Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 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" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 439/2255 | 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 | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: /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_1.13.0.tar.gz |
StartedAt: 2024-08-26 20:30:33 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 20:31:07 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 34.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cosmosR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cosmosR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cosmosR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cosmosR’ version ‘1.13.0’ * 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 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 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 ‘/Users/biocbuild/bbs-3.20-bioc/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/4.4-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 1.867 0.127 1.992
cosmosR.Rcheck/cosmosR-Ex.timings
name | user | system | elapsed | |
HMDB_mapper_vec | 0.109 | 0.003 | 0.113 | |
compress_same_children | 0.002 | 0.000 | 0.002 | |
decompress_solution_network | 0.123 | 0.002 | 0.125 | |
decoupleRnival | 0.343 | 0.002 | 0.344 | |
default_CARNIVAL_options | 0.058 | 0.008 | 0.069 | |
display_node_neighboorhood | 1.195 | 0.058 | 1.255 | |
extract_nodes_for_ORA | 0.965 | 0.041 | 1.010 | |
filter_incohrent_TF_target | 0.162 | 0.004 | 0.167 | |
load_tf_regulon_dorothea | 0.016 | 0.002 | 0.018 | |
meta_network | 0.053 | 0.001 | 0.054 | |
meta_network_cleanup | 0.061 | 0.002 | 0.063 | |
preprocess_COSMOS_metabolism_to_signaling | 0.112 | 0.011 | 0.123 | |
preprocess_COSMOS_signaling_to_metabolism | 0.341 | 0.016 | 0.358 | |
reduce_solution_network | 0.165 | 0.002 | 0.167 | |
run_COSMOS_metabolism_to_signaling | 0.184 | 0.020 | 0.204 | |
run_COSMOS_signaling_to_metabolism | 0.631 | 0.021 | 0.652 | |
toy_RNA | 0.008 | 0.001 | 0.009 | |
toy_metabolic_input | 0.000 | 0.000 | 0.001 | |
toy_network | 0.000 | 0.001 | 0.001 | |
toy_signaling_input | 0.001 | 0.000 | 0.000 | |