Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1967/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sitePath 1.23.0 (landing page) Chengyang Ji
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2024-12-23 21:28:26 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 21:31:31 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 185.3 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/sitePath.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sitePath/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sitePath’ version ‘1.23.0’ * 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 15.0.0 (clang-1500.1.0.2.5)’ * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: addMSA.Rd: seqinr, phylo, ape, ggtree, multi2di, is.binary lineagePath.Rd: seqinr paraFixSites.Rd: seqinr plotFunctions.Rd: ggplot2, ggtree plotSingleSite.Rd: ggtree Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 5.288 0.074 5.368 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/Resources/library’ * installing *source* package ‘sitePath’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c lumpyCluster.cpp -o lumpyCluster.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c minEntropy.cpp -o minEntropy.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c searchNode.cpp -o searchNode.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c searchTree.cpp -o searchTree.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c treemer.cpp -o treemer.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c util.cpp -o util.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 102.591 2.633 137.715
sitePath.Rcheck/sitePath-Ex.timings
name | user | system | elapsed | |
SNPsites | 0.279 | 0.002 | 0.280 | |
addMSA | 0.995 | 0.009 | 1.005 | |
allSitesName | 1.107 | 0.009 | 1.116 | |
as.data.frame | 0.563 | 0.009 | 0.572 | |
extractSite | 0.553 | 0.007 | 0.563 | |
extractTips | 0.573 | 0.005 | 0.580 | |
fixationIndels | 0.608 | 0.005 | 0.612 | |
fixationPath | 0.630 | 0.005 | 0.636 | |
fixationSites | 0.531 | 0.005 | 0.536 | |
groupTips | 0.923 | 0.007 | 0.931 | |
lineagePath | 1.445 | 0.015 | 1.461 | |
paraFixSites | 0.533 | 0.006 | 0.540 | |
parallelSites | 0.512 | 0.005 | 0.518 | |
plotFixationSites | 0.688 | 0.011 | 0.704 | |
plotFunctions | 5.288 | 0.074 | 5.368 | |
plotMutSites | 0.438 | 0.003 | 0.441 | |
plotParallelSites | 3.121 | 0.035 | 3.163 | |
plotSingleSite | 3.497 | 0.034 | 3.544 | |
setSiteNumbering | 0.994 | 0.006 | 1.000 | |
similarityMatrix | 0.910 | 0.006 | 0.916 | |
sitesMinEntropy | 0.495 | 0.007 | 0.502 | |