Niloofar AghaieAbiane
| Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/SGCP |
| git_branch: RELEASE_3_19 |
| git_last_commit: 4b5e64b |
| git_last_commit_date: 2024-07-19 18:20:56 -0400 (Fri, 19 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:06 -0400 (Wed, 24 Jul 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" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| 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 1956/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SGCP 1.4.1 (landing page) Niloofar AghaieAbiane
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the SGCP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SGCP.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: SGCP |
| Version: 1.4.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SGCP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SGCP_1.4.1.tar.gz |
| StartedAt: 2024-07-22 12:35:31 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 12:46:58 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 686.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SGCP.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SGCP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SGCP_1.4.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SGCP.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SGCP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SGCP’ version ‘1.4.1’
* 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 ‘SGCP’ can be installed ... WARNING
Found the following significant warnings:
Warning: object ‘cheng’ is created by more than one data call
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/SGCP.Rcheck/00install.out’ for details.
* 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 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) SGCP_clustering.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_clustering.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_ezSGCP.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SGCP_semiSupervised.Rd:24: Lost braces
24 | \\item{semiSupervised}{An object of the caret train class representing the semi-supervised classification model.}
| ^
checkRd: (-1) SGCP_semiSupervised.Rd:24: Lost braces
24 | \\item{semiSupervised}{An object of the caret train class representing the semi-supervised classification model.}
| ^
checkRd: (-1) resFinalGO.Rd:11: Lost braces
11 | \details{code{resFinalGO} is a list containing the following information:
| ^
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SGCP_semiSupervised 5.653 0.103 6.937
* 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-3.19-bioc/meat/SGCP.Rcheck/00check.log’
for details.
SGCP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SGCP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘SGCP’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB Warning: object ‘cheng’ is created by more than one data call ** 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 (SGCP)
SGCP.Rcheck/SGCP-Ex.timings
| name | user | system | elapsed | |
| SGCP_adjacencyMatrix | 0.227 | 0.041 | 0.331 | |
| SGCP_clustering | 0.381 | 0.026 | 0.500 | |
| SGCP_ezPLOT | 0.327 | 0.028 | 0.417 | |
| SGCP_ezSGCP | 0.421 | 0.030 | 0.529 | |
| SGCP_go | 0.209 | 0.016 | 0.272 | |
| SGCP_plot_bar | 0.655 | 0.018 | 0.808 | |
| SGCP_plot_conductance | 1.024 | 0.039 | 1.281 | |
| SGCP_plot_density | 0.565 | 0.023 | 0.723 | |
| SGCP_plot_heatMap | 0.866 | 0.022 | 1.086 | |
| SGCP_plot_jitter | 0.385 | 0.009 | 0.473 | |
| SGCP_plot_pca | 0.282 | 0.020 | 0.362 | |
| SGCP_plot_pie | 0.973 | 0.030 | 1.233 | |
| SGCP_plot_silhouette | 1.490 | 0.037 | 1.844 | |
| SGCP_semiLabeling | 0.086 | 0.020 | 0.127 | |
| SGCP_semiSupervised | 5.653 | 0.103 | 6.937 | |
| cheng | 0.330 | 0.024 | 0.412 | |
| resClus | 1.390 | 0.398 | 2.121 | |
| resFinalGO | 0.021 | 0.012 | 0.043 | |
| resInitialGO | 0.021 | 0.012 | 0.040 | |
| resSemiLabel | 0.006 | 0.003 | 0.010 | |
| resSemiSupervised | 0.027 | 0.004 | 0.041 | |
| sgcp | 0.096 | 0.020 | 0.144 | |