Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:42:50 -0400 (Thu, 12 Apr 2018).
Package 1013/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
pbcmc 1.6.0 Cristobal Fresno
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![]() |
Package: pbcmc |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pbcmc_1.6.0.tar.gz |
StartedAt: 2018-04-12 07:30:22 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 07:33:18 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 176.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pbcmc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pbcmc_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/pbcmc.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pbcmc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pbcmc’ version ‘1.6.0’ * 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 ‘pbcmc’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed PAM50-class 5.249 0.254 5.949 * 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
pbcmc.Rcheck/00install.out
* installing *source* package ‘pbcmc’ ... ** R ** data ** inst ** preparing package for lazy loading No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘pbcmc’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘pbcmc’ * DONE (pbcmc)
pbcmc.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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("pbcmc") Package 'mclust' version 5.4 Type 'citation("mclust")' for citing this R package in publications. 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:limma': plotMA 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, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'pbcmc' Loading required namespace: breastCancerNKI RUNIT TEST PROTOCOL -- Thu Apr 12 07:33:14 2018 *********************************************** Number of test functions: 14 Number of errors: 0 Number of failures: 0 1 Test Suite : pbcmc RUnit Tests - 14 test functions, 0 errors, 0 failures Number of test functions: 14 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 28.460 1.154 38.045
pbcmc.Rcheck/pbcmc-Ex.timings
name | user | system | elapsed | |
MolecularPermutationClassifierConstructor | 0.699 | 0.048 | 0.767 | |
MolecularPermutationClassifierGenerics | 0.479 | 0.120 | 1.539 | |
MolecularPermutationClassifierGetseters | 0.056 | 0.008 | 0.066 | |
MolecularPermutationClassifierShow | 0.051 | 0.007 | 0.058 | |
PAM50-class | 5.249 | 0.254 | 5.949 | |
PAM50Classify | 0.053 | 0.009 | 0.062 | |
PAM50Constructor | 0.441 | 0.040 | 0.489 | |
PAM50Filtrate | 0.960 | 0.095 | 1.077 | |
PAM50Permutate | 0.121 | 0.064 | 0.523 | |
PAM50SubjectReport | 3.839 | 0.144 | 4.090 | |
PAM50Subtype | 0.054 | 0.006 | 0.063 | |