Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 2198/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
uSORT 1.31.0 (landing page) Hao Chen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the uSORT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/uSORT.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: uSORT |
Version: 1.31.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:uSORT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings uSORT_1.31.0.tar.gz |
StartedAt: 2024-08-27 00:04:22 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 00:08:28 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 246.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: uSORT.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:uSORT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings uSORT_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/uSORT.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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘uSORT/DESCRIPTION’ ... OK * this is package ‘uSORT’ version ‘1.31.0’ * 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 ‘uSORT’ can be installed ... WARNING Found the following significant warnings: Note: break used in wrong context: no loop is visible See ‘/Users/biocbuild/bbs-3.20-bioc/meat/uSORT.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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 ... NOTE mcesApply1: no visible global function definition for ‘clusterEvalQ’ mcesApply1: no visible global function definition for ‘parRapply’ mcesApply1: no visible global function definition for ‘parCapply’ Undefined global functions or variables: clusterEvalQ parCapply parRapply * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed sWanderlust 26.779 4.720 31.517 autoSPIN 15.045 1.321 16.422 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/uSORT.Rcheck/00check.log’ for details.
uSORT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL uSORT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘uSORT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘BiocGenerics’ for request: ‘clusterEvalQ’ when loading ‘uSORT’ No methods found in package ‘BiocGenerics’ for request: ‘parCapply’ when loading ‘uSORT’ No methods found in package ‘BiocGenerics’ for request: ‘parRapply’ when loading ‘uSORT’ Note: break used in wrong context: no loop is visible ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘BiocGenerics’ for request: ‘clusterEvalQ’ when loading ‘uSORT’ No methods found in package ‘BiocGenerics’ for request: ‘parCapply’ when loading ‘uSORT’ No methods found in package ‘BiocGenerics’ for request: ‘parRapply’ when loading ‘uSORT’ ** testing if installed package can be loaded from final location No methods found in package ‘BiocGenerics’ for request: ‘clusterEvalQ’ when loading ‘uSORT’ No methods found in package ‘BiocGenerics’ for request: ‘parCapply’ when loading ‘uSORT’ No methods found in package ‘BiocGenerics’ for request: ‘parRapply’ when loading ‘uSORT’ ** testing if installed package keeps a record of temporary installation path * DONE (uSORT)
uSORT.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > BiocGenerics:::testPackage("uSORT") No methods found in package 'BiocGenerics' for request: 'clusterEvalQ' when loading 'uSORT' No methods found in package 'BiocGenerics' for request: 'parCapply' when loading 'uSORT' No methods found in package 'BiocGenerics' for request: 'parRapply' when loading 'uSORT' No starting point specified, the first row will be used! Building lNN graph... lNN computed in: 0 seconds Randomly Select waypoints... Flock waypoints... Iteratively realign trajectory: Running iterations... 1 Correlation with previous iteration: 0.985372 Running iterations... 2 Correlation with previous iteration: 0.99972 Running iterations... 3 Correlation with previous iteration: 0.999971 Wanderlust Sorting Done! RUNIT TEST PROTOCOL -- Tue Aug 27 00:08:19 2024 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : uSORT RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 7.264 2.298 9.550
uSORT.Rcheck/uSORT-Ex.timings
name | user | system | elapsed | |
Rwanderlust | 0.873 | 0.075 | 0.953 | |
SPIN | 0.067 | 0.004 | 0.072 | |
STS_sortingcost | 0.018 | 0.001 | 0.019 | |
autoSPIN | 15.045 | 1.321 | 16.422 | |
driving_force_gene_selection | 0.002 | 0.002 | 0.002 | |
elbow_detection | 0.003 | 0.001 | 0.004 | |
monocle_wrapper | 0.001 | 0.001 | 0.002 | |
neighborhood_sortingcost | 0.048 | 0.004 | 0.052 | |
pca_gene_selection | 3.039 | 0.154 | 3.204 | |
sWanderlust | 26.779 | 4.720 | 31.517 | |
uSORT | 0.001 | 0.001 | 0.002 | |
uSORT_GUI | 0.001 | 0.000 | 0.001 | |
uSORT_preProcess | 1.739 | 0.114 | 1.860 | |
uSORT_sorting_wrapper | 2.413 | 0.132 | 2.558 | |
uSORT_write_results | 0.001 | 0.001 | 0.002 | |