Michael Love
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/nullranges |
| git_branch: RELEASE_3_19 |
| git_last_commit: a4c4b75 |
| git_last_commit_date: 2024-04-30 11:38:00 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 1446/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nullranges 1.10.0 (landing page) Michael Love
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | 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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:nullranges.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings nullranges_1.10.0.tar.gz |
| StartedAt: 2024-10-17 03:10:48 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 03:18:37 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 469.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: nullranges.Rcheck |
| Warnings: NA |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:nullranges.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings nullranges_1.10.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/nullranges.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘nullranges/DESCRIPTION’ ... OK
* this is package ‘nullranges’ version ‘1.10.0’
* package encoding: UTF-8
* 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 ‘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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘bootRanges.Rmd’ using rmarkdown
--- finished re-building ‘bootRanges.Rmd’
--- re-building ‘matchRanges.Rmd’ using rmarkdown
--- finished re-building ‘matchRanges.Rmd’
--- re-building ‘matching_ginteractions.Rmd’ using rmarkdown
Quitting from lines 202-206 [unnamed-chunk-2] (matching_ginteractions.Rmd)
Error: processing vignette 'matching_ginteractions.Rmd' failed with diagnostics:
failed to connect
reason: Timeout was reached: [bioconductor.org] Resolving timed out after 10000 milliseconds
Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘matching_ginteractions.Rmd’
--- re-building ‘matching_granges.Rmd’ using rmarkdown
--- finished re-building ‘matching_granges.Rmd’
--- re-building ‘matching_pool_set.Rmd’ using rmarkdown
--- finished re-building ‘matching_pool_set.Rmd’
--- re-building ‘nullranges.Rmd’ using rmarkdown
--- finished re-building ‘nullranges.Rmd’
SUMMARY: processing the following file failed:
‘matching_ginteractions.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/nullranges.Rcheck/00check.log’
for details.
nullranges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL nullranges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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
15.251 0.991 16.147
nullranges.Rcheck/nullranges-Ex.timings
| name | user | system | elapsed | |
| MatchedDataFrame | 1.915 | 0.048 | 1.834 | |
| MatchedGInteractions | 1.240 | 0.011 | 1.183 | |
| MatchedGRanges | 0.450 | 0.016 | 0.405 | |
| bootRanges | 0.249 | 0.004 | 0.254 | |
| combnCov | 0.003 | 0.000 | 0.003 | |
| covariates | 0.138 | 0.000 | 0.114 | |
| focal | 0.137 | 0.000 | 0.098 | |
| indices | 0.157 | 0.000 | 0.119 | |
| makeExampleMatchedDataSet | 0.619 | 0.000 | 0.509 | |
| matchRanges | 1.457 | 0.032 | 1.114 | |
| matched | 0.142 | 0.001 | 0.118 | |
| matchedClass | 0.144 | 0.000 | 0.118 | |
| matchedData | 0.162 | 0.012 | 0.141 | |
| method | 0.129 | 0.004 | 0.114 | |
| oneRegionSegment | 0.400 | 0.016 | 0.884 | |
| overview | 0.178 | 0.000 | 0.147 | |
| plotCovariate | 3.462 | 0.136 | 3.538 | |
| plotPropensity | 1.336 | 0.016 | 1.298 | |
| plotSegment | 1.463 | 0.148 | 1.611 | |
| pool | 0.128 | 0.008 | 0.108 | |
| reduceSegment | 0.198 | 0.016 | 0.213 | |
| segmentDensity | 0.441 | 0.004 | 0.446 | |
| unmatched | 0.141 | 0.004 | 0.113 | |
| withReplacement | 0.146 | 0.000 | 0.124 | |