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CHECK report for DMRforPairs on tokay1

This page was generated on 2019-04-13 11:23:47 -0400 (Sat, 13 Apr 2019).

Package 422/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRforPairs 1.18.0
Martin Rijlaarsdam
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/DMRforPairs
Branch: RELEASE_3_8
Last Commit: 6d98e69
Last Changed Date: 2018-10-30 11:41:53 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DMRforPairs
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRforPairs.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DMRforPairs_1.18.0.tar.gz
StartedAt: 2019-04-13 01:51:56 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:58:42 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 406.0 seconds
RetCode: 0
Status:  OK  
CheckDir: DMRforPairs.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRforPairs.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DMRforPairs_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DMRforPairs.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* 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 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 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-3.8-bioc/meat/DMRforPairs.Rcheck/00check.log'
for details.



Installation output

DMRforPairs.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DMRforPairs_1.18.0.tar.gz && rm -rf DMRforPairs.buildbin-libdir && mkdir DMRforPairs.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMRforPairs.buildbin-libdir DMRforPairs_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DMRforPairs_1.18.0.zip && rm DMRforPairs_1.18.0.tar.gz DMRforPairs_1.18.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2132k  100 2132k    0     0  21.3M      0 --:--:-- --:--:-- --:--:-- 22.3M

install for i386

* installing *source* package 'DMRforPairs' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DMRforPairs'
    finding HTML links ... done
    CL.methy                                html  
    DMRforPairs-package                     html  
    DMRforPairs                             html  
    calc_stats                              html  
    example_output_DMRforPairs              html  
    export_data                             html  
    merge_classes                           html  
    plot_annotate_custom_region             html  
    plot_annotate_gene                      html  
    plot_annotate_probes                    html  
    plot_annotate_region                    html  
    regionfinder                            html  
    testregion                              html  
    tune_parameters                         html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DMRforPairs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRforPairs' as DMRforPairs_1.18.0.zip
* DONE (DMRforPairs)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DMRforPairs' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

DMRforPairs.Rcheck/examples_i386/DMRforPairs-Ex.timings

nameusersystemelapsed
DMRforPairs2.060.312.39
calc_stats000
export_data1.800.061.86
merge_classes000
plot_annotate_custom_region2.140.022.15
plot_annotate_gene1.420.041.47
plot_annotate_probes000
plot_annotate_region1.050.041.08
regionfinder000
testregion000
tune_parameters1.380.001.38

DMRforPairs.Rcheck/examples_x64/DMRforPairs-Ex.timings

nameusersystemelapsed
DMRforPairs1.460.031.50
calc_stats000
export_data1.330.071.44
merge_classes000
plot_annotate_custom_region0.990.011.00
plot_annotate_gene1.860.021.87
plot_annotate_probes000
plot_annotate_region0.970.031.00
regionfinder000
testregion000
tune_parameters1.060.031.09