Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FELLA_1.26.0.tar.gz |
StartedAt: 2024-11-20 02:53:56 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 03:25:48 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 1911.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FELLA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FELLA_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed data-funs 5.862 0.071 8.644 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/00check.log’ for details.
FELLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL FELLA ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 30.443 4.780 68.106
FELLA.Rcheck/FELLA-Ex.timings
name | user | system | elapsed | |
FELLA | 0.178 | 0.018 | 0.421 | |
FELLA.sample | 0.009 | 0.000 | 0.020 | |
checkArguments | 0.002 | 0.000 | 0.001 | |
data-funs | 5.862 | 0.071 | 8.644 | |
enrich-funs | 2.013 | 0.035 | 2.350 | |
export-funs | 0.139 | 0.000 | 0.140 | |
getBackground | 0.236 | 0.001 | 0.246 | |
getCom | 0.007 | 0.001 | 0.017 | |
getExcluded | 0.009 | 0.000 | 0.015 | |
getGraph | 0.007 | 0.000 | 0.016 | |
getInfo | 0.007 | 0.000 | 0.013 | |
getInput | 0.009 | 0.000 | 0.015 | |
getMatrix | 0.012 | 0.001 | 0.028 | |
getName | 0.006 | 0.001 | 0.017 | |
getPscores | 0.281 | 0.001 | 0.562 | |
getPvaluesSize | 0.030 | 0.000 | 0.058 | |
getStatus | 0.006 | 0.001 | 0.007 | |
getSums | 0.401 | 0.002 | 0.407 | |
getValid | 0.030 | 0.001 | 0.029 | |
infere.con2ec | 0.001 | 0.000 | 0.001 | |
input.sample | 0.000 | 0.000 | 0.001 | |
is.FELLA.DATA | 0.007 | 0.000 | 0.006 | |
is.FELLA.USER | 0.026 | 0.000 | 0.027 | |
largestcc | 0.045 | 0.000 | 0.045 | |
launchApp | 0.001 | 0.000 | 0.000 | |
listApprox | 0 | 0 | 0 | |
listCategories | 0 | 0 | 0 | |
listInternalDatabases | 0.001 | 0.000 | 0.001 | |
listMethods | 0 | 0 | 0 | |
mytriangle | 0.029 | 0.000 | 0.029 | |
plotBipartite | 0.047 | 0.000 | 0.047 | |
plotLegend | 0.019 | 0.000 | 0.020 | |
sanitise | 0.001 | 0.000 | 0.000 | |