Lanyu Zhang
| Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/rnaEditr |
| git_branch: devel |
| git_last_commit: a074827 |
| git_last_commit_date: 2024-10-29 10:51:31 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-23 11:41 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
| 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 1757/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rnaEditr 1.17.0 (landing page) Lanyu Zhang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.17.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings rnaEditr_1.17.0.tar.gz |
| StartedAt: 2024-12-23 01:36:00 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 01:40:46 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 285.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rnaEditr.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings rnaEditr_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/rnaEditr.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘rnaEditr/DESCRIPTION’ ... OK
* this is package ‘rnaEditr’ version ‘1.17.0’
* 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 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 ... WARNING
checkRd: (-1) AllCoeditedRegions.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:69-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:71-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:76-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:50-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateRdrop.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateRdrop.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindCorrelatedRegions.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindCorrelatedRegions.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GetMinPairwiseCor.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GetMinPairwiseCor.Rd:35-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GetMinPairwiseCor.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OrderSitesByLocation.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OrderSitesByLocation.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OrderSitesByLocation.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:78-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:81-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:83-86: Lost braces in \itemize; \value handles \item{}{} directly
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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.21-bioc/meat/rnaEditr.Rcheck/00check.log’
for details.
rnaEditr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL rnaEditr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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(rnaEditr)
>
> test_check("rnaEditr")
| | 0%
|================= |33.33333% ~0 s remaining
|================================== |66.66667% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|================= |33.33333% ~2 s remaining
|================================== |66.66667% ~1 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 1 s
| | 0%
|================= |33.33333% ~0 s remaining
|================================== |66.66667% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|====== |12.5% ~0 s remaining
|============= | 25% ~0 s remaining
|=================== |37.5% ~0 s remaining
|========================== | 50% ~0 s remaining
|================================ |62.5% ~0 s remaining
|======================================= | 75% ~0 s remaining
|============================================= |87.5% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 1 s
| | 0%
|=== |7.142857% ~1 s remaining
|======= |14.28571% ~1 s remaining
|=========== |21.42857% ~1 s remaining
|============== |28.57143% ~1 s remaining
|================== |35.71429% ~1 s remaining
|====================== |42.85714% ~0 s remaining
|========================== | 50% ~0 s remaining
|============================= |57.14286% ~0 s remaining
|================================= |64.28571% ~0 s remaining
|===================================== |71.42857% ~0 s remaining
|======================================== |78.57143% ~0 s remaining
|============================================ |85.71429% ~0 s remaining
|================================================ |92.85714% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 1 s
| | 0%
|=== |7.142857% ~0 s remaining
|======= |14.28571% ~0 s remaining
|=========== |21.42857% ~0 s remaining
|============== |28.57143% ~0 s remaining
|================== |35.71429% ~0 s remaining
|====================== |42.85714% ~0 s remaining
|========================== | 50% ~0 s remaining
|============================= |57.14286% ~0 s remaining
|================================= |64.28571% ~0 s remaining
|===================================== |71.42857% ~0 s remaining
|======================================== |78.57143% ~0 s remaining
|============================================ |85.71429% ~0 s remaining
|================================================ |92.85714% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|================= |33.33333% ~0 s remaining
|================================== |66.66667% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|==== |7.692308% ~1 s remaining
|======== |15.38462% ~1 s remaining
|============ |23.07692% ~1 s remaining
|================ |30.76923% ~1 s remaining
|==================== |38.46154% ~0 s remaining
|======================== |46.15385% ~0 s remaining
|============================ |53.84615% ~0 s remaining
|================================ |61.53846% ~0 s remaining
|==================================== |69.23077% ~0 s remaining
|======================================== |76.92308% ~0 s remaining
|============================================ |84.61538% ~0 s remaining
|================================================ |92.30769% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 1 s
| | 0%
|================= |33.33333% ~0 s remaining
|================================== |66.66667% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|==== |7.692308% ~1 s remaining
|======== |15.38462% ~1 s remaining
|============ |23.07692% ~0 s remaining
|================ |30.76923% ~0 s remaining
|==================== |38.46154% ~0 s remaining
|======================== |46.15385% ~0 s remaining
|============================ |53.84615% ~0 s remaining
|================================ |61.53846% ~0 s remaining
|==================================== |69.23077% ~0 s remaining
|======================================== |76.92308% ~0 s remaining
|============================================ |84.61538% ~0 s remaining
|================================================ |92.30769% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 1 s
| | 0%
|==== |7.692308% ~0 s remaining
|======== |15.38462% ~0 s remaining
|============ |23.07692% ~0 s remaining
|================ |30.76923% ~0 s remaining
|==================== |38.46154% ~0 s remaining
|======================== |46.15385% ~0 s remaining
|============================ |53.84615% ~0 s remaining
|================================ |61.53846% ~0 s remaining
|==================================== |69.23077% ~0 s remaining
|======================================== |76.92308% ~0 s remaining
|============================================ |84.61538% ~0 s remaining
|================================================ |92.30769% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
>
> proc.time()
user system elapsed
17.927 1.094 19.016
rnaEditr.Rcheck/rnaEditr-Ex.timings
| name | user | system | elapsed | |
| AddMetaData | 0.464 | 0.099 | 0.565 | |
| AllCloseByRegions | 0.362 | 0.011 | 0.372 | |
| AllCoeditedRegions | 0.498 | 0.010 | 0.508 | |
| AnnotateResults | 2.150 | 0.079 | 2.229 | |
| CountSamplesPerGroup | 0.003 | 0.000 | 0.003 | |
| CreateEditingTable | 0.034 | 0.001 | 0.036 | |
| CreateOutputDF | 0.017 | 0.002 | 0.019 | |
| CreateRdrop | 0.01 | 0.00 | 0.01 | |
| FindCorrelatedRegions | 0.011 | 0.001 | 0.012 | |
| GetMinPairwiseCor | 0.005 | 0.000 | 0.005 | |
| GetSitesLocations | 0.076 | 0.001 | 0.077 | |
| MakeModelFormula | 0.000 | 0.001 | 0.000 | |
| MarkCoeditedSites | 0.010 | 0.002 | 0.012 | |
| OrderSitesByLocation | 0.001 | 0.001 | 0.002 | |
| PlotEditingCorrelations | 0.537 | 0.023 | 0.560 | |
| RegionSummaryMethod | 0.044 | 0.001 | 0.045 | |
| SingleCloseByRegion | 0.088 | 0.000 | 0.088 | |
| SingleCoeditedRegion | 0.153 | 0.006 | 0.159 | |
| SitesToRegion | 0.028 | 0.001 | 0.029 | |
| SummarizeAllRegions | 1.301 | 0.023 | 1.324 | |
| SummarizeSingleRegion | 0.087 | 0.001 | 0.087 | |
| TestAssociations | 1.387 | 0.016 | 1.403 | |
| TestSingleRegion | 0.039 | 0.002 | 0.041 | |
| TransformToGR | 0.06 | 0.00 | 0.06 | |