Attila Gabor
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/cosmosR |
| git_branch: devel |
| git_last_commit: 4c05998 |
| git_last_commit_date: 2024-04-30 11:34:23 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 434/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cosmosR 1.13.0 (landing page) Attila Gabor
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
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. |
| Package: cosmosR |
| Version: 1.13.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cosmosR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cosmosR_1.13.0.tar.gz |
| StartedAt: 2024-07-15 23:00:34 -0400 (Mon, 15 Jul 2024) |
| EndedAt: 2024-07-15 23:02:04 -0400 (Mon, 15 Jul 2024) |
| EllapsedTime: 89.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cosmosR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cosmosR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cosmosR_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/cosmosR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'cosmosR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cosmosR' version '1.13.0'
* 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 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 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 ... 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
'C:/Users/biocbuild/bbs-3.20-bioc/meat/cosmosR.Rcheck/00check.log'
for details.
cosmosR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL cosmosR ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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)
cosmosR.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
5.25 0.62 5.89
cosmosR.Rcheck/cosmosR-Ex.timings
| name | user | system | elapsed | |
| HMDB_mapper_vec | 0.18 | 0.01 | 0.20 | |
| compress_same_children | 0 | 0 | 0 | |
| decompress_solution_network | 0.22 | 0.02 | 0.23 | |
| decoupleRnival | 1.44 | 0.03 | 1.47 | |
| default_CARNIVAL_options | 0.16 | 0.02 | 0.17 | |
| display_node_neighboorhood | 2.57 | 0.23 | 2.85 | |
| extract_nodes_for_ORA | 1.94 | 0.17 | 2.14 | |
| filter_incohrent_TF_target | 0.58 | 0.02 | 0.59 | |
| load_tf_regulon_dorothea | 0.05 | 0.00 | 0.05 | |
| meta_network | 0.11 | 0.00 | 0.11 | |
| meta_network_cleanup | 1.03 | 0.00 | 1.03 | |
| preprocess_COSMOS_metabolism_to_signaling | 0.26 | 0.09 | 0.37 | |
| preprocess_COSMOS_signaling_to_metabolism | 0.72 | 0.06 | 0.80 | |
| reduce_solution_network | 0.59 | 0.00 | 0.60 | |
| run_COSMOS_metabolism_to_signaling | 0.46 | 0.14 | 0.64 | |
| run_COSMOS_signaling_to_metabolism | 1.31 | 0.07 | 1.43 | |
| toy_RNA | 0.02 | 0.00 | 0.02 | |
| toy_metabolic_input | 0 | 0 | 0 | |
| toy_network | 0 | 0 | 0 | |
| toy_signaling_input | 0 | 0 | 0 | |