Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-03 11:38:52 -0400 (Fri, 03 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 1937/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sitePath 1.21.0 (landing page) Chengyang Ji
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.21.0 |
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_1.21.0.tar.gz |
StartedAt: 2024-05-02 11:45:52 -0400 (Thu, 02 May 2024) |
EndedAt: 2024-05-02 12:07:08 -0400 (Thu, 02 May 2024) |
EllapsedTime: 1276.0 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_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sitePath.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sitePath/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sitePath’ version ‘1.21.0’ * 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 38.069 0.338 44.786 plotParallelSites 19.878 0.170 22.788 plotSingleSite 19.490 0.345 22.185 lineagePath 7.205 0.103 8.459 plotFixationSites 4.871 0.041 5.807 allSitesName 4.726 0.056 5.351 * 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-3.20-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 Patched (2024-04-24 r86482) -- "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 644.482 9.794 965.841
sitePath.Rcheck/sitePath-Ex.timings
name | user | system | elapsed | |
SNPsites | 1.418 | 0.025 | 1.733 | |
addMSA | 3.808 | 0.045 | 4.587 | |
allSitesName | 4.726 | 0.056 | 5.351 | |
as.data.frame | 3.606 | 0.057 | 4.353 | |
extractSite | 3.601 | 0.038 | 4.275 | |
extractTips | 3.677 | 0.036 | 4.340 | |
fixationIndels | 3.707 | 0.036 | 4.509 | |
fixationPath | 3.785 | 0.061 | 4.451 | |
fixationSites | 3.490 | 0.043 | 4.110 | |
groupTips | 3.653 | 0.056 | 4.319 | |
lineagePath | 7.205 | 0.103 | 8.459 | |
paraFixSites | 3.890 | 0.040 | 4.544 | |
parallelSites | 3.754 | 0.032 | 4.367 | |
plotFixationSites | 4.871 | 0.041 | 5.807 | |
plotFunctions | 38.069 | 0.338 | 44.786 | |
plotMutSites | 2.518 | 0.027 | 2.963 | |
plotParallelSites | 19.878 | 0.170 | 22.788 | |
plotSingleSite | 19.490 | 0.345 | 22.185 | |
setSiteNumbering | 3.892 | 0.039 | 4.051 | |
similarityMatrix | 3.548 | 0.045 | 3.706 | |
sitesMinEntropy | 3.344 | 0.038 | 3.637 | |