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CHECK results for GraphAT on nebbiolo1

This page was generated on 2021-06-11 14:05:41 -0400 (Fri, 11 Jun 2021).

Package 807/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphAT 1.64.0  (landing page)
Thomas LaFramboise
Snapshot Date: 2021-06-10 06:50:12 -0400 (Thu, 10 Jun 2021)
URL: https://git.bioconductor.org/packages/GraphAT
Branch: RELEASE_3_13
Last Commit: cf236c4
Last Changed Date: 2021-05-19 11:34:36 -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
To the developers/maintainers of the GraphAT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GraphAT.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.

Summary

Package: GraphAT
Version: 1.64.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GraphAT.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GraphAT_1.64.0.tar.gz
StartedAt: 2021-06-10 12:15:41 -0400 (Thu, 10 Jun 2021)
EndedAt: 2021-06-10 12:16:36 -0400 (Thu, 10 Jun 2021)
EllapsedTime: 54.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GraphAT.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GraphAT.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GraphAT_1.64.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/GraphAT.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GraphAT/DESCRIPTION’ ... OK
* this is package ‘GraphAT’ version ‘1.64.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘GraphAT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graph’ ‘methods’
A package should be listed in only one of these fields.
* 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 ... NOTE
prepare_Rd: depthmat.Rd:28: Dropping empty section \references
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/GraphAT.Rcheck/00check.log’
for details.



Installation output

GraphAT.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GraphAT
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘GraphAT’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (GraphAT)

Tests output


Example timings

GraphAT.Rcheck/GraphAT-Ex.timings

nameusersystemelapsed
Phenoclusters0.9900.1521.142
causton0.1930.0120.205
cellcycle0.1320.0760.209
clust2Mat0.0010.0000.001
depthmat0.2060.0640.270
getpvalue0.0030.0000.003
giaever0.2150.0000.215
mRNAclusters0.3940.1910.586
makeClustM000
mat2UndirG0.020.000.02
permPower0.5680.0360.604
perms0.0000.0000.001