Back to Build/check report for BioC 3.20 experimental data |
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This page was generated on 2024-12-19 15:42 -0500 (Thu, 19 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4743 |
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 106/431 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
DuoClustering2018 1.24.0 (landing page) Angelo Duò
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||
To the developers/maintainers of the DuoClustering2018 package: - 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: DuoClustering2018 |
Version: 1.24.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DuoClustering2018_1.24.0.tar.gz |
StartedAt: 2024-12-19 12:20:50 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 12:28:27 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 456.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DuoClustering2018.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DuoClustering2018_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/DuoClustering2018.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘DuoClustering2018/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DuoClustering2018’ version ‘1.24.0’ * package encoding: UTF-8 * 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 ‘DuoClustering2018’ 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 whether startup messages can be suppressed ... 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 ... NOTE ari_df: no visible binding for global variable ‘cell’ plot_entropy: no visible binding for global variable ‘dataset’ plot_entropy: no visible binding for global variable ‘method’ plot_entropy: no visible binding for global variable ‘run’ plot_entropy: no visible binding for global variable ‘k’ plot_entropy: no visible binding for global variable ‘cluster’ plot_entropy: no visible binding for global variable ‘trueclass’ plot_entropy: no visible binding for global variable ‘s’ plot_entropy: no visible binding for global variable ‘s.true’ plot_entropy: no visible binding for global variable ‘est_k’ plot_entropy: no visible binding for global variable ‘sce’ plot_entropy: no visible binding for global variable ‘filtering’ plot_entropy: no visible binding for global variable ‘truenclust’ plot_entropy: no visible binding for global variable ‘entropy’ plot_entropy: no visible binding for global variable ‘ARI’ plot_entropy: no visible binding for global variable ‘s.norm’ plot_entropy: no visible binding for global variable ‘s.true.norm’ plot_entropy: no visible binding for global variable ‘ds’ plot_entropy: no visible binding for global variable ‘ds.norm’ plot_k_diff: no visible binding for global variable ‘dataset’ plot_k_diff: no visible binding for global variable ‘method’ plot_k_diff: no visible binding for global variable ‘run’ plot_k_diff: no visible binding for global variable ‘k’ plot_k_diff: no visible binding for global variable ‘cluster’ plot_k_diff: no visible binding for global variable ‘trueclass’ plot_k_diff: no visible binding for global variable ‘est_k’ plot_k_diff: no visible binding for global variable ‘elapsed’ plot_k_diff: no visible binding for global variable ‘sce’ plot_k_diff: no visible binding for global variable ‘filtering’ plot_k_diff: no visible binding for global variable ‘truenclust’ plot_k_diff: no visible binding for global variable ‘ARI’ plot_k_diff: no visible binding for global variable ‘medARI’ plot_k_diff: no visible binding for global variable ‘k_diff’ plot_k_diff: no visible binding for global variable ‘estnclust’ plot_performance: no visible binding for global variable ‘dataset’ plot_performance: no visible binding for global variable ‘method’ plot_performance: no visible binding for global variable ‘run’ plot_performance: no visible binding for global variable ‘k’ plot_performance: no visible binding for global variable ‘cluster’ plot_performance: no visible binding for global variable ‘trueclass’ plot_performance: no visible binding for global variable ‘est_k’ plot_performance: no visible binding for global variable ‘elapsed’ plot_performance: no visible binding for global variable ‘sce’ plot_performance: no visible binding for global variable ‘filtering’ plot_performance: no visible binding for global variable ‘ARI’ plot_performance: no visible binding for global variable ‘truenclust’ plot_performance: no visible binding for global variable ‘medianARI’ plot_performance: no visible binding for global variable ‘estnclust’ plot_stability: no visible binding for global variable ‘dataset’ plot_stability: no visible binding for global variable ‘method’ plot_stability: no visible binding for global variable ‘k’ plot_stability: no visible binding for global variable ‘data.wide’ plot_stability: no visible binding for global variable ‘stability’ plot_stability: no visible binding for global variable ‘truenclust’ plot_stability: no visible binding for global variable ‘sce’ plot_stability: no visible binding for global variable ‘filtering’ plot_stability: no visible binding for global variable ‘ari.stab’ plot_stability: no visible binding for global variable ‘median.stability’ plot_timing: no visible binding for global variable ‘dataset’ plot_timing: no visible binding for global variable ‘method’ plot_timing: no visible binding for global variable ‘run’ plot_timing: no visible binding for global variable ‘k’ plot_timing: no visible binding for global variable ‘cluster’ plot_timing: no visible binding for global variable ‘trueclass’ plot_timing: no visible binding for global variable ‘est_k’ plot_timing: no visible binding for global variable ‘elapsed’ plot_timing: no visible binding for global variable ‘sce’ plot_timing: no visible binding for global variable ‘filtering’ plot_timing: no visible binding for global variable ‘truenclust’ plot_timing: no visible binding for global variable ‘median.elapsed’ plot_timing: no visible binding for global variable ‘med.t’ plot_timing: no visible binding for global variable ‘norm.time’ plot_timing: no visible binding for global variable ‘medianelapsed’ Undefined global functions or variables: ARI ari.stab cell cluster data.wide dataset ds ds.norm elapsed entropy est_k estnclust filtering k k_diff med.t medARI median.elapsed median.stability medianARI medianelapsed method norm.time run s s.norm s.true s.true.norm sce stability trueclass truenclust * checking Rd files ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... 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 NOTE See ‘/home/biocbuild/bbs-3.20-data-experiment/meat/DuoClustering2018.Rcheck/00check.log’ for details.
DuoClustering2018.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DuoClustering2018 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘DuoClustering2018’ ... ** using staged installation ** R ** 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 (DuoClustering2018)
DuoClustering2018.Rcheck/DuoClustering2018-Ex.timings
name | user | system | elapsed | |
clustering_summary_v1 | 2.933 | 0.223 | 3.445 | |
clustering_summary_v2 | 2.070 | 0.209 | 2.355 | |
duo_clustering_all_parameter_settings_v1 | 0.723 | 0.035 | 0.831 | |
duo_clustering_all_parameter_settings_v2 | 0.747 | 0.099 | 0.919 | |
plot_entropy | 3.019 | 0.115 | 3.207 | |
plot_k_diff | 2.163 | 0.046 | 2.284 | |
plot_performance | 1.923 | 0.070 | 2.069 | |
plot_stability | 3.179 | 0.072 | 3.325 | |
plot_timing | 2.175 | 0.087 | 2.335 | |
sce_full_Koh | 4.720 | 0.141 | 4.936 | |
sce_full_Kumar | 1.824 | 0.076 | 1.979 | |
sce_full_SimKumar | 2.387 | 0.118 | 2.580 | |
sce_full_Trapnell | 1.086 | 0.054 | 1.214 | |
sce_full_Zhengmix | 1.966 | 0.098 | 2.144 | |