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This page was generated on 2024-03-04 11:37:14 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 443/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cosmosR 1.10.0  (landing page)
Attila Gabor
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/cosmosR
git_branch: RELEASE_3_18
git_last_commit: 16a439b
git_last_commit_date: 2023-10-24 11:33:21 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for cosmosR on lconway


To the developers/maintainers of the cosmosR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cosmosR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cosmosR
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2024-03-03 19:52:13 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 19:53:55 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 101.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cosmosR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/cosmosR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cosmosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cosmosR’ version ‘1.10.0’
* 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 ... 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 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
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 ... NOTE
  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 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/cosmosR.Rcheck/00check.log’
for details.



Installation output

cosmosR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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)

Tests output

cosmosR.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 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 
  5.362   0.528   5.945 

Example timings

cosmosR.Rcheck/cosmosR-Ex.timings

nameusersystemelapsed
HMDB_mapper_vec0.3090.0190.332
compress_same_children0.0040.0010.006
decompress_solution_network0.3090.0140.326
decoupleRnival1.7370.0331.784
default_CARNIVAL_options0.2230.0340.268
display_node_neighboorhood3.7150.3364.557
extract_nodes_for_ORA2.5660.1472.770
filter_incohrent_TF_target0.8000.0100.817
load_tf_regulon_dorothea0.0490.0010.051
meta_network0.1340.0020.138
meta_network_cleanup0.2470.0100.261
preprocess_COSMOS_metabolism_to_signaling0.3880.0450.441
preprocess_COSMOS_signaling_to_metabolism0.9450.0541.006
reduce_solution_network0.8630.0170.887
run_COSMOS_metabolism_to_signaling0.6530.0660.725
run_COSMOS_signaling_to_metabolism1.7930.0891.897
toy_RNA0.0160.0010.017
toy_metabolic_input0.0000.0010.002
toy_network0.0010.0010.002
toy_signaling_input0.0010.0020.002