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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PPInfer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings PPInfer_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/PPInfer.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PPInfer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PPInfer' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'biomaRt', 'fgsea', 'kernlab', 'ggplot2', 'igraph', 'STRINGdb',
  'yeastExpData'
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 'PPInfer' 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
ORA: no visible global function definition for 'txtProgressBar'
ORA: no visible global function definition for 'fisher.test'
ORA: no visible global function definition for 'setTxtProgressBar'
ORA: no visible global function definition for 'p.adjust'
ORA.barplot: no visible global function definition for 'p.adjust'
enrich.net: no visible global function definition for 'stack'
enrich.net: no visible global function definition for 'adjustcolor'
enrich.net : <anonymous>: no visible global function definition for
  'adjustcolor'
enrich.net: no visible binding for global variable 'legend'
net.infer: no visible global function definition for 'na.omit'
net.infer.ST: no visible global function definition for 'na.omit'
ppi.infer.human: no visible global function definition for 'na.omit'
ppi.infer.mouse: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  adjustcolor fisher.test legend na.omit p.adjust setTxtProgressBar
  stack txtProgressBar
Consider adding
  importFrom("grDevices", "adjustcolor")
  importFrom("graphics", "legend")
  importFrom("stats", "fisher.test", "na.omit", "p.adjust")
  importFrom("utils", "setTxtProgressBar", "stack", "txtProgressBar")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
ppi.infer.human 52.71   1.00   71.52
ppi.infer.mouse 38.25   0.75   52.08
ORA.barplot      0.47   0.03   22.84
ORA              0.34   0.03   22.73
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
ppi.infer.human 39.38   1.38   48.04
ppi.infer.mouse 34.29   1.11   44.51
ORA.barplot      0.38   0.03   22.78
ORA              0.24   0.05   22.63
* 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-3.11-bioc/meat/PPInfer.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/PPInfer_1.14.0.tar.gz && rm -rf PPInfer.buildbin-libdir && mkdir PPInfer.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PPInfer.buildbin-libdir PPInfer_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL PPInfer_1.14.0.zip && rm PPInfer_1.14.0.tar.gz PPInfer_1.14.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

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100  272k  100  272k    0     0  4311k      0 --:--:-- --:--:-- --:--:-- 4870k

install for i386

* installing *source* package 'PPInfer' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PPInfer'
    finding HTML links ... done
    GSEA.barplot                            html  
    ORA                                     html  
    ORA.barplot                             html  
    PPInfer-package                         html  
    enrich.net                              html  
    net.infer                               html  
    net.infer.ST                            html  
    net.kernel                              html  
    ppi.infer.human                         html  
    ppi.infer.mouse                         html  
    self.train.kernel                       html  
** building package indices
** installing vignettes
   'PPInfer.Rnw' 
** 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 'PPInfer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PPInfer' as PPInfer_1.14.0.zip
* DONE (PPInfer)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'PPInfer' successfully unpacked and MD5 sums checked