Attila Gabor
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/cosmosR |
| git_branch: RELEASE_3_17 |
| git_last_commit: 96202c4 |
| git_last_commit_date: 2023-04-25 11:29:42 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 439/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cosmosR 1.8.0 (landing page) Attila Gabor
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the cosmosR package: - 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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2023-10-17 12:07:00 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 12:08:43 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 102.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cosmosR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cosmosR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cosmosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cosmosR’ version ‘1.8.0’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
format_COSMOS_res: no visible binding for global variable
‘HMDB_mapper_vec’
Undefined global functions or variables:
HMDB_mapper_vec
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
display_node_neighboorhood 3.692 0.208 6.026
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cosmosR.Rcheck/00check.log’
for details.
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-arm64/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)
cosmosR.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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
4.333 0.379 7.238
cosmosR.Rcheck/cosmosR-Ex.timings
| name | user | system | elapsed | |
| HMDB_mapper_vec | 0.310 | 0.017 | 0.499 | |
| default_CARNIVAL_options | 0.244 | 0.049 | 0.484 | |
| display_node_neighboorhood | 3.692 | 0.208 | 6.026 | |
| extract_nodes_for_ORA | 2.421 | 0.120 | 4.052 | |
| load_tf_regulon_dorothea | 0.055 | 0.003 | 0.089 | |
| meta_network | 0.194 | 0.005 | 0.331 | |
| preprocess_COSMOS_metabolism_to_signaling | 0.495 | 0.042 | 0.893 | |
| preprocess_COSMOS_signaling_to_metabolism | 1.068 | 0.051 | 1.730 | |
| run_COSMOS_metabolism_to_signaling | 1.019 | 0.082 | 1.752 | |
| run_COSMOS_signaling_to_metabolism | 1.904 | 0.082 | 3.064 | |
| toy_RNA | 0.016 | 0.003 | 0.029 | |
| toy_metabolic_input | 0.001 | 0.001 | 0.003 | |
| toy_network | 0.001 | 0.001 | 0.004 | |
| toy_signaling_input | 0.001 | 0.001 | 0.004 | |