Michael Love
| Snapshot Date: 2024-11-28 13:00 -0500 (Thu, 28 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/nullranges |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9604c3a |
| git_last_commit_date: 2024-10-29 11:05:17 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-02 12:04 -0500 (Mon, 02 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4739 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
| 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 1434/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nullranges 1.12.0 (landing page) Michael Love
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the nullranges package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nullranges.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: nullranges |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:nullranges.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings nullranges_1.12.0.tar.gz |
| StartedAt: 2024-11-29 03:49:00 -0500 (Fri, 29 Nov 2024) |
| EndedAt: 2024-11-29 03:59:17 -0500 (Fri, 29 Nov 2024) |
| EllapsedTime: 617.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nullranges.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:nullranges.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings nullranges_1.12.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/nullranges.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘nullranges/DESCRIPTION’ ... OK
* this is package ‘nullranges’ version ‘1.12.0’
* 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'
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 ‘nullranges’ 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) MatchedDataFrame.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedDataFrame.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedDataFrame.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedDataFrame.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedDataFrame.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedDataFrame.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedDataFrame.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedDataFrame.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedDataFrame.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGInteractions.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGInteractions.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGInteractions.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGInteractions.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGInteractions.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGInteractions.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGInteractions.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGInteractions.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGInteractions.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGRanges.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGRanges.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGRanges.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGRanges.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGRanges.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGRanges.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGRanges.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGRanges.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MatchedGRanges.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) matchRanges.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) matchRanges.Rd:71-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) matchRanges.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) matchedClass.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) matchedClass.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) matchedClass.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) matchedClass.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) matchedClass.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) segmentDensity.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) segmentDensity.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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-3.20-bioc/meat/nullranges.Rcheck/00check.log’
for details.
nullranges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL nullranges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘nullranges’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (nullranges)
nullranges.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(nullranges)
>
> test_check("nullranges")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
>
> proc.time()
user system elapsed
13.887 0.817 14.609
nullranges.Rcheck/nullranges-Ex.timings
| name | user | system | elapsed | |
| MatchedDataFrame | 2.319 | 0.033 | 2.175 | |
| MatchedGInteractions | 0.536 | 0.021 | 0.434 | |
| MatchedGRanges | 0.465 | 0.002 | 0.364 | |
| bootRanges | 0.244 | 0.001 | 0.245 | |
| combnCov | 0.002 | 0.000 | 0.003 | |
| covariates | 0.144 | 0.000 | 0.106 | |
| focal | 0.149 | 0.001 | 0.105 | |
| indices | 0.158 | 0.001 | 0.113 | |
| makeExampleMatchedDataSet | 1.258 | 0.023 | 1.154 | |
| matchRanges | 1.350 | 0.006 | 0.925 | |
| matched | 0.114 | 0.000 | 0.091 | |
| matchedClass | 0.129 | 0.000 | 0.103 | |
| matchedData | 0.121 | 0.000 | 0.089 | |
| method | 0.118 | 0.004 | 0.097 | |
| oneRegionSegment | 0.371 | 0.006 | 0.748 | |
| overview | 0.133 | 0.000 | 0.105 | |
| plotCovariate | 2.388 | 0.076 | 2.382 | |
| plotPropensity | 1.298 | 0.004 | 1.249 | |
| plotSegment | 1.292 | 0.066 | 1.359 | |
| pool | 0.200 | 0.012 | 0.176 | |
| reduceSegment | 0.188 | 0.001 | 0.184 | |
| segmentDensity | 0.382 | 0.002 | 0.383 | |
| unmatched | 0.168 | 0.001 | 0.133 | |
| withReplacement | 0.168 | 0.000 | 0.134 | |