Package: SISPA

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SISPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SISPA_1.10.0.tar.gz

StartedAt: 2018-10-17 04:54:27 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:57:24 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 176.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SISPA.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SISPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SISPA_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SISPA.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.10.0'
* 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
* 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 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'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/SISPA.Rmd'
(Is a VignetteBuilder field missing?)
* 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-3.7-bioc/meat/SISPA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/SISPA_1.10.0.tar.gz && rm -rf SISPA.buildbin-libdir && mkdir SISPA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SISPA.buildbin-libdir SISPA_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL SISPA_1.10.0.zip && rm SISPA_1.10.0.tar.gz SISPA_1.10.0.zip
###
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100  612k  100  612k    0     0  9282k      0 --:--:-- --:--:-- --:--:-- 10.3M

install for i386

* installing *source* package 'SISPA' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SISPA'
    finding HTML links ... done
    SISPA                                   html  
    callGSVA                                html  
    callZSCORE                              html  
    cptSamples                              html  
    expression_data                         html  
    filterVars                              html  
    freqplot                                html  
    sortData                                html  
    variant_data                            html  
    waterfallplot                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SISPA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SISPA' as SISPA_1.10.0.zip
* DONE (SISPA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'SISPA' successfully unpacked and MD5 sums checked
In R CMD INSTALL