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CHECK report for chromPlot on tokay2

This page was generated on 2020-10-17 11:56:16 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE chromPlot PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 294/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromPlot 1.16.0
Karen Y. Orostica
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/chromPlot
Branch: RELEASE_3_11
Last Commit: e2286de
Last Changed Date: 2020-04-27 14:54:48 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromPlot
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromPlot.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings chromPlot_1.16.0.tar.gz
StartedAt: 2020-10-17 02:34:57 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:39:23 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 266.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: chromPlot.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromPlot.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings chromPlot_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/chromPlot.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chromPlot/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chromPlot' version '1.16.0'
* 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 'chromPlot' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'chromPlot'
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/chromPlot.Rcheck/00install.out' for details.
* 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 ... OK
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/chromPlot.Rcheck/00check.log'
for details.



Installation output

chromPlot.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/chromPlot_1.16.0.tar.gz && rm -rf chromPlot.buildbin-libdir && mkdir chromPlot.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromPlot.buildbin-libdir chromPlot_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL chromPlot_1.16.0.zip && rm chromPlot_1.16.0.tar.gz chromPlot_1.16.0.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  762k  100  762k    0     0  10.3M      0 --:--:-- --:--:-- --:--:-- 11.2M

install for i386

* installing *source* package 'chromPlot' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'chromPlot'
** help
*** installing help indices
  converting help for package 'chromPlot'
    finding HTML links ... done
    chromPlot-package                       html  
    chromPlot                               html  
    hg_cytoBandIdeo                         html  
    hg_gap                                  html  
    mm10_cytoBandIdeo                       html  
    mm10_gap                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'chromPlot'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'chromPlot'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'chromPlot' ...
** testing if installed package can be loaded
Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'chromPlot'
* MD5 sums
packaged installation of 'chromPlot' as chromPlot_1.16.0.zip
* DONE (chromPlot)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'chromPlot' successfully unpacked and MD5 sums checked

Tests output


Example timings

chromPlot.Rcheck/examples_i386/chromPlot-Ex.timings

nameusersystemelapsed
chromPlot0.200.020.22
hg_cytoBandIdeo0.020.000.01
hg_gap000
mm10_cytoBandIdeo0.010.000.01
mm10_gap000

chromPlot.Rcheck/examples_x64/chromPlot-Ex.timings

nameusersystemelapsed
chromPlot0.230.010.25
hg_cytoBandIdeo0.020.000.02
hg_gap0.000.020.01
mm10_cytoBandIdeo000
mm10_gap000