Package: pathRender

Version: 1.52.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathRender.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pathRender_1.52.0.tar.gz

StartedAt: 2019-10-16 05:51:18 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:53:33 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 135.5 seconds

RetCode: 0

Status:  OK

CheckDir: pathRender.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathRender.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pathRender_1.52.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pathRender.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pathRender/DESCRIPTION' ... OK
* this is package 'pathRender' version '1.52.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'graph', 'Rgraphviz', 'RColorBrewer', 'cMAP', 'AnnotationDbi',
  'stats4'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'pathRender' 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
graphcMAP: no visible binding for global variable 'cMAPKEGGPATHWAY'
graphcMAP: no visible binding for global variable 'cMAPCARTAPATHWAY'
graphcMAP: no visible binding for global variable 'cMAPKEGGINTERACTION'
graphcMAP: no visible binding for global variable 'cMAPKEGGMOLECULE'
graphcMAP: no visible binding for global variable
  'cMAPCARTAINTERACTION'
graphcMAP: no visible binding for global variable 'cMAPCARTAMOLECULE'
plotExGraph: no visible global function definition for
  'colorRampPalette'
plotExGraph: no visible global function definition for 'exprs'
quantizeByRow : : no visible global function definition for
  'quantile'
quantizeByRow: no visible global function definition for 'featureNames'
quantizeByRow: no visible global function definition for 'exprs<-'
quantizeByRow: no visible global function definition for 'exprs'
quantizeByRow: no visible global function definition for
  'featureNames<-'
reduceES: no visible global function definition for 'na.omit'
reduceES: no visible global function definition for 'featureData<-'
reduceES: no visible global function definition for 'exprs'
reduceES: no visible global function definition for 'phenoData'
rendercMAPPathway: no visible binding for global variable
  'cMAPKEGGPATHWAY'
rendercMAPPathway: no visible binding for global variable
  'cMAPCARTAPATHWAY'
rendercMAPPathway: no visible binding for global variable
  'cMAPKEGGINTERACTION'
rendercMAPPathway: no visible binding for global variable
  'cMAPKEGGMOLECULE'
rendercMAPPathway: no visible binding for global variable
  'cMAPCARTAINTERACTION'
rendercMAPPathway: no visible binding for global variable
  'cMAPCARTAMOLECULE'
plot,coloredGraph-ANY: no visible global function definition for
  'palette'
Undefined global functions or variables:
  cMAPCARTAINTERACTION cMAPCARTAMOLECULE cMAPCARTAPATHWAY
  cMAPKEGGINTERACTION cMAPKEGGMOLECULE cMAPKEGGPATHWAY colorRampPalette
  exprs exprs<- featureData<- featureNames featureNames<- na.omit
  palette phenoData quantile
Consider adding
  importFrom("grDevices", "colorRampPalette", "palette")
  importFrom("stats", "na.omit", "quantile")
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 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/pathRender.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/pathRender_1.52.0.tar.gz && rm -rf pathRender.buildbin-libdir && mkdir pathRender.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathRender.buildbin-libdir pathRender_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL pathRender_1.52.0.zip && rm pathRender_1.52.0.tar.gz pathRender_1.52.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 11583  100 11583    0     0   180k      0 --:--:-- --:--:-- --:--:--  201k

install for i386

* installing *source* package 'pathRender' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pathRender'
    finding HTML links ... done
    colorNodes                              html  
    coloredGraph-class                      html  
    graphcMAP                               html  
    plotExGraph                             html  
    pwayGraph-class                         html  
    reduceES                                html  
    rendercMAP                              html  
** building package indices
** installing vignettes
** 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 'pathRender' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathRender' as pathRender_1.52.0.zip
* DONE (pathRender)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'pathRender' successfully unpacked and MD5 sums checked