Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-31 19:28:42 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 243/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BubbleTree 2.35.0 (landing page) Todd Creasy
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the BubbleTree package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BubbleTree.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: BubbleTree |
Version: 2.35.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BubbleTree_2.35.0.tar.gz |
StartedAt: 2024-05-31 02:03:05 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 02:10:27 -0400 (Fri, 31 May 2024) |
EllapsedTime: 441.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BubbleTree.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BubbleTree_2.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BubbleTree.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘BubbleTree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BubbleTree’ version ‘2.35.0’ * 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 ‘BubbleTree’ can be installed ... OK * checking installed package size ... NOTE installed size is 23.9Mb sub-directories of 1Mb or more: data 23.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. 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 annoByOverlap,Annotate: no visible binding for global variable 'queryHits' Undefined global functions or variables: queryHits * checking Rd files ... OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'Annotate.Rd': ‘Annotate-package’ Invalid package aliases in Rd file 'BTreePlotter.Rd': ‘BTreePlotter-package’ Invalid package aliases in Rd file 'BTreePredictor.Rd': ‘BTreePredictor-package’ Invalid package aliases in Rd file 'RBD.Rd': ‘RBD-package’ Invalid package aliases in Rd file 'TrackPlotter.Rd': ‘TrackPlotter-package’ * 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 makeRBD 13.243 0.244 13.486 heteroLociTrack 6.179 0.372 6.550 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/BubbleTree.Rcheck/00check.log’ for details.
BubbleTree.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BubbleTree ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘BubbleTree’ ... ** using staged installation Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. ** 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 (BubbleTree)
BubbleTree.Rcheck/BubbleTree-Ex.timings
name | user | system | elapsed | |
Annotate | 0 | 0 | 0 | |
BTreePlotter | 0.161 | 0.051 | 0.213 | |
BTreePredictor | 0.007 | 0.000 | 0.007 | |
RBD | 0.001 | 0.000 | 0.000 | |
RscoreTrack | 0.451 | 0.075 | 0.527 | |
TrackPlotter | 0.001 | 0.001 | 0.001 | |
annoByGenesAndCyto | 0.525 | 0.016 | 0.541 | |
bafTrack | 0.236 | 0.012 | 0.249 | |
btcompare | 0.002 | 0.000 | 0.002 | |
btpredict | 2.196 | 0.168 | 2.364 | |
drawBTree | 0.258 | 0.008 | 0.266 | |
drawBubbles | 0.265 | 0.015 | 0.281 | |
drawFeatures | 0.867 | 0.033 | 0.899 | |
getTracks | 0.591 | 0.020 | 0.611 | |
heteroLociTrack | 6.179 | 0.372 | 6.550 | |
info | 2.097 | 0.044 | 2.141 | |
loadRBD | 0.023 | 0.000 | 0.023 | |
makeRBD | 13.243 | 0.244 | 13.486 | |
saveXLS | 0.311 | 0.029 | 0.357 | |
trackBTree | 0.284 | 0.001 | 0.284 | |
xyTrack | 0.244 | 0.000 | 0.243 | |