Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:44:36 -0400 (Tue, 09 Apr 2019).
Package 787/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
IHW 1.11.1 Nikos Ignatiadis
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: IHW |
Version: 1.11.1 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IHW.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IHW_1.11.1.tar.gz |
StartedAt: 2019-04-09 01:20:34 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 01:21:29 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 55.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IHW.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IHW.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IHW_1.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IHW.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘IHW/DESCRIPTION’ ... OK * this is package ‘IHW’ version ‘1.11.1’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘IHW’ 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 ... NOTE filter_pvals_for_optim: no visible global function definition for ‘p.adjust’ groups_by_filter: no visible global function definition for ‘runif’ ihw.DESeqResults: no visible global function definition for ‘mcols’ ihw.DESeqResults: no visible global function definition for ‘mcols<-’ ihw.DESeqResults: no visible global function definition for ‘metadata’ ihw.DESeqResults: no visible global function definition for ‘metadata<-’ ihw.default: no visible global function definition for ‘runif’ ihw.default: no visible global function definition for ‘p.adjust’ ihw_convex: no visible global function definition for ‘gurobi’ ihw_internal: no visible global function definition for ‘p.adjust’ ihw_milp: no visible global function definition for ‘str’ ihw_milp: no visible global function definition for ‘gurobi’ plot_decisionboundary: no visible binding for global variable ‘stratum’ plot_decisionboundary: no visible binding for global variable ‘covariate’ plot_decisionboundary: no visible binding for global variable ‘pvalue’ plot_decisionboundary: no visible binding for global variable ‘fold’ rand_cbum: no visible global function definition for ‘rbinom’ rand_cbum: no visible global function definition for ‘runif’ rand_cbum: no visible global function definition for ‘qbeta’ rand_cbum: no visible global function definition for ‘pbeta’ thresholds_ihwResult: no visible global function definition for ‘na.exclude’ thresholds,ihwResult: no visible global function definition for ‘na.exclude’ Undefined global functions or variables: covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude p.adjust pbeta pvalue qbeta rbinom runif str stratum Consider adding importFrom("stats", "na.exclude", "p.adjust", "pbeta", "qbeta", "rbinom", "runif") importFrom("utils", "str") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed ihw.default 5.222 0.039 5.345 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/IHW.Rcheck/00check.log’ for details.
IHW.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IHW ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘IHW’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘nrow’ from package ‘base’ in package ‘IHW’ ** 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 (IHW)
IHW.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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("IHW") > > test_check("IHW") List of 3 $ solution: num [1:2000] 0 0 0 0 0 0 0 0 0 0 ... $ objval : num 70 $ status : Named int 0 ..- attr(*, "names")= chr "TM_OPTIMAL_SOLUTION_FOUND" NULL ══ testthat results ═══════════════════════════════════════════════════════════ OK: 36 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 13.990 0.112 14.157
IHW.Rcheck/IHW-Ex.timings
name | user | system | elapsed | |
get_bh_threshold | 0.004 | 0.001 | 0.004 | |
groups_by_filter | 0.003 | 0.000 | 0.003 | |
ihw.DESeqResults | 0.001 | 0.000 | 0.000 | |
ihw.default | 5.222 | 0.039 | 5.345 | |
ihwResult-class | 2.947 | 0.004 | 2.951 | |
plot-ihwResult-ANY-method | 3.951 | 0.016 | 3.967 | |