE_3_5
Last Commit: a40967d
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: M3D
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings M3D_1.10.0.tar.gz
StartedAt: 2017-10-18 00:59:53 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:04:28 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 274.9 seconds
RetCode: 0
Status:  OK  
CheckDir: M3D.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings M3D_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/M3D.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.10.0'
* 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-3.5-bioc/meat/M3D.Rcheck/00check.log'
for details.


M3D.Rcheck/00install.out:

* installing *source* package 'M3D' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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˜1.5-B/R/bin/x64 -lR
C:\Rtools\mingw_32\bin\nm.exe: C:/Users/biocbuild/bbs-3.5-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-3.5-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-3.5-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-3.5-bioc/meat/M3D.Rcheck/00_pkg_src/M3D/src/cpp_fns.o"' had status 1 
installing to C:/Users/biocbuild/bbs-3.5-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)

M3D.Rcheck/M3D-Ex.timings:

nameusersystemelapsed
M3D_Wrapper0.50.00.5
M3D_Wrapper_lite0.330.010.34
determineGroupComps0.280.030.31
findComps0.330.000.33
median_freq000
plotCoverageSampleProfiles0.180.020.20
plotMethProfile0.330.000.33
plotMethSampleProfiles0.20.00.2
pvals0.520.030.55
pvals_lite0.610.020.62
readBedFiles000
readBedRaw000