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 12:07 -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 2259/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
vulcan 1.28.0 (landing page) Federico M. Giorgi
| 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 | OK | OK | ||||||||||
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: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vulcan.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vulcan_1.28.0.tar.gz |
StartedAt: 2024-11-20 03:50:56 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 04:00:07 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 550.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: vulcan.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vulcan.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vulcan_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/vulcan.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘vulcan/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘vulcan’ version ‘1.28.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' NOTE 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 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 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 vulcan 4.891 0.171 5.089 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/vulcan.Rcheck/00check.log’ for details.
vulcan.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL vulcan ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 3.409 | 0.428 | 3.885 | |
corr2p | 0.001 | 0.000 | 0.001 | |
densityauc | 0.023 | 0.002 | 0.026 | |
dpareto | 0.005 | 0.001 | 0.006 | |
fisherp | 0.000 | 0.001 | 0.001 | |
gsea | 0.136 | 0.014 | 0.152 | |
kmgformat | 0.042 | 0.005 | 0.048 | |
null_gsea | 0.034 | 0.004 | 0.038 | |
p2corr | 0.001 | 0.000 | 0.000 | |
p2z | 0.000 | 0.001 | 0.001 | |
pareto.fit | 0.021 | 0.001 | 0.023 | |
plot_gsea | 0.029 | 0.003 | 0.033 | |
ppareto | 0.002 | 0.001 | 0.003 | |
rea | 0.002 | 0.000 | 0.002 | |
slice | 0.000 | 0.000 | 0.001 | |
stouffer | 0.000 | 0.001 | 0.001 | |
textplot2 | 0.126 | 0.002 | 0.129 | |
val2col | 0.007 | 0.001 | 0.008 | |
vulcan | 4.891 | 0.171 | 5.089 | |
vulcan.annotate | 1.663 | 0.090 | 1.763 | |
vulcan.import | 0.022 | 0.005 | 0.027 | |
vulcan.normalize | 0.000 | 0.001 | 0.000 | |
vulcan.pathways | 2.633 | 0.118 | 2.769 | |
wstouffer | 0.000 | 0.001 | 0.000 | |
z2p | 0 | 0 | 0 | |