| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:48 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 661/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epigenomix 1.44.0 (landing page) Hans-Ulrich Klein
| 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 | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the epigenomix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epigenomix.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: epigenomix |
| Version: 1.44.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings epigenomix_1.44.0.tar.gz |
| StartedAt: 2024-05-09 07:09:25 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 07:15:51 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 386.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epigenomix.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings epigenomix_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/epigenomix.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 ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.44.0’
* 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 ‘epigenomix’ 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) MixModel-class.Rd:77-81: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModel-class.Rd:85-86: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModel-class.Rd:87: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModel-class.Rd:88-89: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:55: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:56-58: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:59-60: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:65-66: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:67-68: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:69-70: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:71-72: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelML-class.Rd:51-53: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelML-class.Rd:58: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelML-class.Rd:59-60: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelML-class.Rd:61: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalize.Rd:50-55: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalize.Rd:56-60: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalize.Rd:61-63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalize.Rd:64-72: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalizeChIP.Rd:35-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalizeChIP.Rd:39-46: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalizeChIP.Rd:47-51: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalizeChIP.Rd:52-53: Lost braces in \enumerate; meant \describe ?
* 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 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
plotChains 38.698 0.199 44.501
bayesMixModel 28.521 0.338 36.214
mlMixModel 16.684 0.180 16.900
* 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 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/epigenomix.Rcheck/00check.log’
for details.
epigenomix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL epigenomix ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘epigenomix’ ... ** 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 (epigenomix)
epigenomix.Rcheck/epigenomix-Ex.timings
| name | user | system | elapsed | |
| ChIPseqSet-class | 0.002 | 0.000 | 0.002 | |
| MixModel-class | 0.001 | 0.000 | 0.000 | |
| MixModelBayes-class | 0.001 | 0.000 | 0.000 | |
| MixModelML-class | 0.001 | 0.000 | 0.001 | |
| MixtureComponent-class | 0.000 | 0.000 | 0.001 | |
| bayesMixModel | 28.521 | 0.338 | 36.214 | |
| calculateCrossCorrelation | 0.984 | 0.036 | 1.022 | |
| eSet | 0.016 | 0.000 | 0.017 | |
| fpkm | 0.033 | 0.000 | 0.034 | |
| getAlignmentQuality | 0 | 0 | 0 | |
| integrateData | 0.237 | 0.004 | 0.242 | |
| mappedReads | 0.042 | 0.004 | 0.047 | |
| matchProbeToPromoter | 0.441 | 0.024 | 0.466 | |
| mlMixModel | 16.684 | 0.180 | 16.900 | |
| normalize | 0.233 | 0.024 | 0.257 | |
| normalizeChIP | 0.151 | 0.008 | 0.159 | |
| plotChains | 38.698 | 0.199 | 44.501 | |
| plotClassification | 0.035 | 0.008 | 0.043 | |
| plotComponents | 0.049 | 0.012 | 0.060 | |
| summarizeReads | 0.469 | 0.008 | 0.478 | |
| transToTSS | 0.003 | 0.000 | 0.003 | |