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 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (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 2256/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
vsclust 1.8.0 (landing page) Veit Schwaemmle
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the vsclust package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vsclust.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: vsclust |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vsclust.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vsclust_1.8.0.tar.gz |
StartedAt: 2024-11-20 03:50:29 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 03:58:18 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 469.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: vsclust.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vsclust.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vsclust_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/vsclust.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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘vsclust/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘vsclust’ version ‘1.8.0’ * 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 ‘vsclust’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 runFuncEnrich: no visible global function definition for ‘compareCluster’ runFuncEnrich: no visible global function definition for ‘new’ Undefined global functions or variables: compareCluster new Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: vsclust-package.Rd:29-31: Dropping empty section \seealso prepare_Rd: vsclust-package.Rd:32-33: Dropping empty section \examples * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'estimClustNum.Rd': estimClustNum Code: function(dat, maxClust = 25, scaling = "standardize", cores = 1) Docs: function(dat, maxClust = 25, cores = 1) Argument names in code not in docs: scaling Mismatches in argument names: Position: 3 Code: scaling Docs: cores Codoc mismatches from Rd file 'runClustWrapper.Rd': runClustWrapper Code: function(dat, NClust, proteins = NULL, VSClust = TRUE, scaling = "standardize", cores, verbose = FALSE) Docs: function(dat, NClust, proteins = NULL, VSClust = TRUE, cores, verbose = FALSE) Argument names in code not in docs: scaling Mismatches in argument names: Position: 5 Code: scaling Docs: cores Position: 6 Code: cores Docs: verbose * 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 calcBHI 4.083 0.453 13.156 optimalClustNum 0.085 0.026 11.882 estimClust.plot 0.076 0.020 11.648 estimClustNum 0.045 0.012 9.219 runClustWrapper 0.028 0.007 6.720 ClustComp 0.011 0.006 6.388 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/vsclust.Rcheck/00check.log’ for details.
vsclust.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL vsclust ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘vsclust’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vsclust_algo.cpp -o vsclust_algo.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o vsclust.so RcppExports.o vsclust_algo.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-vsclust/00new/vsclust/libs ** R ** data ** 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 ** 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 (vsclust)
vsclust.Rcheck/tests/testthat.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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(vsclust) > > test_check("vsclust") Running cluster number 3 Running cluster number 4 Running cluster number 5 Running cluster number 6 Running cluster number 7 Running cluster number 8 Running cluster number 9 Running cluster number 10 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ] Warning message: In for (i in seq_len(n)) { : closing unused connection 5 (<-localhost:11099) > > proc.time() user system elapsed 6.977 0.458 43.592
vsclust.Rcheck/vsclust-Ex.timings
name | user | system | elapsed | |
ClustComp | 0.011 | 0.006 | 6.388 | |
PrepareForVSClust | 0.124 | 0.002 | 0.126 | |
PrepareSEForVSClust | 0.590 | 0.009 | 0.601 | |
SignAnalysis | 0.013 | 0.001 | 0.014 | |
SignAnalysisPaired | 0.011 | 0.000 | 0.012 | |
SwitchOrder | 0.009 | 0.000 | 0.009 | |
averageCond | 0.001 | 0.000 | 0.001 | |
calcBHI | 4.083 | 0.453 | 13.156 | |
cvalidate.xiebeni | 0.008 | 0.000 | 0.009 | |
determine_fuzz | 0.006 | 0.000 | 0.006 | |
estimClust.plot | 0.076 | 0.020 | 11.648 | |
estimClustNum | 0.045 | 0.012 | 9.219 | |
mfuzz.plot | 0.039 | 0.001 | 0.040 | |
optimalClustNum | 0.085 | 0.026 | 11.882 | |
pcaWithVar | 0.008 | 0.001 | 0.010 | |
runClustWrapper | 0.028 | 0.007 | 6.720 | |
runVSClustApp | 0 | 0 | 0 | |
vsclust_algorithm | 0.009 | 0.000 | 0.009 | |