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 363/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clstutils 1.55.0 (landing page) Noah Hoffman
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the clstutils package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clstutils.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: clstutils |
Version: 1.55.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:clstutils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings clstutils_1.55.0.tar.gz |
StartedAt: 2024-12-24 05:25:04 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 05:26:06 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 62.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: clstutils.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:clstutils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings clstutils_1.55.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/clstutils.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clstutils/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘clstutils’ version ‘1.55.0’ * 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 ‘clstutils’ can be installed ... OK * checking installed package size ... OK * 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 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘rjson’ which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: ‘ape’ ‘rjson’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call("seq_root2tip", ..., PACKAGE = "ape") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE edgeMap: no visible global function definition for ‘fromJSON’ prettyTree: no visible binding for global variable ‘.PlotPhyloEnv’ refpkgContents: no visible global function definition for ‘fromJSON’ Undefined global functions or variables: .PlotPhyloEnv fromJSON * 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: clstutils-package.Rd: clst 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: tests/unit/Makefile Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runalltests.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 ‘/home/biocbuild/bbs-3.21-bioc/meat/clstutils.Rcheck/00check.log’ for details.
clstutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL clstutils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘clstutils’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (clstutils)
clstutils.Rcheck/tests/runalltests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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("RUnit") > > options(warn=1) > > dirs <- 'unit' > > testFilePat <- ".*_test\\.R$" > > allSuite <- defineTestSuite(name="allSuite", + dirs=dirs, + testFileRegexp=testFilePat, + rngKind="default", + rngNormalKind="default" + ) > > testData <- runTestSuite(allSuite) Loading required package: clst Loading required package: rjson Loading required package: ape Executing test function test_seqdata ... done successfully. Executing test function test_seqs ... done successfully. Executing test function test_classifyPlacements01 ... tax_id tax_name rank below above score match min median max d 1 33958 Lactobacillaceae family 106 12 0.89 1 0.03 0.73 1.12 0.9 at 1 860 done successfully. Executing test function test_distfile ... done successfully. Executing test function test_edgeMap01 ... done successfully. Executing test function test_placeMat01 ... done successfully. Executing test function test_placeMat02 ... done successfully. Executing test function test_placefile ... done successfully. Executing test function test_treeDists01 ... done successfully. Executing test function test_findOutliers01 ... done successfully. Executing test function test_findOutliers02 ... done successfully. Executing test function test_maxDists01 ... done successfully. Executing test function test_maxDists02 ... done successfully. Executing test function test_maxDists03 ... done successfully. Executing test function test_refpkgContents ... done successfully. Executing test function test_taxonomyFromRefpkg01 ... done successfully. > > printTextProtocol(testData, showDetails=TRUE) RUNIT TEST PROTOCOL -- Tue Dec 24 05:26:02 2024 *********************************************** Number of test functions: 16 Number of errors: 0 Number of failures: 0 1 Test Suite : allSuite - 16 test functions, 0 errors, 0 failures Details *************************** Test Suite: allSuite Test function regexp: ^test.+ Test file regexp: .*_test\.R$ Involved directory: unit --------------------------- Test file: unit/data_test.R test_seqdata: (3 checks) ... OK (0.01 seconds) test_seqs: (1 checks) ... OK (0 seconds) --------------------------- Test file: unit/placeTools_test.R test_classifyPlacements01: (0 checks) ... OK (5.67 seconds) test_distfile: (1 checks) ... OK (0 seconds) test_edgeMap01: (2 checks) ... OK (0.57 seconds) test_placeMat01: (2 checks) ... OK (2.41 seconds) test_placeMat02: (3 checks) ... OK (3.51 seconds) test_placefile: (1 checks) ... OK (0 seconds) test_treeDists01: (2 checks) ... OK (3.12 seconds) --------------------------- Test file: unit/taxTools_test.R test_findOutliers01: (1 checks) ... OK (0.04 seconds) test_findOutliers02: (3 checks) ... OK (0.05 seconds) test_maxDists01: (2 checks) ... OK (0.03 seconds) test_maxDists02: (2 checks) ... OK (0.04 seconds) test_maxDists03: (3 checks) ... OK (0.04 seconds) test_refpkgContents: (2 checks) ... OK (0 seconds) test_taxonomyFromRefpkg01: (24 checks) ... OK (0.01 seconds) > > #q(runLast=FALSE) > > proc.time() user system elapsed 19.004 0.389 19.405
clstutils.Rcheck/clstutils-Ex.timings
name | user | system | elapsed | |
classifyPlacements | 4.821 | 0.097 | 4.932 | |
clstutils-package | 0.01 | 0.00 | 0.01 | |
findOutliers | 0.033 | 0.008 | 0.041 | |
maxDists | 0.341 | 0.008 | 0.350 | |
prettyTree | 0.117 | 0.000 | 0.118 | |
refpkgContents | 0.011 | 0.013 | 0.019 | |
seqdat | 0.002 | 0.000 | 0.002 | |
seqs | 0.005 | 0.000 | 0.005 | |
taxonomyFromRefpkg | 0.035 | 0.013 | 0.043 | |
treeDists | 3.517 | 0.040 | 3.564 | |