Back to Build/check report for BioC 3.16
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2022-06-27 11:05:27 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for PPInfer on nebbiolo2


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? 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 1468/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PPInfer 1.23.0  (landing page)
Dongmin Jung
Snapshot Date: 2022-06-26 14:00:03 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/PPInfer
git_branch: master
git_last_commit: cac0cc8
git_last_commit_date: 2022-04-26 11:40:40 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PPInfer
Version: 1.23.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:PPInfer.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings PPInfer_1.23.0.tar.gz
StartedAt: 2022-06-26 21:09:48 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 21:16:18 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 390.2 seconds
RetCode: 0
Status:   OK  
CheckDir: PPInfer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:PPInfer.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings PPInfer_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/PPInfer.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PPInfer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PPInfer’ version ‘1.23.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
ppi.infer.human 32.825  1.450 102.788
ppi.infer.mouse 26.971  1.146  91.755
ORA.barplot      2.089  0.060  16.552
ORA              1.895  0.092  16.377
* 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
  ‘/home/biocbuild/bbs-3.16-bioc/meat/PPInfer.Rcheck/00check.log’
for details.



Installation output

PPInfer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL PPInfer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘PPInfer’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (PPInfer)

Tests output


Example timings

PPInfer.Rcheck/PPInfer-Ex.timings

nameusersystemelapsed
GSEA.barplot3.2060.2323.399
ORA 1.895 0.09216.377
ORA.barplot 2.089 0.06016.552
enrich.net2.0490.1432.150
net.infer1.6550.1001.755
net.infer.ST0.0580.0040.062
net.kernel0.0160.0070.023
ppi.infer.human 32.825 1.450102.788
ppi.infer.mouse26.971 1.14691.755
self.train.kernel0.0470.0200.066