##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cosmosR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cosmosR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/cosmosR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cosmosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cosmosR’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘cosmosR’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘scales’
  All declared Imports should be used.
* 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 ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
load_tf_regulon_dorothea_omnipath 6.936  0.228  31.326
convert_ensembl_to_entrezid       6.030  0.254   6.290
display_node_neighboorhood        5.160  0.318   5.491
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/cosmosR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cosmosR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘cosmosR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (cosmosR)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(cosmosR)
> 
> test_check("cosmosR")
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: removing unexpressed nodes from PKN..."
[1] "COSMOS: 0 interactions removed"
[1] "COSMOS: removing nodes that are not reachable from inputs within 8 steps"
[1] "COSMOS: 197 from  720 interactions are removed from the PKN"
[1] "COSMOS: 3 input/measured nodes are not in PKN any more: X8317, X2101, X5629 and 0 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 8 steps"
[1] "COSMOS: 186 from  523 interactions are removed from the PKN"
[1] "COSMOS: 62 input/measured nodes are not in PKN any more: X2931, X1025, X891, X9134, X4137, X196 and 56 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 33 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: removing unexpressed nodes from PKN..."
[1] "COSMOS: 0 interactions removed"
[1] "COSMOS: removing nodes that are not reachable from inputs within 8 steps"
[1] "COSMOS: 401 from  720 interactions are removed from the PKN"
[1] "COSMOS: 25 input/measured nodes are not in PKN any more: X1457, X1022, X983, X8317, X1459, X9134 and 19 more."
[1] "COSMOS: 18 input/measured nodes are not in PKN any more: XMetab__6132___n____, XMetab__6132___m____, XMetab__6132___c____, XMetab__6132___e____, XMetab__9750___c____, XMetab__700___c____ and 12 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 8 steps"
[1] "COSMOS: 62 from  319 interactions are removed from the PKN"
[1] "COSMOS: 5 input/measured nodes are not in PKN any more: XMetab__790___c____, XMetab__6021___c____, XMetab__6426851___c____, XMetab__107738___c____, XMetab__6029___c____ and 0 more."
[1] "COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 73 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 2 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 184 from  720 interactions are removed from the PKN"
[1] "COSMOS: 4 input/measured nodes are not in PKN any more: X1457, X983, X6667, X6772 and 0 more."
[1] "COSMOS: 1 input/measured nodes are not in PKN any more: XMetab__6132___e____ and 0 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 202 from  536 interactions are removed from the PKN"
[1] "COSMOS: 22 input/measured nodes are not in PKN any more: XMetab__6132___n____, XMetab__6132___m____, XMetab__6132___c____, XMetab__9750___c____, XMetab__700___c____, XMetab__5961___c____ and 16 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 94 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 2 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 175 from  720 interactions are removed from the PKN"
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 197 from  545 interactions are removed from the PKN"
[1] "COSMOS: 65 input/measured nodes are not in PKN any more: X8317, X2931, X1025, X891, X9134, X4137 and 59 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 33 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 30 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• CPLEX optimization based test skipped. (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 30 ]
> 
> proc.time()
   user  system elapsed 
 15.139   0.650  15.781