Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the biomformat package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biomformat.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 181/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biomformat 1.20.0 (landing page) Paul J. McMurdie
| 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: biomformat |
Version: 1.20.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomformat.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings biomformat_1.20.0.tar.gz |
StartedAt: 2021-10-14 20:14:51 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:16:18 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 87.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: biomformat.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomformat.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings biomformat_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/biomformat.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'biomformat/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'biomformat' version '1.20.0' * 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 whether package 'biomformat' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpUl3Fcr/R.INSTALL10fc1eb452c/biomformat/man/biom_data-methods.Rd:46: missing link 'plyr-package' Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpUl3Fcr/R.INSTALL10fc1eb452c/biomformat/man/observation_metadata-methods.Rd:30: missing link 'plyr-package' Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpUl3Fcr/R.INSTALL10fc1eb452c/biomformat/man/sample_metadata-methods.Rd:30: missing link 'plyr-package' See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/biomformat.Rcheck/00install.out' for details. * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... WARNING Missing link or links in documentation object 'biom_data-methods.Rd': 'plyr-package' Missing link or links in documentation object 'observation_metadata-methods.Rd': 'plyr-package' Missing link or links in documentation object 'sample_metadata-methods.Rd': 'plyr-package' See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat-biomformat.R' OK ** running tests for arch 'x64' ... 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: 2 WARNINGs, 1 NOTE See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/biomformat.Rcheck/00check.log' for details.
biomformat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/biomformat_1.20.0.tar.gz && rm -rf biomformat.buildbin-libdir && mkdir biomformat.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biomformat.buildbin-libdir biomformat_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL biomformat_1.20.0.zip && rm biomformat_1.20.0.tar.gz biomformat_1.20.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 30313 100 30313 0 0 254k 0 --:--:-- --:--:-- --:--:-- 255k install for i386 * installing *source* package 'biomformat' ... ** using staged installation ** R ** inst ** byte-compile and prepare 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 converting help for package 'biomformat' finding HTML links ... done biom-class html biom-methods html finding level-2 HTML links ... done biom-package html biom_data-methods html Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpUl3Fcr/R.INSTALL10fc1eb452c/biomformat/man/biom_data-methods.Rd:46: missing link 'plyr-package' biom_shape-methods html colnames-methods html header-methods html make_biom html matrix_element_type-methods html ncol-methods html nrow-methods html observation_metadata-methods html Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpUl3Fcr/R.INSTALL10fc1eb452c/biomformat/man/observation_metadata-methods.Rd:30: missing link 'plyr-package' read_biom html read_hdf5_biom html rownames-methods html sample_metadata-methods html Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpUl3Fcr/R.INSTALL10fc1eb452c/biomformat/man/sample_metadata-methods.Rd:30: missing link 'plyr-package' show-methods html write_biom html ** 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 install for x64 * installing *source* package 'biomformat' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'biomformat' as biomformat_1.20.0.zip * DONE (biomformat) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'biomformat' successfully unpacked and MD5 sums checked
biomformat.Rcheck/tests_i386/testthat-biomformat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 [ FAIL 0 | WARN 4 | SKIP 0 | PASS 136 ] > > proc.time() user system elapsed 3.14 0.15 3.34 |
biomformat.Rcheck/tests_x64/testthat-biomformat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 [ FAIL 0 | WARN 4 | SKIP 0 | PASS 136 ] > > proc.time() user system elapsed 2.78 0.15 2.92 |
biomformat.Rcheck/examples_i386/biomformat-Ex.timings
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biomformat.Rcheck/examples_x64/biomformat-Ex.timings
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