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This page was generated on 2021-10-21 12:05:05 -0400 (Thu, 21 Oct 2021).

CHECK results for SEtools on riesling1

To the developers/maintainers of the SEtools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SEtools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1769/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SEtools 1.7.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/SEtools
git_branch: master
git_last_commit: cd35cc2
git_last_commit_date: 2021-05-19 12:46:08 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: SEtools
Version: 1.7.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SEtools.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SEtools_1.7.0.tar.gz
StartedAt: 2021-10-21 03:56:55 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 04:01:22 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 266.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SEtools.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SEtools.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SEtools_1.7.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/SEtools.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 'SEtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SEtools' version '1.7.0'
* 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 'SEtools' 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
castSE : <anonymous>: warning in sparseMatrix(i = as.integer(rowNames),
  j = as.integer(colNames), x = x[[y]], dim =
  c(length(levels(rowNames)), length(levels(colNames))), dimnames =
  list(levels(rowNames), levels(colNames))): partial argument match of
  'dim' to 'dims'
* 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 ... WARNING
Undocumented arguments in documentation object 'SE-heatmap'
  'annorow_title_side'
Documented arguments not in \usage in documentation object 'SE-heatmap':
  'annorows_title_side'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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, 1 NOTE
See
  'D:/biocbuild/bbs-3.14-bioc/meat/SEtools.Rcheck/00check.log'
for details.



Installation output

SEtools.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SEtools_1.7.0.tar.gz && rm -rf SEtools.buildbin-libdir && mkdir SEtools.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SEtools.buildbin-libdir SEtools_1.7.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SEtools_1.7.0.zip && rm SEtools_1.7.0.tar.gz SEtools_1.7.0.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
 13  312k   13 41639    0     0   249k      0  0:00:01 --:--:--  0:00:01  247k
100  312k  100  312k    0     0  1300k      0 --:--:-- --:--:-- --:--:-- 1295k

install for i386

* installing *source* package 'SEtools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SEtools'
    finding HTML links ... done
    SE-heatmap                              html  
    aggSE                                   html  
    castSE                                  html  
    crossHm                                 html  
    data                                    html  
    flattenPB                               html  
    getBreaks                               html  
    log2FC                                  html  
    meltSE                                  html  
    mergeSEs                                html  
    qualitativeColors                       html  
    resetAllSEtoolsOptions                  html  
    scale2                                  html  
    se2xls                                  html  
    sortRows                                html  
    svacor                                  html  
    finding level-2 HTML links ... done

** 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 'SEtools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SEtools' as SEtools_1.7.0.zip
* DONE (SEtools)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'SEtools' successfully unpacked and MD5 sums checked

Tests output


Example timings

SEtools.Rcheck/examples_i386/SEtools-Ex.timings

nameusersystemelapsed
SE-heatmap0.330.030.79
aggSE0.290.050.79
castSE0.050.000.17
crossHm0.250.001.06
getBreaks000
log2FC0.010.000.02
meltSE0.030.000.17
mergeSEs0.190.000.31
resetAllSEtoolsOptions000
scale20.000.000.02
se2xls000
sortRows000

SEtools.Rcheck/examples_x64/SEtools-Ex.timings

nameusersystemelapsed
SE-heatmap0.210.020.22
aggSE0.170.030.20
castSE0.040.000.03
crossHm0.170.010.18
getBreaks000
log2FC000
meltSE0.010.020.04
mergeSEs0.100.000.09
resetAllSEtoolsOptions000
scale2000
se2xls000
sortRows000