Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 351/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CHRONOS 1.34.0  (landing page)
Panos Balomenos
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CHRONOS
git_branch: RELEASE_3_20
git_last_commit: 8f10df2
git_last_commit_date: 2024-10-29 10:10:44 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    TIMEOUT  skippedskipped


CHECK results for CHRONOS on palomino8

To the developers/maintainers of the CHRONOS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CHRONOS.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.

raw results


Summary

Package: CHRONOS
Version: 1.34.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CHRONOS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CHRONOS_1.34.0.tar.gz
StartedAt: 2024-12-20 00:00:45 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 00:04:12 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 206.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CHRONOS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CHRONOS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CHRONOS_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CHRONOS.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CHRONOS/DESCRIPTION' ... OK
* this is package 'CHRONOS' version '1.34.0'
* 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 'CHRONOS' 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 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) extractLinearSubpathways.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractLinearSubpathways.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractLinearSubpathways.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractNonLinearSubpathways.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractNonLinearSubpathways.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractNonLinearSubpathways.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
CHRONOSrun       2.05   0.15   10.49
visualizeResults 0.06   0.05    6.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/CHRONOS.Rcheck/00check.log'
for details.


Installation output

CHRONOS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CHRONOS
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'CHRONOS' ...
** using staged installation
** R
** 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 (CHRONOS)

Tests output

CHRONOS.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> BiocGenerics:::testPackage('CHRONOS')
Testing test_CHRONOSrun...Importing entrezgene data...done.
Importing miRNA data...done.
Downloading files...done.
Creating adjacency matrices...done.
Extracting Linear Subpathways...done.
	#98 subpathways initially
Calculating subscores...done.
	#21 subpathways after subscore.
Calculating mirscores......end.
Extracting Non Linear Subpathways...done.
	#24 subpathways initially
Calculating subscores...done.
	#19 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_pathwayToGraph...Creating adjacency matrices...done.
done.
Testing test_subExtractionLinear...Importing entrezgene data...done.
Extracting Linear Subpathways...done.
done.
Testing test_subExtractionNonLinear...Importing entrezgene data...done.
Extracting Non Linear Subpathways...done.
done.
Testing test_subRefinement...Importing entrezgene data...done.
Importing miRNA data...done.
	#98 subpathways initially
Calculating subscores...done.
	#21 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_subVisualization...Importing entrezgene data...done.
Summarising scores...done.
Summarising scores...done.
done.


RUNIT TEST PROTOCOL -- Fri Dec 20 00:04:01 2024 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CHRONOS RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
  10.87    1.18   14.89 

Example timings

CHRONOS.Rcheck/CHRONOS-Ex.timings

nameusersystemelapsed
CHRONOSrun 2.05 0.1510.49
convertMiRNANomenclature0.000.020.02
convertNomenclature000
createPathwayGraphs0.230.060.29
downloadKEGGPathwayList0.020.010.03
downloadMiRecords0.030.020.05
downloadPathways000
extractLinearSubpathways0.500.061.45
extractNonLinearSubpathways0.230.060.30
getEdgeTypes000
importExpressions0.060.000.06
pathwayMeasures0.110.000.11
scoreSubpathways0.110.020.17
subpathwayKEGGmap0.050.000.05
subpathwayMiRNAs1.800.061.86
visualizeResults0.060.056.55