Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:35 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 487/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cytoKernel 1.8.0 (landing page) Tusharkanti Ghosh
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the cytoKernel package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cytoKernel.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. |
Package: cytoKernel |
Version: 1.8.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:cytoKernel.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings cytoKernel_1.8.0.tar.gz |
StartedAt: 2023-11-02 09:44:46 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 09:49:52 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 306.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cytoKernel.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:cytoKernel.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings cytoKernel_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/cytoKernel.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 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 ‘cytoKernel/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cytoKernel’ version ‘1.8.0’ * 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 ‘cytoKernel’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * 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 R 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotCytoK 7.050 5.262 8.283 CytoK 5.816 2.295 4.948 CytoKProc 2.527 3.955 4.330 CytoKDEData 2.672 2.567 4.449 CytoK-class 2.600 2.519 3.561 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/cytoKernel.Rcheck/00check.log’ for details.
cytoKernel.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL cytoKernel ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘cytoKernel’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cytoKernelUtility.cpp -o cytoKernelUtility.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o cytoKernel.so RcppExports.o cytoKernelUtility.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-cytoKernel/00new/cytoKernel/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cytoKernel)
cytoKernel.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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(cytoKernel) > > test_check("cytoKernel") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ] > > proc.time() user system elapsed 15.887 2.777 16.089
cytoKernel.Rcheck/cytoKernel-Ex.timings
name | user | system | elapsed | |
CytoK-class | 2.600 | 2.519 | 3.561 | |
CytoK | 5.816 | 2.295 | 4.948 | |
CytoKDEData | 2.672 | 2.567 | 4.449 | |
CytoKDEfeatures | 2.391 | 2.201 | 4.796 | |
CytoKData | 2.528 | 1.710 | 3.184 | |
CytoKFeatureVars | 2.628 | 1.495 | 2.587 | |
CytoKFeatures | 2.509 | 1.387 | 2.438 | |
CytoKFeaturesOrdered | 2.490 | 1.114 | 2.313 | |
CytoKProc | 2.527 | 3.955 | 4.330 | |
CytoKalpha | 2.502 | 1.208 | 2.327 | |
cytoHDBMW | 0.031 | 0.031 | 0.005 | |
plotCytoK | 7.050 | 5.262 | 8.283 | |