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This page was generated on 2023-05-31 05:44:32 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 430/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cosmosR 1.9.1 (landing page) Attila Gabor
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: cosmosR |
| Version: 1.9.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:cosmosR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings cosmosR_1.9.1.tar.gz |
| StartedAt: 2023-05-30 04:18:31 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 04:20:23 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 112.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cosmosR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:cosmosR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings cosmosR_1.9.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/cosmosR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘cosmosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cosmosR’ version ‘1.9.1’
* 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 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 ... 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 4.993 0.162 5.162
* 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 ...
‘tutorial.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/cosmosR.Rcheck/00check.log’
for details.
cosmosR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL cosmosR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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)
cosmosR.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
6.877 0.315 7.174
cosmosR.Rcheck/cosmosR-Ex.timings
| name | user | system | elapsed | |
| HMDB_mapper_vec | 0.327 | 0.004 | 0.331 | |
| compress_same_children | 0.004 | 0.000 | 0.005 | |
| decompress_solution_network | 0.287 | 0.025 | 0.311 | |
| decoupleRnival | 2.974 | 0.047 | 3.022 | |
| default_CARNIVAL_options | 0.233 | 0.012 | 0.245 | |
| display_node_neighboorhood | 4.993 | 0.162 | 5.162 | |
| extract_nodes_for_ORA | 3.587 | 0.100 | 3.687 | |
| filter_incohrent_TF_target | 1.37 | 0.04 | 1.41 | |
| load_tf_regulon_dorothea | 0.068 | 0.004 | 0.072 | |
| meta_network | 0.126 | 0.000 | 0.127 | |
| meta_network_cleanup | 0.271 | 0.004 | 0.275 | |
| preprocess_COSMOS_metabolism_to_signaling | 0.516 | 0.012 | 0.528 | |
| preprocess_COSMOS_signaling_to_metabolism | 1.816 | 0.044 | 1.860 | |
| reduce_solution_network | 1.292 | 0.020 | 1.312 | |
| run_COSMOS_metabolism_to_signaling | 0.820 | 0.012 | 0.832 | |
| run_COSMOS_signaling_to_metabolism | 2.843 | 0.016 | 2.859 | |
| toy_RNA | 0.015 | 0.000 | 0.015 | |
| toy_metabolic_input | 0.001 | 0.000 | 0.001 | |
| toy_network | 0.001 | 0.000 | 0.001 | |
| toy_signaling_input | 0.001 | 0.000 | 0.001 | |