Package: geneplotter

Version: 1.60.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneplotter.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings geneplotter_1.60.0.tar.gz

StartedAt: 2019-04-13 02:29:24 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:32:14 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 169.6 seconds

RetCode: 0

Status:  OK

CheckDir: geneplotter.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneplotter.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings geneplotter_1.60.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/geneplotter.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneplotter/DESCRIPTION' ... OK
* this is package 'geneplotter' version '1.60.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'geneplotter' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to 'annotate' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'Rgraphviz' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotExpressionGraph: no visible global function definition for
  'selectMethod'
Undefined global functions or variables:
  selectMethod
Consider adding
  importFrom("methods", "selectMethod")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
** 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/geneplotter.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/geneplotter_1.60.0.tar.gz && rm -rf geneplotter.buildbin-libdir && mkdir geneplotter.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneplotter.buildbin-libdir geneplotter_1.60.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL geneplotter_1.60.0.zip && rm geneplotter_1.60.0.tar.gz geneplotter_1.60.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 1002k  100 1002k    0     0  18.2M      0 --:--:-- --:--:-- --:--:-- 19.5M

install for i386

* installing *source* package 'geneplotter' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geneplotter'
    finding HTML links ... done
    GetColor                                html  
    Makesense                               html  
    alongChrom                              html  
    amplicon.plot                           html  
    cColor                                  html  
    cPlot                                   html  
    cScale                                  html  
    eset133a                                html  
    groupedHeatmap                          html  
    histStack                               html  
    imageMap                                html  
    make.chromOrd                           html  
    multiecdf                               html  
    openHtmlPage                            html  
    plotChr                                 html  
    plotExpressionGraph                     html  
    plotMA                                  html  
    savepng                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'geneplotter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneplotter' as geneplotter_1.60.0.zip
* DONE (geneplotter)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'geneplotter' successfully unpacked and MD5 sums checked
In R CMD INSTALL