Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:06:08 -0400 (Fri, 24 Sep 2021).

CHECK results for diffUTR on tokay2

To the developers/maintainers of the diffUTR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffUTR.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 503/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffUTR 1.0.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/diffUTR
git_branch: RELEASE_3_13
git_last_commit: 948e593
git_last_commit_date: 2021-05-19 13:03:14 -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: diffUTR
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffUTR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings diffUTR_1.0.0.tar.gz
StartedAt: 2021-09-23 21:33:51 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 21:40:09 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 377.8 seconds
RetCode: 0
Status:   OK  
CheckDir: diffUTR.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:diffUTR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings diffUTR_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/diffUTR.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 'diffUTR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'diffUTR' version '1.0.0'
* 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 'diffUTR' 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
deuBinPlot: no visible binding for global variable 'x_start'
deuBinPlot: no visible binding for global variable 'x_end'
deuBinPlot: no visible binding for global variable 'y_start'
deuBinPlot: no visible binding for global variable 'y_end'
plotTopGenes: no visible binding for global variable 'sizeScore'
plotTopGenes: no visible binding for global variable 'q.value'
plotTopGenes: no visible binding for global variable 'density.ratio'
plotTopGenes: no visible binding for global variable 'geneMeanDensity'
plotTopGenes: no visible binding for global variable 'w.abs.coef'
plotTopGenes: no visible binding for global variable 'tmp'
plotTopGenes: no visible binding for global variable 'name'
Undefined global functions or variables:
  density.ratio geneMeanDensity name q.value sizeScore tmp w.abs.coef
  x_end x_start y_end y_start
* 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-3.13-bioc/meat/diffUTR.Rcheck/00check.log'
for details.



Installation output

diffUTR.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/diffUTR_1.0.0.tar.gz && rm -rf diffUTR.buildbin-libdir && mkdir diffUTR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diffUTR.buildbin-libdir diffUTR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL diffUTR_1.0.0.zip && rm diffUTR_1.0.0.tar.gz diffUTR_1.0.0.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  445k  100  445k    0     0  1657k      0 --:--:-- --:--:-- --:--:-- 1662k

install for i386

* installing *source* package 'diffUTR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'diffUTR'
    finding HTML links ... done
    DEUwrappers                             html  
    addNormalizedAssays                     html  
    countFeatures                           html  
    deuBinPlot                              html  
    diffSplice2                             html  
    example_bin_se                          html  
    example_gene_annotation                 html  
    geneBinHeatmap                          html  
    geneLevelStats                          html  
    plotTopGenes                            html  
    prepareBins                             html  
    rn6_PAS                                 html  
    simesAggregation                        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 'diffUTR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'diffUTR' as diffUTR_1.0.0.zip
* DONE (diffUTR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'diffUTR' successfully unpacked and MD5 sums checked

Tests output


Example timings

diffUTR.Rcheck/examples_i386/diffUTR-Ex.timings

nameusersystemelapsed
DEUwrappers2.400.382.78
addNormalizedAssays0.120.090.22
countFeatures3.110.143.33
deuBinPlot1.260.001.27
diffSplice20.350.030.37
geneBinHeatmap2.860.153.02
geneLevelStats1.140.081.22
plotTopGenes0.860.000.86
prepareBins1.610.031.64
simesAggregation000

diffUTR.Rcheck/examples_x64/diffUTR-Ex.timings

nameusersystemelapsed
DEUwrappers1.420.001.42
addNormalizedAssays0.110.000.11
countFeatures3.880.114.03
deuBinPlot1.260.001.27
diffSplice20.350.030.37
geneBinHeatmap2.820.052.88
geneLevelStats1.390.001.39
plotTopGenes1.190.011.20
prepareBins2.000.052.05
simesAggregation000