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BioC 3.6: CHECK report for SISPA on tokay1

This page was generated on 2017-08-16 13:35:16 -0400 (Wed, 16 Aug 2017).

Package 1255/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SISPA 1.7.0
Bhakti Dwivedi
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SISPA
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SISPA
Version: 1.7.0
Command: rm -rf SISPA.buildbin-libdir SISPA.Rcheck && mkdir SISPA.buildbin-libdir SISPA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SISPA.buildbin-libdir SISPA_1.7.0.tar.gz >SISPA.Rcheck\00install.out 2>&1 && cp SISPA.Rcheck\00install.out SISPA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SISPA.buildbin-libdir --install="check:SISPA-install.out" --force-multiarch --no-vignettes --timings SISPA_1.7.0.tar.gz
StartedAt: 2017-08-16 02:33:12 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:36:25 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 192.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SISPA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SISPA.buildbin-libdir SISPA.Rcheck && mkdir SISPA.buildbin-libdir SISPA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SISPA.buildbin-libdir SISPA_1.7.0.tar.gz >SISPA.Rcheck\00install.out 2>&1 && cp SISPA.Rcheck\00install.out SISPA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SISPA.buildbin-libdir --install="check:SISPA-install.out" --force-multiarch --no-vignettes --timings SISPA_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SISPA.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.7.0'
* 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 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'SISPA.Rmd', 'SISPA.md', 'SISPA_data.Rda',
    'SISPA_files/figure-html/unnamed-chunk-2-1.png',
    'SISPA_files/figure-html/unnamed-chunk-3-1.png',
    'SISPA_files/figure-html/unnamed-chunk-4-1.png',
    'SISPA_files/figure-html/unnamed-chunk-5-1.png',
    'SISPA_files/figure-html/unnamed-chunk-6-1.png',
    'SISPA_files/figure-html/unnamed-chunk-7-1.png',
    'sispa_overview.png'
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/SISPA.Rcheck/00check.log'
for details.


SISPA.Rcheck/00install.out:


install for i386

* installing *source* package 'SISPA' ...
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'SISPA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SISPA' as SISPA_1.7.0.zip
* DONE (SISPA)

SISPA.Rcheck/examples_i386/SISPA-Ex.timings:

nameusersystemelapsed
SISPA0.010.000.01
callGSVA0.410.000.41
callZSCORE000
cptSamples0.470.030.50
filterVars000
freqplot0.820.010.82
sortData000
waterfallplot0.610.000.61

SISPA.Rcheck/examples_x64/SISPA-Ex.timings:

nameusersystemelapsed
SISPA0.030.000.03
callGSVA0.330.000.33
callZSCORE000
cptSamples1.110.001.11
filterVars000
freqplot1.610.001.61
sortData000
waterfallplot0.770.000.76