Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:41:58 -0400 (Thu, 12 Apr 2018).
Package 135/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
biomformat 1.6.0 Paul J. McMurdie
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![]() |
Package: biomformat |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biomformat_1.6.0.tar.gz |
StartedAt: 2018-04-12 00:58:26 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 00:59:22 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 56.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biomformat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biomformat_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/biomformat.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 ‘biomformat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘biomformat’ 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 ‘biomformat’ 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 make_biom: no visible global function definition for ‘packageVersion’ namedList: no visible global function definition for ‘setNames’ Undefined global functions or variables: packageVersion setNames Consider adding importFrom("stats", "setNames") importFrom("utils", "packageVersion") 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat-biomformat.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: 1 NOTE See ‘/Users/biocbuild/bbs-3.6-bioc/meat/biomformat.Rcheck/00check.log’ for details.
biomformat.Rcheck/00install.out
* installing *source* package ‘biomformat’ ... ** R ** inst ** preparing package for lazy loading Creating a generic function for ‘nrow’ from package ‘base’ in package ‘biomformat’ Creating a generic function for ‘ncol’ from package ‘base’ in package ‘biomformat’ Creating a generic function for ‘rownames’ from package ‘base’ in package ‘biomformat’ Creating a generic function for ‘colnames’ from package ‘base’ in package ‘biomformat’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (biomformat)
biomformat.Rcheck/tests/testthat-biomformat.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. > library("testthat") > # As suggested for opt-out option on testing by users, recommended by CRAN > # http://adv-r.had.co.nz/Testing.html > # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R: > # library(testthat) > # library(yourpackage) > # test_package("yourpackage") > # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R: > # library(testthat) > # test_check("yourpackage") > # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers. > test_check("biomformat") Loading required package: biomformat ══ testthat results ═══════════════════════════════════════════════════════════ OK: 136 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 4.235 0.140 4.600
biomformat.Rcheck/biomformat-Ex.timings
name | user | system | elapsed | |
biom-class | 0.372 | 0.012 | 0.385 | |
biom-methods | 0.586 | 0.003 | 0.602 | |
biom_data-methods | 0.188 | 0.003 | 0.197 | |
biom_shape-methods | 0.006 | 0.000 | 0.006 | |
colnames-methods | 0.004 | 0.000 | 0.003 | |
header-methods | 0.004 | 0.000 | 0.005 | |
make_biom | 0.128 | 0.002 | 0.131 | |
matrix_element_type-methods | 0.005 | 0.000 | 0.005 | |
ncol-methods | 0.005 | 0.000 | 0.005 | |
nrow-methods | 0.003 | 0.000 | 0.003 | |
observation_metadata-methods | 0.047 | 0.002 | 0.050 | |
read_biom | 0.009 | 0.001 | 0.010 | |
read_hdf5_biom | 0.236 | 0.003 | 0.247 | |
rownames-methods | 0.005 | 0.000 | 0.005 | |
sample_metadata-methods | 0.037 | 0.002 | 0.039 | |
show-methods | 0.005 | 0.000 | 0.006 | |
write_biom | 0.013 | 0.000 | 0.014 | |