Package: SRGnet

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SRGnet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SRGnet_1.12.0.tar.gz

StartedAt: 2020-04-15 05:56:18 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:58:54 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 156.2 seconds

RetCode: 0

Status:  OK

CheckDir: SRGnet.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SRGnet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SRGnet_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/SRGnet.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SRGnet/DESCRIPTION’ ... OK
* this is package ‘SRGnet’ version ‘1.12.0’
* 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 ‘plot’
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 plot predict terrain.colors write.table
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "boxplot", "par", "plot")
  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 or elapsed time > 5s
         user system elapsed
SRGnet 53.562  0.519  54.911
* 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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/SRGnet.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SRGnet
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

name	user	system	elapsed
SRGnet	53.562	0.519	54.911