Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:36:24 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 1978/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sitePath 1.18.0 (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 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 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: 1.18.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sitePath.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sitePath_1.18.0.tar.gz |
StartedAt: 2024-03-28 02:51:26 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 02:59:11 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 464.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sitePath.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sitePath.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sitePath_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sitePath.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘sitePath/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sitePath’ version ‘1.18.0’ * 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: extdata 1.3Mb libs 5.5Mb * 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 R 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 loading without being on the library search path ... 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 14.912 0.096 15.008 plotParallelSites 8.487 0.008 8.497 plotSingleSite 7.916 0.056 7.972 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘sitePath.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/sitePath.Rcheck/00check.log’ for details.
sitePath.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL sitePath ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘sitePath’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c lumpyCluster.cpp -o lumpyCluster.o lumpyCluster.cpp: In member function ‘void LumpyCluster::Base::mergeClusters(const clusters&, int)’: lumpyCluster.cpp:96:24: warning: comparison of integer expressions of different signedness: ‘std::vector<Treemer::TipSeqLinker*>::size_type’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 96 | if (allTips.size() >= m_maxSNPnum) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c minEntropy.cpp -o minEntropy.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c searchNode.cpp -o searchNode.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c searchTree.cpp -o searchTree.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c treemer.cpp -o treemer.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c util.cpp -o util.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o sitePath.so RcppExports.o lumpyCluster.o minEntropy.o searchNode.o searchTree.o treemer.o util.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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 260.563 1.379 339.292
sitePath.Rcheck/sitePath-Ex.timings
name | user | system | elapsed | |
SNPsites | 0.569 | 0.044 | 0.613 | |
addMSA | 1.761 | 0.013 | 1.773 | |
allSitesName | 2.182 | 0.027 | 2.210 | |
as.data.frame | 1.327 | 0.036 | 1.362 | |
extractSite | 1.366 | 0.004 | 1.370 | |
extractTips | 1.446 | 0.016 | 1.462 | |
fixationIndels | 1.583 | 0.032 | 1.615 | |
fixationPath | 1.278 | 0.008 | 1.285 | |
fixationSites | 1.265 | 0.024 | 1.289 | |
groupTips | 1.781 | 0.004 | 1.784 | |
lineagePath | 3.145 | 0.036 | 3.181 | |
paraFixSites | 1.403 | 0.004 | 1.407 | |
parallelSites | 1.395 | 0.004 | 1.400 | |
plotFixationSites | 1.870 | 0.044 | 1.914 | |
plotFunctions | 14.912 | 0.096 | 15.008 | |
plotMutSites | 1.103 | 0.000 | 1.103 | |
plotParallelSites | 8.487 | 0.008 | 8.497 | |
plotSingleSite | 7.916 | 0.056 | 7.972 | |
setSiteNumbering | 1.921 | 0.000 | 1.921 | |
similarityMatrix | 1.804 | 0.000 | 1.804 | |
sitesMinEntropy | 1.351 | 0.000 | 1.351 | |