Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:37 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the gespeR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gespeR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 760/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gespeR 1.24.0 (landing page) Fabian Schmich
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: gespeR |
Version: 1.24.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gespeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gespeR_1.24.0.tar.gz |
StartedAt: 2021-10-14 19:32:16 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:37:30 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 314.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: gespeR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gespeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gespeR_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/gespeR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gespeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gespeR’ version ‘1.24.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt 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 ‘gespeR’ 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 .gespeR.cv: no visible global function definition for ‘coef’ .select.model: no visible global function definition for ‘predict’ concordance: no visible global function definition for ‘cor’ lasso.rand: no visible global function definition for ‘runif’ plot.gespeR: no visible global function definition for ‘hist’ stability.selection: no visible global function definition for ‘lm’ Phenotypes,character: no visible global function definition for ‘read.delim’ Undefined global functions or variables: coef cor hist lm predict read.delim runif Consider adding importFrom("graphics", "hist") importFrom("stats", "coef", "cor", "lm", "predict", "runif") importFrom("utils", "read.delim") 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 ... WARNING Codoc mismatches from documentation object 'c,Phenotypes-method': \S4method{c}{Phenotypes} Code: function(x, ...) Docs: function(x, ..., recursive = FALSE) Argument names in docs not in code: recursive * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed gespeR-package 5.332 0.320 56.418 gespeR-class 0.800 0.022 13.427 stability-methods 0.143 0.019 12.548 * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/gespeR.Rcheck/00check.log’ for details.
gespeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gespeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘gespeR’ ... ** using staged installation ** R ** data ** 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 (gespeR)
gespeR.Rcheck/gespeR-Ex.timings
name | user | system | elapsed | |
Phenotypes-class | 0.019 | 0.001 | 0.022 | |
TargetRelations-class | 0.011 | 0.002 | 0.012 | |
annotate.gsp-methods | 0.138 | 0.007 | 0.147 | |
as.data.frame-Phenotypes-method | 0.156 | 0.006 | 0.162 | |
c-Phenotypes-method | 0.044 | 0.002 | 0.045 | |
concordance | 0.836 | 0.034 | 0.871 | |
gespeR-class | 0.800 | 0.022 | 13.427 | |
gespeR-package | 5.332 | 0.320 | 56.418 | |
gspssp-methods | 0.205 | 0.009 | 0.216 | |
join-methods | 0.017 | 0.001 | 0.019 | |
lasso.rand | 0.010 | 0.003 | 0.013 | |
na.rem-methods | 0.044 | 0.005 | 0.049 | |
path-methods | 0.006 | 0.000 | 0.007 | |
rbo | 0.001 | 0.001 | 0.001 | |
scores-methods | 0.160 | 0.007 | 0.168 | |
simData | 0.013 | 0.001 | 0.015 | |
stability-methods | 0.143 | 0.019 | 12.548 | |
stabilityfits | 0.122 | 0.002 | 0.124 | |
target-relations-methods | 0.121 | 0.002 | 0.123 | |
trmatrix-methods | 0.108 | 0.002 | 0.111 | |
values-methods | 0.017 | 0.011 | 0.028 | |