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CHECK report for PPInfer on tokay2

This page was generated on 2019-10-16 12:38:25 -0400 (Wed, 16 Oct 2019).

Package 1237/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PPInfer 1.10.0
Dongmin Jung
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/PPInfer
Branch: RELEASE_3_9
Last Commit: 7dcf551
Last Changed Date: 2019-05-02 11:54:07 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PPInfer
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PPInfer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PPInfer_1.10.0.tar.gz
StartedAt: 2019-10-16 06:04:58 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:15:41 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 643.3 seconds
RetCode: 0
Status:  OK  
CheckDir: PPInfer.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PPInfer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PPInfer_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PPInfer.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 'PPInfer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PPInfer' version '1.10.0'
* 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 : : 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 or elapsed time > 5s
                 user system elapsed
ppi.infer.human 64.17   1.17  103.72
ppi.infer.mouse 36.66   1.35   94.75
ORA.barplot      0.61   0.03   22.99
ORA              0.21   0.03   24.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
ppi.infer.human 42.97   1.86   89.17
ppi.infer.mouse 34.39   2.13   65.75
ORA.barplot      0.73   0.02   23.12
ORA              0.17   0.03   22.58
* 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/PPInfer.Rcheck/00check.log'
for details.



Installation output

PPInfer.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PPInfer_1.10.0.tar.gz && rm -rf PPInfer.buildbin-libdir && mkdir PPInfer.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PPInfer.buildbin-libdir PPInfer_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PPInfer_1.10.0.zip && rm PPInfer_1.10.0.tar.gz PPInfer_1.10.0.zip
###
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  % 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  272k  100  272k    0     0  4035k      0 --:--:-- --:--:-- --:--:-- 4471k

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_1.10.0.zip
* DONE (PPInfer)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PPInfer' successfully unpacked and MD5 sums checked

Tests output


Example timings

PPInfer.Rcheck/examples_i386/PPInfer-Ex.timings

nameusersystemelapsed
GSEA.barplot3.780.224.00
ORA 0.21 0.0324.09
ORA.barplot 0.61 0.0322.99
enrich.net2.690.072.75
net.infer2.780.002.86
net.infer.ST0.090.010.11
net.kernel0.050.000.04
ppi.infer.human 64.17 1.17103.72
ppi.infer.mouse36.66 1.3594.75
self.train.kernel0.110.000.11

PPInfer.Rcheck/examples_x64/PPInfer-Ex.timings

nameusersystemelapsed
GSEA.barplot2.440.062.43
ORA 0.17 0.0322.58
ORA.barplot 0.73 0.0223.12
enrich.net2.360.052.41
net.infer2.050.002.05
net.infer.ST0.080.000.08
net.kernel0.020.010.03
ppi.infer.human42.97 1.8689.17
ppi.infer.mouse34.39 2.1365.75
self.train.kernel0.080.000.08