Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:28 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for DMRforPairs on tokay2


To the developers/maintainers of the DMRforPairs package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DMRforPairs.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 527/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRforPairs 1.30.0  (landing page)
Martin Rijlaarsdam
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/DMRforPairs
git_branch: RELEASE_3_14
git_last_commit: 93fa270
git_last_commit_date: 2021-10-26 12:13:07 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DMRforPairs
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRforPairs.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DMRforPairs_1.30.0.tar.gz
StartedAt: 2022-04-12 18:46:34 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:53:02 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 387.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DMRforPairs.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRforPairs.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DMRforPairs_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DMRforPairs.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.30.0'
* 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
* 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 '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 png rainbow seqlevels<- wilcox.test
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "extendrange", "pdf", "png",
             "rainbow")
  importFrom("graphics", "axis", "box", "legend", "lines", "par")
  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-3.14-bioc/meat/DMRforPairs.Rcheck/00check.log'
for details.



Installation output

DMRforPairs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/DMRforPairs_1.30.0.tar.gz && rm -rf DMRforPairs.buildbin-libdir && mkdir DMRforPairs.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMRforPairs.buildbin-libdir DMRforPairs_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DMRforPairs_1.30.0.zip && rm DMRforPairs_1.30.0.tar.gz DMRforPairs_1.30.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 28 2132k   28  614k    0     0   968k      0  0:00:02 --:--:--  0:00:02  968k
100 2132k  100 2132k    0     0  1446k      0  0:00:01  0:00:01 --:--:-- 1447k

install for i386

* installing *source* package 'DMRforPairs' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DMRforPairs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRforPairs' as DMRforPairs_1.30.0.zip
* DONE (DMRforPairs)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DMRforPairs' successfully unpacked and MD5 sums checked

Tests output


Example timings

DMRforPairs.Rcheck/examples_i386/DMRforPairs-Ex.timings

nameusersystemelapsed
DMRforPairs1.300.071.38
calc_stats000
export_data1.360.081.44
merge_classes000
plot_annotate_custom_region1.000.031.03
plot_annotate_gene1.820.031.86
plot_annotate_probes000
plot_annotate_region0.960.040.99
regionfinder000
testregion000
tune_parameters1.040.011.06

DMRforPairs.Rcheck/examples_x64/DMRforPairs-Ex.timings

nameusersystemelapsed
DMRforPairs1.380.041.42
calc_stats000
export_data1.010.031.06
merge_classes000
plot_annotate_custom_region0.860.020.87
plot_annotate_gene0.720.010.74
plot_annotate_probes000
plot_annotate_region0.730.040.76
regionfinder000
testregion000
tune_parameters1.860.001.86