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This page was generated on 2021-08-02 15:05:23 -0400 (Mon, 02 Aug 2021).

CHECK results for PPInfer on tokay2

To the developers/maintainers of the PPInfer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PPInfer.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1420/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PPInfer 1.18.0  (landing page)
Dongmin Jung
Snapshot Date: 2021-08-01 04:50:10 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/PPInfer
Branch: RELEASE_3_13
Last Commit: 7713f20
Last Changed Date: 2021-05-19 12:27:35 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PPInfer
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PPInfer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PPInfer_1.18.0.tar.gz
StartedAt: 2021-08-02 03:51:00 -0400 (Mon, 02 Aug 2021)
EndedAt: 2021-08-02 04:00:16 -0400 (Mon, 02 Aug 2021)
EllapsedTime: 556.3 seconds
RetCode: 0
Status:   OK  
CheckDir: PPInfer.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PPInfer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PPInfer_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PPInfer.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.18.0'
* 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 41.50   0.90   62.03
ppi.infer.mouse 35.54   0.89   57.11
ORA.barplot      0.44   0.03   22.85
ORA              0.21   0.04   22.58
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
ppi.infer.human 43.38   1.28   64.61
ppi.infer.mouse 34.34   1.08   55.36
ORA.barplot      0.45   0.01   22.84
ORA              0.20   0.05   22.59
* 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-3.13-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 http://155.52.207.165/BBS/3.13/bioc/src/contrib/PPInfer_1.18.0.tar.gz && rm -rf PPInfer.buildbin-libdir && mkdir PPInfer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PPInfer.buildbin-libdir PPInfer_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL PPInfer_1.18.0.zip && rm PPInfer_1.18.0.tar.gz PPInfer_1.18.0.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
  5  273k    5 14877    0     0   193k      0  0:00:01 --:--:--  0:00:01  193k
100  273k  100  273k    0     0  1815k      0 --:--:-- --:--:-- --:--:-- 1820k

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_1.18.0.zip
* DONE (PPInfer)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'PPInfer' successfully unpacked and MD5 sums checked

Tests output


Example timings

PPInfer.Rcheck/examples_i386/PPInfer-Ex.timings

nameusersystemelapsed
GSEA.barplot2.450.062.52
ORA 0.21 0.0422.58
ORA.barplot 0.44 0.0322.85
enrich.net3.140.223.36
net.infer2.030.002.11
net.infer.ST0.060.000.06
net.kernel0.030.000.03
ppi.infer.human41.50 0.9062.03
ppi.infer.mouse35.54 0.8957.11
self.train.kernel0.060.000.06

PPInfer.Rcheck/examples_x64/PPInfer-Ex.timings

nameusersystemelapsed
GSEA.barplot3.120.053.17
ORA 0.20 0.0522.59
ORA.barplot 0.45 0.0122.84
enrich.net2.410.052.45
net.infer2.220.002.35
net.infer.ST0.080.000.08
net.kernel0.030.000.03
ppi.infer.human43.38 1.2864.61
ppi.infer.mouse34.34 1.0855.36
self.train.kernel0.060.000.06