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BioC 3.4: CHECK report for M3D on zin1

This page was generated on 2016-09-21 03:39:10 -0700 (Wed, 21 Sep 2016).

Package 674/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3D 1.7.11
Tom Mayo
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/M3D
Last Changed Rev: 120733 / Revision: 121152
Last Changed Date: 2016-09-05 09:36:51 -0700 (Mon, 05 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: M3D
Version: 1.7.11
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings M3D_1.7.11.tar.gz
StartedAt: 2016-09-20 08:43:46 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:46:53 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 186.5 seconds
RetCode: 0
Status:  OK 
CheckDir: M3D.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings M3D_1.7.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/M3D.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.7.11’
* 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 ‘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 sizes of PDF files under ‘inst/doc’ ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/M3D.Rcheck/00check.log’
for details.


M3D.Rcheck/00install.out:

* installing *source* package ‘M3D’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c cpp_fns.cpp -o cpp_fns.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o M3D.so RcppExports.o cpp_fns.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/M3D.Rcheck/M3D/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 (M3D)

M3D.Rcheck/M3D-Ex.timings:

nameusersystemelapsed
M3D_Para1.8680.4361.546
M3D_Para_lite1.5440.4361.044
M3D_Wrapper0.4960.0400.534
M3D_Wrapper_lite0.1640.0040.166
determineGroupComps0.2040.0120.215
findComps0.5160.0080.522
median_freq0.0000.0000.001
plotCoverageSampleProfiles0.1720.0040.175
plotMethProfile0.1800.0000.179
plotMethSampleProfiles0.180.000.18
pvals0.3440.0080.354
pvals_lite0.3080.0080.317
readBedFiles000
readBedRaw000