Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-03 12:03 -0400 (Wed, 03 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4826 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4616 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4563 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 251/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BubbleTree 2.39.0 (landing page) Todd Creasy
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 2.39.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BubbleTree_2.39.0.tar.gz |
StartedAt: 2025-09-02 21:40:11 -0400 (Tue, 02 Sep 2025) |
EndedAt: 2025-09-02 21:50:42 -0400 (Tue, 02 Sep 2025) |
EllapsedTime: 631.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BubbleTree.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BubbleTree_2.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BubbleTree.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘BubbleTree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BubbleTree’ version ‘2.39.0’ * 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 ... INFO installed size is 23.8Mb sub-directories of 1Mb or more: data 23.4Mb * 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 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 18.371 0.313 19.842 heteroLociTrack 7.839 0.477 8.547 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/BubbleTree.Rcheck/00check.log’ for details.
BubbleTree.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BubbleTree ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BubbleTree’ ... ** this is package ‘BubbleTree’ version ‘2.39.0’ ** 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 | 0.213 | 0.049 | 0.296 | |
BTreePredictor | 0.006 | 0.002 | 0.020 | |
RBD | 0.000 | 0.000 | 0.001 | |
RscoreTrack | 0.623 | 0.010 | 0.844 | |
TrackPlotter | 0 | 0 | 0 | |
annoByGenesAndCyto | 0.702 | 0.008 | 0.726 | |
bafTrack | 0.382 | 0.025 | 0.445 | |
btcompare | 0.004 | 0.000 | 0.004 | |
btpredict | 3.558 | 0.183 | 3.846 | |
drawBTree | 0.318 | 0.009 | 0.351 | |
drawBubbles | 0.358 | 0.024 | 0.382 | |
drawFeatures | 1.039 | 0.006 | 1.066 | |
getTracks | 0.799 | 0.015 | 0.830 | |
heteroLociTrack | 7.839 | 0.477 | 8.547 | |
info | 3.700 | 0.005 | 3.925 | |
loadRBD | 0.027 | 0.000 | 0.027 | |
makeRBD | 18.371 | 0.313 | 19.842 | |
saveXLS | 0.382 | 0.042 | 0.660 | |
trackBTree | 0.415 | 0.007 | 0.522 | |
xyTrack | 0.375 | 0.007 | 0.382 | |