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CHECK report for SISPA on tokay1

This page was generated on 2021-05-06 12:33:39 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SISPA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1728/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SISPA 1.20.0  (landing page)
Bhakti Dwivedi
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SISPA
Branch: RELEASE_3_12
Last Commit: aa0aff3
Last Changed Date: 2020-10-27 11:08:51 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SISPA
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SISPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SISPA_1.20.0.tar.gz
StartedAt: 2021-05-06 07:02:22 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:07:01 -0400 (Thu, 06 May 2021)
EllapsedTime: 279.8 seconds
RetCode: 0
Status:   OK   
CheckDir: SISPA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SISPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SISPA_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SISPA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SISPA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SISPA' version '1.20.0'
* 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 'SISPA' 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
cptSamples : cptsPlot: no visible global function definition for
  'abline'
cptSamples : cptsPlot: no visible global function definition for 'text'
Undefined global functions or variables:
  abline text
Consider adding
  importFrom("graphics", "abline", "text")
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 installed files from 'inst/doc' ... 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-3.12-bioc/meat/SISPA.Rcheck/00check.log'
for details.



Installation output

SISPA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SISPA_1.20.0.tar.gz && rm -rf SISPA.buildbin-libdir && mkdir SISPA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SISPA.buildbin-libdir SISPA_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SISPA_1.20.0.zip && rm SISPA_1.20.0.tar.gz SISPA_1.20.0.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  431k  100  431k    0     0  22.0M      0 --:--:-- --:--:-- --:--:-- 23.4M

install for i386

* installing *source* package 'SISPA' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SISPA'
    finding HTML links ... done
    ExpressionSet                           html  
    SISPA                                   html  
    VariantSet                              html  
    callGSVA                                html  
    callZSCORE                              html  
    cptSamples                              html  
    filterVars                              html  
    freqplot                                html  
    sortData                                html  
    waterfallplot                           html  
** building package indices
** installing vignettes
   'SISPA.Rmd' using 'UTF-8' 
** 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 'SISPA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SISPA' as SISPA_1.20.0.zip
* DONE (SISPA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SISPA' successfully unpacked and MD5 sums checked

Tests output


Example timings

SISPA.Rcheck/examples_i386/SISPA-Ex.timings

nameusersystemelapsed
SISPA1.120.001.13
callGSVA0.210.000.20
callZSCORE0.010.000.02
cptSamples1.390.001.39
filterVars000
freqplot0.320.000.31
sortData000
waterfallplot0.210.020.23

SISPA.Rcheck/examples_x64/SISPA-Ex.timings

nameusersystemelapsed
SISPA1.420.021.44
callGSVA0.360.000.36
callZSCORE000
cptSamples1.780.001.78
filterVars000
freqplot0.310.010.33
sortData000
waterfallplot0.220.000.22