Lanyu Zhang
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/rnaEditr |
| git_branch: RELEASE_3_17 |
| git_last_commit: 19beb2c |
| git_last_commit_date: 2023-04-25 11:23:33 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:42 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1739/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rnaEditr 1.10.0 (landing page) Lanyu Zhang
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the rnaEditr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rnaEditr.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: rnaEditr |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rnaEditr_1.10.0.tar.gz |
| StartedAt: 2023-10-16 00:30:29 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 00:35:19 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 290.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rnaEditr.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rnaEditr_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rnaEditr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rnaEditr/DESCRIPTION’ ... OK
* this is package ‘rnaEditr’ 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 ‘rnaEditr’ 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 R 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 ... WARNING
checkRd: (7) TestSingleRegion.Rd:38: Invalid URL: "https://www.jstor.org/stable/2336755"
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘introduction_to_rnaEditr.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.17-bioc/meat/rnaEditr.Rcheck/00check.log’
for details.
rnaEditr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rnaEditr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘rnaEditr’ ... ** 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 (rnaEditr)
rnaEditr.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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(rnaEditr)
>
> test_check("rnaEditr")
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
>
> proc.time()
user system elapsed
17.971 0.652 18.613
rnaEditr.Rcheck/rnaEditr-Ex.timings
| name | user | system | elapsed | |
| AddMetaData | 0.546 | 0.011 | 0.560 | |
| AllCloseByRegions | 0.390 | 0.008 | 0.398 | |
| AllCoeditedRegions | 0.608 | 0.000 | 0.608 | |
| AnnotateResults | 2.178 | 0.039 | 2.218 | |
| CountSamplesPerGroup | 0.000 | 0.003 | 0.003 | |
| CreateEditingTable | 0.034 | 0.001 | 0.035 | |
| CreateOutputDF | 0.02 | 0.00 | 0.02 | |
| CreateRdrop | 0.012 | 0.000 | 0.011 | |
| FindCorrelatedRegions | 0.009 | 0.004 | 0.014 | |
| GetMinPairwiseCor | 0.001 | 0.004 | 0.005 | |
| GetSitesLocations | 0.078 | 0.000 | 0.078 | |
| MakeModelFormula | 0.000 | 0.001 | 0.000 | |
| MarkCoeditedSites | 0.010 | 0.002 | 0.012 | |
| OrderSitesByLocation | 0.002 | 0.000 | 0.001 | |
| PlotEditingCorrelations | 0.549 | 0.028 | 0.577 | |
| RegionSummaryMethod | 0.045 | 0.000 | 0.046 | |
| SingleCloseByRegion | 0.081 | 0.012 | 0.093 | |
| SingleCoeditedRegion | 1.020 | 0.108 | 1.127 | |
| SitesToRegion | 0.03 | 0.00 | 0.03 | |
| SummarizeAllRegions | 1.233 | 0.044 | 1.278 | |
| SummarizeSingleRegion | 0.082 | 0.004 | 0.086 | |
| TestAssociations | 1.938 | 0.084 | 2.022 | |
| TestSingleRegion | 0.036 | 0.004 | 0.040 | |
| TransformToGR | 0.057 | 0.000 | 0.056 | |