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This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 399/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cosmosR 1.0.1 (landing page) Katharina Zirngibl
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: cosmosR |
Version: 1.0.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cosmosR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cosmosR_1.0.1.tar.gz |
StartedAt: 2021-10-14 17:51:36 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 17:53:21 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 104.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cosmosR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cosmosR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cosmosR_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/cosmosR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cosmosR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cosmosR’ version ‘1.0.1’ * 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 ... 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 * 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 ... 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed load_tf_regulon_dorothea_omnipath 6.401 0.193 11.259 convert_ensembl_to_entrezid 5.319 0.228 5.552 * 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: OK
cosmosR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cosmosR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘cosmosR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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" ══ Skipped tests ═══════════════════════════════════════════════════════════════ • CPLEX optimization based test skipped. (2) [ FAIL 0 | WARN 0 | SKIP 2 | PASS 30 ] > > proc.time() user system elapsed 14.453 0.619 15.067
cosmosR.Rcheck/cosmosR-Ex.timings
name | user | system | elapsed | |
convert_ensembl_to_entrezid | 5.319 | 0.228 | 5.552 | |
convert_genesymbols_to_entrezid | 0.300 | 0.012 | 0.315 | |
default_CARNIVAL_options | 0.001 | 0.000 | 0.001 | |
display_node_neighboorhood | 3.384 | 0.199 | 3.595 | |
format_COSMOS_res | 1.629 | 0.060 | 1.688 | |
load_tf_regulon_dorothea | 0.641 | 0.018 | 0.658 | |
load_tf_regulon_dorothea_omnipath | 6.401 | 0.193 | 11.259 | |
meta_network | 0.260 | 0.002 | 0.261 | |
metabolite_to_pubchem | 0.007 | 0.002 | 0.009 | |
omnipath_ptm | 0.294 | 0.002 | 0.297 | |
prepare_metabolomics_data | 0.297 | 0.007 | 0.304 | |
preprocess_COSMOS_metabolism_to_signaling | 1.056 | 0.027 | 1.084 | |
preprocess_COSMOS_signaling_to_metabolism | 1.098 | 0.031 | 1.130 | |
run_COSMOS_metabolism_to_signaling | 1.180 | 0.032 | 1.213 | |
run_COSMOS_signaling_to_metabolism | 1.043 | 0.037 | 1.086 | |
toy_RNA | 0.032 | 0.002 | 0.034 | |
toy_metabolic_input | 0.001 | 0.001 | 0.002 | |
toy_network | 0.000 | 0.001 | 0.002 | |
toy_signaling_input | 0.001 | 0.001 | 0.001 | |