Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-03-28 11:32:18 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
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 360/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clipper 1.42.0 (landing page) Paolo Martini
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the clipper package: - 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: clipper |
Version: 1.42.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clipper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clipper_1.42.0.tar.gz |
StartedAt: 2024-03-27 08:55:23 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 09:02:13 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 409.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: clipper.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clipper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clipper_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/clipper.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * 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 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clipper/DESCRIPTION’ ... OK * this is package ‘clipper’ version ‘1.42.0’ * 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 ‘clipper’ 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 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 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 ... OK * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed clipperAllRoots 11.000 0.394 12.028 pathwayTest 7.208 2.428 9.993 clipper 7.408 0.148 7.956 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
clipper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL clipper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘clipper’ ... ** using staged installation ** R ** 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 (clipper)
clipper.Rcheck/tests/runTests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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. > BiocGenerics:::testPackage("clipper") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'gRbase' The following objects are masked from 'package:graph': addEdge, adj, connComp, edges, nodes, removeEdge, subGraph RUNIT TEST PROTOCOL -- Wed Mar 27 09:02:02 2024 *********************************************** Number of test functions: 10 Number of errors: 0 Number of failures: 0 1 Test Suite : clipper RUnit Tests - 10 test functions, 0 errors, 0 failures Number of test functions: 10 Number of errors: 0 Number of failures: 0 Warning message: In (function (edges, n = max(edges), directed = TRUE) : At vendor/cigraph/src/cliques/maximal_cliques_template.h:220 : Edge directions are ignored for maximal clique calculation. > > pattern="^test_.*\\.R$" > > proc.time() user system elapsed 17.594 0.618 18.894
clipper.Rcheck/clipper-Ex.timings
name | user | system | elapsed | |
clipper | 7.408 | 0.148 | 7.956 | |
clipperAllRoots | 11.000 | 0.394 | 12.028 | |
cliqueMeanTest | 3.899 | 0.075 | 4.104 | |
cliqueMixedTest | 4.058 | 0.072 | 4.280 | |
cliquePairedTest | 4.067 | 0.064 | 4.251 | |
cliqueVarianceTest | 4.004 | 0.069 | 4.231 | |
deleteEdge | 1.338 | 0.011 | 1.401 | |
easyClip | 4.352 | 0.133 | 4.649 | |
getGraphEntryGenes | 1.378 | 0.013 | 1.474 | |
getJunctionTreePaths | 2.681 | 0.022 | 2.737 | |
nameCliques | 0.001 | 0.000 | 0.001 | |
pathwayTest | 7.208 | 2.428 | 9.993 | |
plotInCytoscape | 0.000 | 0.000 | 0.001 | |
prunePaths | 0.005 | 0.001 | 0.005 | |