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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:cosmosR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings cosmosR_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/cosmosR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘cosmosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cosmosR’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘keep_controllable_neighbours’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
decompress_solution_network: no visible binding for global variable
  ‘HMDB_mapper_vec’
format_COSMOS_res: no visible binding for global variable
  ‘HMDB_mapper_vec’
meta_network_cleanup: no visible binding for global variable ‘target’
meta_network_cleanup: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . HMDB_mapper_vec target
* 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 ... INFO
  Note: found 1029 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/cosmosR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL cosmosR
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 3 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: 2975 of the 9300 genes in expression data were found as transcription factor target"
[1] "COSMOS: 2975 of the 5321 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: 26 from  101 interactions are removed from the PKN"
[1] "COSMOS: 1 input/measured nodes are not in PKN any more: Metab__HMDB0000190_c and 0 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 8 steps"
[1] "COSMOS: 50 from  75 interactions are removed from the PKN"
[1] "COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF 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 1 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 1 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target"
[1] "COSMOS: 2975 of the 5321 transcription factor targets were found in expression data"
[1] "COSMOS: all 3 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: 2975 of the 9300 genes in expression data were found as transcription factor target"
[1] "COSMOS: 2975 of the 5321 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: 0 from  101 interactions are removed from the PKN"
[1] "COSMOS: removing nodes that are not observable by measurements within 8 steps"
[1] "COSMOS: 54 from  101 interactions are removed from the PKN"
[1] "COSMOS: 1 input/measured nodes are not in PKN any more: Metab__HMDB0000190_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 3 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 1 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target"
[1] "COSMOS: 2975 of the 5321 transcription factor targets were found in expression data"
[1] "COSMOS: all 3 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: 2975 of the 9300 genes in expression data were found as transcription factor target"
[1] "COSMOS: 2975 of the 5321 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 0 from  101 interactions are removed from the PKN"
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 54 from  101 interactions are removed from the PKN"
[1] "COSMOS: 1 input/measured nodes are not in PKN any more: Metab__HMDB0000190_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 3 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 1 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target"
[1] "COSMOS: 2975 of the 5321 transcription factor targets were found in expression data"
[1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."
[1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."
[1] "COSMOS: all 3 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: 2975 of the 9300 genes in expression data were found as transcription factor target"
[1] "COSMOS: 2975 of the 5321 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 0 from  101 interactions are removed from the PKN"
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 52 from  101 interactions are removed from the PKN"
[1] "COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF 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 1 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: 2975 of the 9300 genes in expression data were found as transcription factor target"
[1] "COSMOS: 2975 of the 5321 transcription factor targets were found in expression data"
[1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."
[1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  4.150   0.339   4.475