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 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (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 708/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FELLA 1.26.0 (landing page) Sergio Picart-Armada
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the FELLA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FELLA.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: FELLA |
Version: 1.26.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FELLA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings FELLA_1.26.0.tar.gz |
StartedAt: 2024-12-20 01:32:55 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:36:33 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 218.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FELLA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FELLA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings FELLA_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/FELLA.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 'FELLA/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'FELLA' version '1.26.0' * 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 'FELLA' 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 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 ... NOTE buildGraphFromKEGGREST: no visible global function definition for 'capture.output' Undefined global functions or variables: capture.output Consider adding importFrom("utils", "capture.output") to your NAMESPACE file. * 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 ... NOTE Documented arguments not in \usage in Rd file 'dot-params.Rd': 'databaseDir' 'internalDir' 'object' 'data' 'type' 'level' 'method' 'methods' 'approx' 'loadMatrix' 'threshold' 'thresholdConnectedComponent' 'plimit' 'nlimit' 'niter' 'layout' 'graph' 'GOterm' 'GONamesAsLabels' 'LabelLengthAtPlot' 'godata.options' 'mart.options' 'p.adjust' 'dampingFactor' 't.df' 'compounds' 'compoundsBackground' 'NamesAsLabels' 'capPscores' Documented arguments not in \usage in Rd file 'infere.con2ec.Rd': 'gene2enyzme' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 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 data-funs 8.3 0.44 8.78 * 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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/00check.log' for details.
FELLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL FELLA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'FELLA' ... ** 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 (FELLA)
FELLA.Rcheck/tests/testthat.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. > library(testthat) > library(FELLA) > > test_check("FELLA") | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% [ FAIL 0 | WARN 14 | SKIP 0 | PASS 168 ] [ FAIL 0 | WARN 14 | SKIP 0 | PASS 168 ] > > proc.time() user system elapsed 41.78 4.42 74.04
FELLA.Rcheck/FELLA-Ex.timings
name | user | system | elapsed | |
FELLA | 0.64 | 0.05 | 1.05 | |
FELLA.sample | 0.02 | 0.00 | 0.02 | |
checkArguments | 0 | 0 | 0 | |
data-funs | 8.30 | 0.44 | 8.78 | |
enrich-funs | 4.36 | 0.03 | 4.55 | |
export-funs | 0.27 | 0.00 | 0.28 | |
getBackground | 0.34 | 0.01 | 0.36 | |
getCom | 0 | 0 | 0 | |
getExcluded | 0.00 | 0.02 | 0.01 | |
getGraph | 0 | 0 | 0 | |
getInfo | 0.02 | 0.01 | 0.03 | |
getInput | 0.01 | 0.00 | 0.01 | |
getMatrix | 0.00 | 0.02 | 0.02 | |
getName | 0.02 | 0.00 | 0.01 | |
getPscores | 0.08 | 0.00 | 0.08 | |
getPvaluesSize | 0.03 | 0.00 | 0.03 | |
getStatus | 0.01 | 0.00 | 0.02 | |
getSums | 0.39 | 0.02 | 0.41 | |
getValid | 0.07 | 0.01 | 0.07 | |
infere.con2ec | 0.01 | 0.00 | 0.02 | |
input.sample | 0 | 0 | 0 | |
is.FELLA.DATA | 0.02 | 0.00 | 0.02 | |
is.FELLA.USER | 0.04 | 0.03 | 0.07 | |
largestcc | 0.08 | 0.00 | 0.08 | |
launchApp | 0 | 0 | 0 | |
listApprox | 0 | 0 | 0 | |
listCategories | 0 | 0 | 0 | |
listInternalDatabases | 0 | 0 | 0 | |
listMethods | 0 | 0 | 0 | |
mytriangle | 0.04 | 0.00 | 0.04 | |
plotBipartite | 0.11 | 0.00 | 0.11 | |
plotLegend | 0.04 | 0.00 | 0.03 | |
sanitise | 0 | 0 | 0 | |