Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1942/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SGCP 1.6.0  (landing page)
Niloofar AghaieAbiane
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/SGCP
git_branch: RELEASE_3_20
git_last_commit: e164401
git_last_commit_date: 2024-10-29 11:16:51 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for SGCP on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: SGCP
Version: 1.6.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SGCP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SGCP_1.6.0.tar.gz
StartedAt: 2024-11-20 12:26:00 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 12:32:16 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 375.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SGCP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SGCP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SGCP_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SGCP.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SGCP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SGCP’ version ‘1.6.0’
* 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 ‘SGCP’ 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) 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
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/SGCP.Rcheck/00check.log’
for details.


Installation output

SGCP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SGCP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘SGCP’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB


** 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)

Tests output


Example timings

SGCP.Rcheck/SGCP-Ex.timings

nameusersystemelapsed
SGCP_adjacencyMatrix1.3530.0281.367
SGCP_clustering0.2680.0000.240
SGCP_ezPLOT0.2020.0080.210
SGCP_ezSGCP0.2250.0080.235
SGCP_go0.1330.0040.137
SGCP_plot_bar0.3930.0160.410
SGCP_plot_conductance0.5190.0080.529
SGCP_plot_density0.2810.0320.314
SGCP_plot_heatMap0.4950.0680.546
SGCP_plot_jitter0.2030.0320.236
SGCP_plot_pca0.1840.0110.196
SGCP_plot_pie0.5010.0280.530
SGCP_plot_silhouette0.70.00.7
SGCP_semiLabeling0.0460.0040.050
SGCP_semiSupervised2.7360.0482.789
cheng0.2140.0000.215
resClus0.6910.0360.728
resFinalGO0.0110.0000.011
resInitialGO0.0110.0000.011
resSemiLabel0.0040.0000.004
resSemiSupervised0.1430.0120.156
sgcp0.0660.0000.066