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CHECK report for GraphAT on malbec2

This page was generated on 2019-10-16 11:55:25 -0400 (Wed, 16 Oct 2019).

Package 714/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphAT 1.56.0
Thomas LaFramboise
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GraphAT
Branch: RELEASE_3_9
Last Commit: 3ea1867
Last Changed Date: 2019-05-02 11:53:02 -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: GraphAT
Version: 1.56.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GraphAT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GraphAT_1.56.0.tar.gz
StartedAt: 2019-10-16 02:11:11 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:12:24 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 73.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GraphAT.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GraphAT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GraphAT_1.56.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GraphAT.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.56.0’
* 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-3.9-bioc/meat/GraphAT.Rcheck/00check.log’
for details.



Installation output

GraphAT.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GraphAT
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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
Phenoclusters1.0790.1521.231
causton0.2470.0080.255
cellcycle0.1420.0760.219
clust2Mat0.0000.0000.001
depthmat0.2820.0600.342
getpvalue0.0040.0000.004
giaever0.3630.0000.363
mRNAclusters0.8440.2001.044
makeClustM0.0010.0000.001
mat2UndirG0.0220.0000.022
permPower0.4030.0360.439
perms000