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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).

CHECK results for CNVRanger on tokay2

To the developers/maintainers of the CNVRanger package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVRanger.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 353/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVRanger 1.8.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CNVRanger
git_branch: RELEASE_3_13
git_last_commit: dfb9864
git_last_commit_date: 2021-05-19 12:40:54 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: CNVRanger
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVRanger.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVRanger_1.8.0.tar.gz
StartedAt: 2021-10-14 21:20:55 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 21:26:37 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 342.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVRanger.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVRanger.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVRanger_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNVRanger.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNVRanger/DESCRIPTION' ... OK
* this is package 'CNVRanger' version '1.8.0'
* package encoding: UTF-8
* 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 'CNVRanger' 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 ... NOTE
Unexported object imported by a ':::' call: 'rappdirs:::get_os'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRecurrentRegions: no visible binding for global variable 'type'
plotRecurrentRegions: no visible binding for global variable 'pvalue'
Undefined global functions or variables:
  pvalue type
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
plotRecurrentRegions 19.49   0.11   22.51
plotEQTL             16.23   1.45   22.83
plotManhattan         8.47   0.01   10.64
cnvGWAS               7.14   0.03    7.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
plotRecurrentRegions 24.83   0.04   29.04
plotEQTL             17.74   0.56   22.45
plotManhattan        10.03   0.08   10.14
cnvGWAS               7.94   0.04    7.99
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNVRanger.Rcheck/00check.log'
for details.



Installation output

CNVRanger.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CNVRanger_1.8.0.tar.gz && rm -rf CNVRanger.buildbin-libdir && mkdir CNVRanger.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVRanger.buildbin-libdir CNVRanger_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CNVRanger_1.8.0.zip && rm CNVRanger_1.8.0.tar.gz CNVRanger_1.8.0.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
 37  989k   37  375k    0     0  1112k      0 --:--:-- --:--:-- --:--:-- 1111k
100  989k  100  989k    0     0  1383k      0 --:--:-- --:--:-- --:--:-- 1382k

install for i386

* installing *source* package 'CNVRanger' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNVRanger'
    finding HTML links ... done
    cnvEQTL                                 html  
    finding level-2 HTML links ... done

    cnvGWAS                                 html  
    cnvOncoPrint                            html  
    generateGDS                             html  
    importLrrBaf                            html  
    plotEQTL                                html  
    plotManhattan                           html  
    plotRecurrentRegions                    html  
    populationRanges                        html  
    setupCnvGWAS                            html  
** 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 'CNVRanger' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVRanger' as CNVRanger_1.8.0.zip
* DONE (CNVRanger)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CNVRanger' successfully unpacked and MD5 sums checked

Tests output


Example timings

CNVRanger.Rcheck/examples_i386/CNVRanger-Ex.timings

nameusersystemelapsed
cnvEQTL2.120.282.40
cnvGWAS7.140.037.48
cnvOncoPrint1.740.211.97
generateGDS0.900.000.93
importLrrBaf0.020.000.02
plotEQTL16.23 1.4522.83
plotManhattan 8.47 0.0110.64
plotRecurrentRegions19.49 0.1122.51
populationRanges1.830.021.85
setupCnvGWAS0.010.000.01

CNVRanger.Rcheck/examples_x64/CNVRanger-Ex.timings

nameusersystemelapsed
cnvEQTL3.050.093.14
cnvGWAS7.940.047.99
cnvOncoPrint1.500.031.53
generateGDS1.270.001.30
importLrrBaf0.010.000.01
plotEQTL17.74 0.5622.45
plotManhattan10.03 0.0810.14
plotRecurrentRegions24.83 0.0429.04
populationRanges1.860.001.86
setupCnvGWAS0.010.000.01