Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:58:13 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE clipper PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 308/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
clipper 1.28.0 Paolo Martini
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
Package: clipper |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clipper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clipper_1.28.0.tar.gz |
StartedAt: 2020-10-16 23:44:08 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 23:52:28 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 500.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: clipper.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clipper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clipper_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/clipper.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clipper/DESCRIPTION’ ... OK * this is package ‘clipper’ version ‘1.28.0’ * 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 19.202 0.441 19.725 pathwayTest 9.734 0.055 9.870 clipper 8.500 0.229 8.809 cliqueMixedTest 5.658 0.090 5.779 cliquePairedTest 5.050 0.062 5.139 * 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/Versions/Current/Resources/bin/R CMD INSTALL clipper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘clipper’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’ ** testing if installed package can be loaded from final location No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’ ** testing if installed package keeps a record of temporary installation path * DONE (clipper)
clipper.Rcheck/tests/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from 'package:Matrix': which 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, 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, which.max, which.min No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph' RUNIT TEST PROTOCOL -- Fri Oct 16 23:52:18 2020 *********************************************** 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 > > pattern="^test_.*\\.R$" > > proc.time() user system elapsed 21.792 0.831 25.494
clipper.Rcheck/clipper-Ex.timings
name | user | system | elapsed | |
clipper | 8.500 | 0.229 | 8.809 | |
clipperAllRoots | 19.202 | 0.441 | 19.725 | |
cliqueMeanTest | 4.868 | 0.066 | 4.961 | |
cliqueMixedTest | 5.658 | 0.090 | 5.779 | |
cliquePairedTest | 5.050 | 0.062 | 5.139 | |
cliqueVarianceTest | 4.662 | 0.068 | 4.769 | |
deleteEdge | 1.252 | 0.021 | 1.280 | |
easyClip | 4.417 | 0.044 | 4.532 | |
getGraphEntryGenes | 1.400 | 0.025 | 1.432 | |
getJunctionTreePaths | 1.298 | 0.016 | 1.318 | |
nameCliques | 0.001 | 0.000 | 0.001 | |
pathwayTest | 9.734 | 0.055 | 9.870 | |
plotInCytoscape | 0.001 | 0.001 | 0.002 | |
prunePaths | 0.007 | 0.002 | 0.008 | |