Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-04-29 11:41:17 -0400 (Mon, 29 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4752 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4475 |
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 1747/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rfaRm 1.15.2 (landing page) Lara Selles Vidal
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | 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 | OK | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the rfaRm package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rfaRm.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: rfaRm |
Version: 1.15.2 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:rfaRm.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings rfaRm_1.15.2.tar.gz |
StartedAt: 2024-04-29 09:44:20 -0000 (Mon, 29 Apr 2024) |
EndedAt: 2024-04-29 09:48:35 -0000 (Mon, 29 Apr 2024) |
EllapsedTime: 254.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: rfaRm.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:rfaRm.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings rfaRm_1.15.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/rfaRm.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rfaRm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rfaRm’ version ‘1.15.2’ * 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 ‘rfaRm’ 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 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 ... NOTE rfamSeedAlignment: no visible global function definition for ‘as’ Undefined global functions or variables: as Consider adding importFrom("methods", "as") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘rfaRm-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: rfamSequenceRegions > ### Title: Retrieve all sequence regions belonging to an Rfam family > ### Aliases: rfamSequenceRegions > > ### ** Examples > > # Generate a data frame with the sequence regions belonging to the Rfam family > # with ID "FMN" > > head(rfamSequenceRegions("FMN")) No encoding supplied: defaulting to UTF-8. No encoding supplied: defaulting to UTF-8. Error in names(x) <- value : 'names' attribute [7] must be the same length as the vector [1] Calls: head -> rfamSequenceRegions -> colnames<- -> colnames<- Execution halted * 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 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/rfaRm.Rcheck/00check.log’ for details.
rfaRm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL rfaRm ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘rfaRm’ ... ** 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 (rfaRm)
rfaRm.Rcheck/tests/runTests.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > BiocGenerics:::testPackage("rfaRm") Linking to librsvg 2.50.5 No encoding supplied: defaulting to UTF-8. format width height colorspace matte filesize density 1 SVG 700 550 sRGB TRUE 17458 +96x+96 format width height colorspace matte filesize density 1 GIF 600 2056 sRGB FALSE 62234 +72x+72 Running sequence search query. This might take a long time. RUNIT TEST PROTOCOL -- Mon Apr 29 09:48:32 2024 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : rfaRm RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 5.285 0.350 41.936
rfaRm.Rcheck/rfaRm-Ex.timings
name | user | system | elapsed | |
rfamConsensusSecondaryStructure | 0.273 | 0.012 | 6.364 | |
rfamCovarianceModel | 0.120 | 0.012 | 1.817 | |
rfamFamilyAccessionToID | 0.026 | 0.004 | 0.315 | |
rfamFamilyIDToAccession | 0.012 | 0.004 | 0.298 | |
rfamFamilySummary | 0.132 | 0.004 | 1.859 | |
rfamPDBMapping | 0.136 | 0.024 | 2.069 | |
rfamSecondaryStructurePlot | 0.263 | 0.017 | 1.758 | |
rfamSecondaryStructureXMLSVG | 0.063 | 0.001 | 1.746 | |
rfamSeedAlignment | 0.574 | 0.087 | 6.483 | |
rfamSeedTree | 0.110 | 0.004 | 1.256 | |
rfamSeedTreeImage | 0.096 | 0.008 | 1.553 | |