Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:23 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for cosmosR on tokay2


To the developers/maintainers of the cosmosR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 406/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cosmosR 1.2.0  (landing page)
Katharina Zirngibl
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/cosmosR
git_branch: RELEASE_3_14
git_last_commit: dcb4b9c
git_last_commit_date: 2021-10-26 13:09:43 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cosmosR
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cosmosR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cosmosR_1.2.0.tar.gz
StartedAt: 2022-04-12 17:56:42 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:59:40 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 178.3 seconds
RetCode: 0
Status:   OK  
CheckDir: cosmosR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cosmosR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cosmosR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cosmosR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cosmosR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cosmosR' version '1.2.0'
* 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 ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Namespaces in Imports field not imported from:
  'ggplot2' 'scales'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
load_tf_regulon_dorothea_omnipath 16.8   0.14   39.42
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
load_tf_regulon_dorothea_omnipath   12   0.22   28.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/cosmosR.Rcheck/00check.log'
for details.

Installation output

cosmosR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cosmosR_1.2.0.tar.gz && rm -rf cosmosR.buildbin-libdir && mkdir cosmosR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cosmosR.buildbin-libdir cosmosR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cosmosR_1.2.0.zip && rm cosmosR_1.2.0.tar.gz cosmosR_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 12 3836k   12  478k    0     0  1261k      0  0:00:03 --:--:--  0:00:03 1262k
 82 3836k   82 3167k    0     0  2296k      0  0:00:01  0:00:01 --:--:-- 2297k
100 3836k  100 3836k    0     0  2445k      0  0:00:01  0:00:01 --:--:-- 2446k

install for i386

* installing *source* package 'cosmosR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cosmosR'
    finding HTML links ... done
    convert_ensembl_to_entrezid             html  
    convert_genesymbols_to_entrezid         html  
    cosmos_data                             html  
    default_CARNIVAL_options                html  
    display_node_neighboorhood              html  
    extract_nodes_for_ORA                   html  
    format_COSMOS_res                       html  
    gmt_to_dataframe                        html  
    load_tf_regulon_dorothea                html  
    load_tf_regulon_dorothea_omnipath       html  
    meta_network                            html  
    metabolite_to_pubchem                   html  
    omnipath_ptm                            html  
    prepare_metabolomics_data               html  
    preprocess_COSMOS_metabolism_to_signaling
                                            html  
    preprocess_COSMOS_signaling_to_metabolism
                                            html  
    print.cosmos_data                       html  
    run_COSMOS_metabolism_to_signaling      html  
    run_COSMOS_signaling_to_metabolism      html  
    toy_RNA                                 html  
    toy_metabolic_input                     html  
    toy_network                             html  
    toy_signaling_input                     html  
*** 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

install for x64

* installing *source* package 'cosmosR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cosmosR' as cosmosR_1.2.0.zip
* DONE (cosmosR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cosmosR' successfully unpacked and MD5 sums checked

Tests output

cosmosR.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 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: 197 from  720 interactions are removed from the PKN"
[1] "COSMOS: 3 input/measured nodes are not in PKN any more: X8317, X2101, X5629 and 0 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 8 steps"
[1] "COSMOS: 186 from  523 interactions are removed from the PKN"
[1] "COSMOS: 62 input/measured nodes are not in PKN any more: X2931, X1025, X891, X9134, X4137, X196 and 56 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 33 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 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: 401 from  720 interactions are removed from the PKN"
[1] "COSMOS: 25 input/measured nodes are not in PKN any more: X1457, X1022, X983, X8317, X1459, X9134 and 19 more."
[1] "COSMOS: 18 input/measured nodes are not in PKN any more: XMetab__6132___n____, XMetab__6132___m____, XMetab__6132___c____, XMetab__6132___e____, XMetab__9750___c____, XMetab__700___c____ and 12 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 8 steps"
[1] "COSMOS: 62 from  319 interactions are removed from the PKN"
[1] "COSMOS: 5 input/measured nodes are not in PKN any more: XMetab__790___c____, XMetab__6021___c____, XMetab__6426851___c____, XMetab__107738___c____, XMetab__6029___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 73 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: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 184 from  720 interactions are removed from the PKN"
[1] "COSMOS: 4 input/measured nodes are not in PKN any more: X1457, X983, X6667, X6772 and 0 more."
[1] "COSMOS: 1 input/measured nodes are not in PKN any more: XMetab__6132___e____ and 0 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 202 from  536 interactions are removed from the PKN"
[1] "COSMOS: 22 input/measured nodes are not in PKN any more: XMetab__6132___n____, XMetab__6132___m____, XMetab__6132___c____, XMetab__9750___c____, XMetab__700___c____, XMetab__5961___c____ and 16 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 94 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: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 175 from  720 interactions are removed from the PKN"
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 197 from  545 interactions are removed from the PKN"
[1] "COSMOS: 65 input/measured nodes are not in PKN any more: X8317, X2931, X1025, X891, X9134, X4137 and 59 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 33 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 30 ]

== Skipped tests ===============================================================
* CPLEX optimization based test skipped. (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 30 ]
> 
> proc.time()
   user  system elapsed 
  10.65    0.67   11.34

cosmosR.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 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: 197 from  720 interactions are removed from the PKN"
[1] "COSMOS: 3 input/measured nodes are not in PKN any more: X8317, X2101, X5629 and 0 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 8 steps"
[1] "COSMOS: 186 from  523 interactions are removed from the PKN"
[1] "COSMOS: 62 input/measured nodes are not in PKN any more: X2931, X1025, X891, X9134, X4137, X196 and 56 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 33 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 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: 401 from  720 interactions are removed from the PKN"
[1] "COSMOS: 25 input/measured nodes are not in PKN any more: X1457, X1022, X983, X8317, X1459, X9134 and 19 more."
[1] "COSMOS: 18 input/measured nodes are not in PKN any more: XMetab__6132___n____, XMetab__6132___m____, XMetab__6132___c____, XMetab__6132___e____, XMetab__9750___c____, XMetab__700___c____ and 12 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 8 steps"
[1] "COSMOS: 62 from  319 interactions are removed from the PKN"
[1] "COSMOS: 5 input/measured nodes are not in PKN any more: XMetab__790___c____, XMetab__6021___c____, XMetab__6426851___c____, XMetab__107738___c____, XMetab__6029___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 73 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: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 184 from  720 interactions are removed from the PKN"
[1] "COSMOS: 4 input/measured nodes are not in PKN any more: X1457, X983, X6667, X6772 and 0 more."
[1] "COSMOS: 1 input/measured nodes are not in PKN any more: XMetab__6132___e____ and 0 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 202 from  536 interactions are removed from the PKN"
[1] "COSMOS: 22 input/measured nodes are not in PKN any more: XMetab__6132___n____, XMetab__6132___m____, XMetab__6132___c____, XMetab__9750___c____, XMetab__700___c____, XMetab__5961___c____ and 16 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 94 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: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: all 98 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 175 from  720 interactions are removed from the PKN"
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 197 from  545 interactions are removed from the PKN"
[1] "COSMOS: 65 input/measured nodes are not in PKN any more: X8317, X2931, X1025, X891, X9134, X4137 and 59 more."
[1] "COSMOS:  3 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "COSMOS: all 33 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 25 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 30 ]

== Skipped tests ===============================================================
* CPLEX optimization based test skipped. (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 30 ]
> 
> proc.time()
   user  system elapsed 
  10.35    0.53   10.87

Example timings

cosmosR.Rcheck/examples_i386/cosmosR-Ex.timings

nameusersystemelapsed
convert_ensembl_to_entrezid3.500.223.72
convert_genesymbols_to_entrezid0.190.020.20
default_CARNIVAL_options000
display_node_neighboorhood3.580.233.92
extract_nodes_for_ORA1.650.081.74
format_COSMOS_res1.920.122.05
load_tf_regulon_dorothea0.580.000.58
load_tf_regulon_dorothea_omnipath16.80 0.1439.42
meta_network0.110.000.11
metabolite_to_pubchem000
omnipath_ptm0.310.000.31
prepare_metabolomics_data0.110.020.13
preprocess_COSMOS_metabolism_to_signaling1.080.031.10
preprocess_COSMOS_signaling_to_metabolism0.900.050.96
run_COSMOS_metabolism_to_signaling1.040.011.04
run_COSMOS_signaling_to_metabolism1.200.021.22
toy_RNA0.030.010.05
toy_metabolic_input000
toy_network000
toy_signaling_input000

cosmosR.Rcheck/examples_x64/cosmosR-Ex.timings

nameusersystemelapsed
convert_ensembl_to_entrezid3.740.133.86
convert_genesymbols_to_entrezid0.170.000.18
default_CARNIVAL_options000
display_node_neighboorhood3.650.173.82
extract_nodes_for_ORA2.460.052.50
format_COSMOS_res2.020.062.08
load_tf_regulon_dorothea0.480.030.51
load_tf_regulon_dorothea_omnipath12.00 0.2228.27
meta_network0.080.000.08
metabolite_to_pubchem000
omnipath_ptm0.200.020.22
prepare_metabolomics_data0.130.000.12
preprocess_COSMOS_metabolism_to_signaling1.030.031.06
preprocess_COSMOS_signaling_to_metabolism1.310.031.35
run_COSMOS_metabolism_to_signaling1.360.001.36
run_COSMOS_signaling_to_metabolism1.380.081.45
toy_RNA0.030.000.03
toy_metabolic_input0.010.000.02
toy_network000
toy_signaling_input000