Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
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 1998/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sitePath 1.20.0 (landing page) Chengyang Ji
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the sitePath package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sitePath.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: sitePath |
Version: 1.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sitePath.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sitePath_1.20.0.tar.gz |
StartedAt: 2024-06-09 23:08:21 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 23:17:27 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 546.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sitePath.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sitePath.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sitePath_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sitePath.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘sitePath/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sitePath’ version ‘1.20.0’ * 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 ‘sitePath’ 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 ... NOTE License stub is invalid DCF. * 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 .createSNPplot: no visible binding for global variable ‘Pos’ .createSNPplot: no visible binding for global variable ‘Accession’ .createSNPplot: no visible binding for global variable ‘SNP’ plot.fixationPath: no visible binding for global variable ‘branch’ plot.fixationPath: no visible binding for global variable ‘SNPs’ plot.fixationSites: no visible binding for global variable ‘group’ plot.fixationSites: no visible binding for global variable ‘branch’ plot.fixationSites: no visible binding for global variable ‘SNPs’ plot.parallelSites: no visible binding for global variable ‘branch’ plot.parallelSites: no visible binding for global variable ‘SNPs’ plot.sitePath: no visible binding for global variable ‘branch’ plot.sitePath: no visible binding for global variable ‘SNPs’ plotMutSites.lineagePath: no visible binding for global variable ‘node’ plotMutSites.paraFixSites: no visible binding for global variable ‘group’ plotMutSites.paraFixSites: no visible binding for global variable ‘branch’ plotMutSites.paraFixSites: no visible binding for global variable ‘SNPs’ plotSingleSite.parallelSites: no visible binding for global variable ‘branch’ plotSingleSite.parallelSites: no visible binding for global variable ‘SNPs’ Undefined global functions or variables: Accession Pos SNP SNPs branch group node * 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 plotFunctions 14.855 0.169 15.049 plotSingleSite 9.157 0.071 9.248 plotParallelSites 8.089 0.080 8.184 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/sitePath.Rcheck/00check.log’ for details.
sitePath.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sitePath ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘sitePath’ ... ** 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 lumpyCluster.cpp -o lumpyCluster.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 minEntropy.cpp -o minEntropy.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 searchNode.cpp -o searchNode.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 searchTree.cpp -o searchTree.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 treemer.cpp -o treemer.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 util.cpp -o util.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 sitePath.so RcppExports.o lumpyCluster.o minEntropy.o searchNode.o searchTree.o treemer.o util.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-sitePath/00new/sitePath/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 (sitePath)
sitePath.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" 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. > library(testthat) > library(sitePath) > > test_check("sitePath") Using 2 cores.. Multiprocessing ended. Using 2 cores.. Multiprocessing ended. [ FAIL 0 | WARN 1 | SKIP 0 | PASS 2312 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 2312 ] > > proc.time() user system elapsed 304.912 6.137 414.487
sitePath.Rcheck/sitePath-Ex.timings
name | user | system | elapsed | |
SNPsites | 0.753 | 0.011 | 0.764 | |
addMSA | 2.214 | 0.024 | 2.245 | |
allSitesName | 2.569 | 0.025 | 2.599 | |
as.data.frame | 1.502 | 0.024 | 1.528 | |
extractSite | 1.403 | 0.017 | 1.423 | |
extractTips | 1.660 | 0.016 | 1.680 | |
fixationIndels | 1.632 | 0.017 | 1.651 | |
fixationPath | 1.460 | 0.012 | 1.475 | |
fixationSites | 1.391 | 0.013 | 1.406 | |
groupTips | 2.079 | 0.017 | 2.100 | |
lineagePath | 3.505 | 0.054 | 3.563 | |
paraFixSites | 1.297 | 0.016 | 1.315 | |
parallelSites | 1.296 | 0.020 | 1.318 | |
plotFixationSites | 1.695 | 0.021 | 1.718 | |
plotFunctions | 14.855 | 0.169 | 15.049 | |
plotMutSites | 1.295 | 0.013 | 1.312 | |
plotParallelSites | 8.089 | 0.080 | 8.184 | |
plotSingleSite | 9.157 | 0.071 | 9.248 | |
setSiteNumbering | 2.323 | 0.010 | 2.336 | |
similarityMatrix | 1.813 | 0.007 | 1.821 | |
sitesMinEntropy | 1.585 | 0.015 | 1.602 | |