Package: SigFuge

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SigFuge.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SigFuge_1.18.0.tar.gz

StartedAt: 2018-10-17 04:50:28 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:53:42 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 193.3 seconds

RetCode: 0

Status:  OK

CheckDir: SigFuge.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SigFuge.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SigFuge_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SigFuge.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 'SigFuge/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SigFuge' version '1.18.0'
* 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 'SigFuge' 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
SFfigure: no visible binding for global variable 'base'
SFfigure: no visible binding for global variable 's'
SFfigure: no visible binding for global variable 'e'
SFfigure: no visible global function definition for 'rgb'
SFfigure: no visible global function definition for 'hcl'
SFfigure: no visible binding for global variable 'cluster'
SFfigure: no visible binding for global variable 'median'
SFfigure: no visible binding for global variable 'x'
SFfigure: no visible binding for global variable 'y1'
SFfigure: no visible binding for global variable 'label'
SFfigure: no visible binding for global variable 'value'
SFfigure: no visible binding for global variable 'Clusters'
SFfigure: no visible binding for global variable 'y2'
SFfigure: no visible global function definition for 'pdf'
SFfigure: no visible global function definition for 'dev.off'
SFlabels: no visible global function definition for 'kmeans'
SFnormalize : <anonymous>: no visible global function definition for
  'median'
Undefined global functions or variables:
  Clusters base cluster dev.off e hcl kmeans label median pdf rgb s
  value x y1 y2
Consider adding
  importFrom("grDevices", "dev.off", "hcl", "pdf", "rgb")
  importFrom("stats", "kmeans", "median")
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
SFfigure 21.05   0.89   21.98
SFpval   15.77   0.76   16.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
SFfigure 19.85   0.78   20.65
SFpval   10.77   0.61   11.38
* 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-3.7-bioc/meat/SigFuge.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/SigFuge_1.18.0.tar.gz && rm -rf SigFuge.buildbin-libdir && mkdir SigFuge.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SigFuge.buildbin-libdir SigFuge_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL SigFuge_1.18.0.zip && rm SigFuge_1.18.0.tar.gz SigFuge_1.18.0.zip
###
##############################################################################
##############################################################################


  % 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  131k  100  131k    0     0  2249k      0 --:--:-- --:--:-- --:--:-- 2536k

install for i386

* installing *source* package 'SigFuge' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SigFuge'
    finding HTML links ... done
    SFfigure                                html  
    SFlabels                                html  
    SFnormalize                             html  
    SFpval                                  html  
    finding level-2 HTML links ... done

    SigFuge-package                         html  
    geneAnnot                               html  
    geneDepth                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SigFuge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SigFuge' as SigFuge_1.18.0.zip
* DONE (SigFuge)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'SigFuge' successfully unpacked and MD5 sums checked
In R CMD INSTALL