Marzia A Cremona
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/IWTomics |
| git_branch: devel |
| git_last_commit: 87c60ab |
| git_last_commit_date: 2024-10-29 10:15:51 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:39 -0500 (Mon, 25 Nov 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" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 1067/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IWTomics 1.31.0 (landing page) Marzia A Cremona
| 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 | | ||||||||
|
To the developers/maintainers of the IWTomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IWTomics.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: IWTomics |
| Version: 1.31.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IWTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IWTomics_1.31.0.tar.gz |
| StartedAt: 2024-11-24 23:08:42 -0500 (Sun, 24 Nov 2024) |
| EndedAt: 2024-11-24 23:15:01 -0500 (Sun, 24 Nov 2024) |
| EllapsedTime: 379.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: IWTomics.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IWTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IWTomics_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/IWTomics.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IWTomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IWTomics’ version ‘1.31.0’
* 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 ‘IWTomics’ 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
0.99.0 First submission
Cannot process chunk/lines:
0.99.11 Revised package
Cannot process chunk/lines:
0.99.12 Fixed bug in plotTest and plotSummary
Cannot process chunk/lines:
1.1.1 Fixed bug in IWTomicsTest statistics=variance
Cannot process chunk/lines:
1.1.2 Fixed alpha
Cannot process chunk/lines:
1.1.3 Fixed bug in IWTomicsData constructor
Cannot process chunk/lines:
1.3.3 Citation added
* 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 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) IWTomicsData-class.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:75-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:97-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:103-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:108-109: Lost braces in \itemize; meant \describe ?
checkRd: (5) IWTomicsData-class.Rd:122-126: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:127-170: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:177-179: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:180-182: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:183-186: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:187-189: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:190-193: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:194-196: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:197-200: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:201-204: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:205-208: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:209-211: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:212-214: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:215-217: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:218-220: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:221-223: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:224-226: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:227-229: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:230-234: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:235-237: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:238-248: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:256-261: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:269-274: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:275-280: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:281-286: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:292-299: \item in \describe must have non-empty label
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
IWTomicsTest 38.053 1.558 39.687
IWTomics-package 7.078 1.203 8.329
IWTomicsData-class 7.316 0.049 7.377
plotSummary 3.928 1.067 5.038
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/IWTomics.Rcheck/00check.log’
for details.
IWTomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IWTomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘IWTomics’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘smooth’ in package ‘IWTomics’ ** 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 (IWTomics)
IWTomics.Rcheck/IWTomics-Ex.timings
| name | user | system | elapsed | |
| ETn_example | 0.117 | 0.009 | 0.126 | |
| IWTomics-package | 7.078 | 1.203 | 8.329 | |
| IWTomicsData-class | 7.316 | 0.049 | 7.377 | |
| IWTomicsTest | 38.053 | 1.558 | 39.687 | |
| features_example | 0.001 | 0.001 | 0.003 | |
| plot-IWTomicsData | 0.301 | 0.019 | 0.323 | |
| plotSummary | 3.928 | 1.067 | 5.038 | |
| plotTest | 2.607 | 0.628 | 3.322 | |
| regionsFeatures_center | 0.008 | 0.001 | 0.009 | |
| regionsFeatures_scale | 0.008 | 0.001 | 0.009 | |
| regions_example | 0.001 | 0.001 | 0.002 | |
| smooth-IWTomicsData | 0.917 | 0.067 | 0.989 | |