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CHECK report for SRGnet on malbec2

This page was generated on 2020-10-17 11:55:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SRGnet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1729/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SRGnet 1.14.0
Isar Nassiri
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SRGnet
Branch: RELEASE_3_11
Last Commit: 9fac514
Last Changed Date: 2020-04-27 14:58:06 -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  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SRGnet
Version: 1.14.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SRGnet.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SRGnet_1.14.0.tar.gz
StartedAt: 2020-10-17 05:48:13 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:50:27 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 134.0 seconds
RetCode: 0
Status:  OK 
CheckDir: SRGnet.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SRGnet.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SRGnet_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/SRGnet.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SRGnet/DESCRIPTION’ ... OK
* this is package ‘SRGnet’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'EBcoexpress', 'MASS', 'igraph', 'pvclust', 'gbm', 'limma', 'DMwR',
  'matrixStats', 'Hmisc'
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 ‘SRGnet’ 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 ... NOTE
SRGnet: no visible binding for global variable
  ‘Differentially_expressed_genes’
SRGnet: no visible binding for global variable ‘Transcriptomics’
SRGnet: no visible binding for global variable ‘PLCRG’
SRGnet: no visible global function definition for ‘ebPatterns’
SRGnet: no visible global function definition for ‘par’
SRGnet: no visible global function definition for ‘boxplot’
SRGnet: no visible global function definition for ‘predict’
SRGnet: no visible global function definition for ‘terrain.colors’
SRGnet: no visible global function definition for ‘na.omit’
SRGnet: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  Differentially_expressed_genes PLCRG Transcriptomics boxplot
  ebPatterns na.omit par predict terrain.colors write.table
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "boxplot", "par")
  importFrom("stats", "na.omit", "predict")
  importFrom("utils", "write.table")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
SRGnet 44.824  0.076  44.919
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/SRGnet.Rcheck/00check.log’
for details.



Installation output

SRGnet.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL SRGnet
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘SRGnet’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SRGnet)

Tests output


Example timings

SRGnet.Rcheck/SRGnet-Ex.timings

nameusersystemelapsed
SRGnet44.824 0.07644.919