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CHECK report for GraphAT on machv2

This page was generated on 2020-10-17 11:58:38 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GraphAT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 773/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphAT 1.60.0
Thomas LaFramboise
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GraphAT
Branch: RELEASE_3_11
Last Commit: 54e84ab
Last Changed Date: 2020-04-27 14:10:01 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GraphAT
Version: 1.60.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GraphAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GraphAT_1.60.0.tar.gz
StartedAt: 2020-10-17 01:50:44 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:52:25 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 100.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GraphAT.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GraphAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GraphAT_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GraphAT.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GraphAT/DESCRIPTION’ ... OK
* this is package ‘GraphAT’ version ‘1.60.0’
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/GraphAT.Rcheck/00check.log’
for details.



Installation output

GraphAT.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GraphAT
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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
Phenoclusters1.2720.1231.396
causton0.4670.0440.512
cellcycle0.4300.0520.481
clust2Mat0.0000.0010.001
depthmat0.4770.0520.529
getpvalue0.0060.0010.006
giaever0.5060.0180.524
mRNAclusters0.5830.0480.632
makeClustM0.0010.0000.001
mat2UndirG0.0470.0010.047
permPower1.2090.1481.359
perms0.0010.0000.000