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CHECK report for Roleswitch on tokay1

This page was generated on 2020-04-15 12:22:06 -0400 (Wed, 15 Apr 2020).

Package 1467/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Roleswitch 1.24.0
Yue Li
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Roleswitch
Branch: RELEASE_3_10
Last Commit: dfb087a
Last Changed Date: 2019-10-29 13:08:46 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Roleswitch
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Roleswitch.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Roleswitch_1.24.0.tar.gz
StartedAt: 2020-04-15 06:14:53 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:19:14 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 260.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Roleswitch.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Roleswitch.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Roleswitch_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Roleswitch.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Roleswitch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Roleswitch' version '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'pracma', 'reshape', 'plotrix', 'microRNA', 'biomaRt', 'Biostrings',
  'Biobase', 'DBI'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'Roleswitch' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCGldor/R.INSTALLd706423a6b/Roleswitch/man/roleswitch.Rd:42: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCGldor/R.INSTALLd706423a6b/Roleswitch/man/roleswitch.Rd:42: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCGldor/R.INSTALLd706423a6b/Roleswitch/man/roleswitch.Rd:45: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Roleswitch.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 ... NOTE
diagnosticPlot: no visible global function definition for 'par'
diagnosticPlot: no visible global function definition for 'axis'
diagnosticPlot: no visible global function definition for 'plot'
getSeedMatrix: no visible global function definition for 'data'
getTranscriptIDwithLongest3UTR: no visible global function definition
  for 'aggregate'
roleswitch: no visible global function definition for 'aggregate'
Undefined global functions or variables:
  aggregate axis data par plot
Consider adding
  importFrom("graphics", "axis", "par", "plot")
  importFrom("stats", "aggregate")
  importFrom("utils", "data")
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
Examples with CPU or elapsed time > 5s
              user system elapsed
getSeedMatrix 4.12   0.31  104.91
** 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/Roleswitch.Rcheck/00check.log'
for details.



Installation output

Roleswitch.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Roleswitch_1.24.0.tar.gz && rm -rf Roleswitch.buildbin-libdir && mkdir Roleswitch.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Roleswitch.buildbin-libdir Roleswitch_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Roleswitch_1.24.0.zip && rm Roleswitch_1.24.0.tar.gz Roleswitch_1.24.0.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  369k  100  369k    0     0  5567k      0 --:--:-- --:--:-- --:--:-- 5859k

install for i386

* installing *source* package 'Roleswitch' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Roleswitch'
    finding HTML links ... done
    Roleswitch-package                      html  
    diagnosticPlot                          html  
    getSeedMatrix                           html  
    roleswitch                              html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCGldor/R.INSTALLd706423a6b/Roleswitch/man/roleswitch.Rd:42: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCGldor/R.INSTALLd706423a6b/Roleswitch/man/roleswitch.Rd:42: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCGldor/R.INSTALLd706423a6b/Roleswitch/man/roleswitch.Rd:45: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
    tcga_gbm_testdata                       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 'Roleswitch' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Roleswitch' as Roleswitch_1.24.0.zip
* DONE (Roleswitch)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Roleswitch' successfully unpacked and MD5 sums checked

Tests output


Example timings

Roleswitch.Rcheck/examples_i386/Roleswitch-Ex.timings

nameusersystemelapsed
Roleswitch-package000
diagnosticPlot0.030.000.04
getSeedMatrix 4.12 0.31104.91
roleswitch0.020.000.01
tcga_gbm_testdata0.560.200.77

Roleswitch.Rcheck/examples_x64/Roleswitch-Ex.timings

nameusersystemelapsed
Roleswitch-package000
diagnosticPlot0.040.000.05
getSeedMatrix2.520.094.74
roleswitch000
tcga_gbm_testdata0.230.050.28