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BioC 3.6: CHECK report for DMRforPairs on tokay1

This page was generated on 2017-08-16 13:32:40 -0400 (Wed, 16 Aug 2017).

Package 362/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRforPairs 1.13.0
Martin Rijlaarsdam
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRforPairs
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 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: DMRforPairs
Version: 1.13.0
Command: rm -rf DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && mkdir DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRforPairs.buildbin-libdir DMRforPairs_1.13.0.tar.gz >DMRforPairs.Rcheck\00install.out 2>&1 && cp DMRforPairs.Rcheck\00install.out DMRforPairs-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DMRforPairs.buildbin-libdir --install="check:DMRforPairs-install.out" --force-multiarch --no-vignettes --timings DMRforPairs_1.13.0.tar.gz
StartedAt: 2017-08-15 23:02:22 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:09:44 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 442.0 seconds
RetCode: 0
Status:  OK  
CheckDir: DMRforPairs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && mkdir DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRforPairs.buildbin-libdir DMRforPairs_1.13.0.tar.gz >DMRforPairs.Rcheck\00install.out 2>&1 && cp DMRforPairs.Rcheck\00install.out DMRforPairs-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DMRforPairs.buildbin-libdir --install="check:DMRforPairs-install.out" --force-multiarch --no-vignettes --timings DMRforPairs_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DMRforPairs.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DMRforPairs/DESCRIPTION' ... OK
* this is package 'DMRforPairs' version '1.13.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'DMRforPairs' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
DMRforPairs: no visible global function definition for 'combn'
DMRforPairs: no visible global function definition for 'p.adjust'
calc_stats: no visible global function definition for 'combn'
calc_stats: no visible binding for global variable 'median'
calc_stats: no visible global function definition for 'wilcox.test'
calc_stats: no visible global function definition for 'kruskal.test'
export_data: no visible global function definition for 'write.table'
plot_annotate_probes: no visible global function definition for
  'rainbow'
plot_annotate_probes: no visible global function definition for 'png'
plot_annotate_probes: no visible global function definition for 'par'
plot_annotate_probes: no visible global function definition for 'plot'
plot_annotate_probes: no visible global function definition for 'lines'
plot_annotate_probes: no visible global function definition for
  'extendrange'
plot_annotate_probes: no visible global function definition for
  'dev.off'
plot_annotate_probes: no visible global function definition for 'pdf'
plot_annotate_probes: no visible global function definition for 'combn'
plot_annotate_probes: no visible global function definition for
  'legend'
plot_annotate_probes: no visible global function definition for 'axis'
plot_annotate_probes: no visible global function definition for 'box'
plot_annotate_probes: no visible global function definition for
  'seqlevels<-'
plot_annotate_probes: no visible global function definition for 'Rle'
plot_annotate_probes: no visible global function definition for
  'IRanges'
Undefined global functions or variables:
  IRanges Rle axis box combn dev.off extendrange kruskal.test legend
  lines median p.adjust par pdf plot png rainbow seqlevels<-
  wilcox.test write.table
Consider adding
  importFrom("grDevices", "dev.off", "extendrange", "pdf", "png",
             "rainbow")
  importFrom("graphics", "axis", "box", "legend", "lines", "par", "plot")
  importFrom("stats", "kruskal.test", "median", "p.adjust",
             "wilcox.test")
  importFrom("utils", "combn", "write.table")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/DMRforPairs.Rcheck/00check.log'
for details.


DMRforPairs.Rcheck/00install.out:


install for i386

* installing *source* package 'DMRforPairs' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'DMRforPairs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRforPairs' as DMRforPairs_1.13.0.zip
* DONE (DMRforPairs)

DMRforPairs.Rcheck/examples_i386/DMRforPairs-Ex.timings:

nameusersystemelapsed
DMRforPairs1.740.131.86
calc_stats000
export_data2.410.122.54
merge_classes000
plot_annotate_custom_region1.420.061.48
plot_annotate_gene1.240.021.25
plot_annotate_probes000
plot_annotate_region1.170.031.20
regionfinder000
testregion000
tune_parameters1.360.021.38

DMRforPairs.Rcheck/examples_x64/DMRforPairs-Ex.timings:

nameusersystemelapsed
DMRforPairs1.460.031.50
calc_stats000
export_data2.410.052.46
merge_classes000
plot_annotate_custom_region0.980.031.01
plot_annotate_gene0.950.010.97
plot_annotate_probes000
plot_annotate_region0.970.051.02
regionfinder000
testregion000
tune_parameters1.170.001.17