Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 2244/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
vulcan 1.29.0 (landing page) Federico M. Giorgi
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
To the developers/maintainers of the vulcan package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vulcan.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: vulcan |
Version: 1.29.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings vulcan_1.29.0.tar.gz |
StartedAt: 2024-12-24 03:16:31 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 03:23:54 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 442.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: vulcan.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings vulcan_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/vulcan.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘vulcan/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘vulcan’ version ‘1.29.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Depends: includes the non-default packages: 'ChIPpeakAnno', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'zoo', 'GenomicRanges', 'S4Vectors', 'viper', 'DiffBind', 'locfit' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘vulcan’ 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 vulcan.normalize: no visible global function definition for 'assay' Undefined global functions or variables: assay * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed average_fragment_length 5.292 0.265 5.579 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/vulcan.Rcheck/00check.log’ for details.
vulcan.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL vulcan ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘vulcan’ ... ** 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 (vulcan)
vulcan.Rcheck/vulcan-Ex.timings
name | user | system | elapsed | |
average_fragment_length | 5.292 | 0.265 | 5.579 | |
corr2p | 0.000 | 0.002 | 0.002 | |
densityauc | 0.020 | 0.002 | 0.022 | |
dpareto | 0.007 | 0.000 | 0.006 | |
fisherp | 0.000 | 0.001 | 0.000 | |
gsea | 0.163 | 0.001 | 0.163 | |
kmgformat | 0.053 | 0.000 | 0.054 | |
null_gsea | 0.024 | 0.000 | 0.024 | |
p2corr | 0.000 | 0.001 | 0.000 | |
p2z | 0.000 | 0.001 | 0.000 | |
pareto.fit | 0.021 | 0.001 | 0.022 | |
plot_gsea | 0.029 | 0.001 | 0.029 | |
ppareto | 0.002 | 0.002 | 0.003 | |
rea | 0.002 | 0.001 | 0.003 | |
slice | 0.000 | 0.001 | 0.001 | |
stouffer | 0.000 | 0.000 | 0.001 | |
textplot2 | 0.136 | 0.000 | 0.137 | |
val2col | 0.014 | 0.000 | 0.014 | |
vulcan | 4.021 | 0.119 | 4.141 | |
vulcan.annotate | 3.26 | 0.12 | 3.38 | |
vulcan.import | 0.046 | 0.002 | 0.049 | |
vulcan.normalize | 0 | 0 | 0 | |
vulcan.pathways | 2.735 | 0.077 | 2.811 | |
wstouffer | 0.001 | 0.000 | 0.001 | |
z2p | 0 | 0 | 0 | |