Paul J. McMurdie
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/biomformat |
| git_branch: master |
| git_last_commit: 0ddeea2 |
| git_last_commit_date: 2021-10-26 12:24:06 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:03 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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 181/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biomformat 1.23.0 (landing page) Paul J. McMurdie
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: biomformat |
| Version: 1.23.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biomformat.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biomformat_1.23.0.tar.gz |
| StartedAt: 2022-03-17 18:34:03 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:34:56 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 53.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biomformat.Rcheck |
| Warnings: 2 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biomformat.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biomformat_1.23.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/biomformat.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.23.0'
* 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: D:/biocbuild/bbs-3.15-bioc/meat/biomformat/man/biom_data-methods.Rd:46: missing link 'plyr-package'
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/biomformat/man/observation_metadata-methods.Rd:30: missing link 'plyr-package'
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/biomformat/man/sample_metadata-methods.Rd:30: missing link 'plyr-package'
See 'D:/biocbuild/bbs-3.15-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
* 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 ... 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: 2 WARNINGs, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/biomformat.Rcheck/00check.log'
for details.
biomformat.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL biomformat
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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: D:/biocbuild/bbs-3.15-bioc/meat/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: D:/biocbuild/bbs-3.15-bioc/meat/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: D:/biocbuild/bbs-3.15-bioc/meat/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
* DONE (biomformat)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'sights' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'UNDO' is missing or broken
done
biomformat.Rcheck/tests/testthat-biomformat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 136 ]
>
> proc.time()
user system elapsed
2.39 0.20 2.56
biomformat.Rcheck/biomformat-Ex.timings
| name | user | system | elapsed | |
| biom-class | 0.06 | 0.00 | 0.06 | |
| biom-methods | 0.00 | 0.02 | 0.02 | |
| biom_data-methods | 0.01 | 0.01 | 0.03 | |
| biom_shape-methods | 0.02 | 0.00 | 0.01 | |
| colnames-methods | 0 | 0 | 0 | |
| header-methods | 0 | 0 | 0 | |
| make_biom | 0.05 | 0.00 | 0.14 | |
| matrix_element_type-methods | 0 | 0 | 0 | |
| ncol-methods | 0 | 0 | 0 | |
| nrow-methods | 0.01 | 0.00 | 0.02 | |
| observation_metadata-methods | 0.02 | 0.00 | 0.01 | |
| read_biom | 0.01 | 0.00 | 0.02 | |
| read_hdf5_biom | 0.03 | 0.00 | 0.06 | |
| rownames-methods | 0 | 0 | 0 | |
| sample_metadata-methods | 0.04 | 0.00 | 0.03 | |
| show-methods | 0 | 0 | 0 | |
| write_biom | 0.00 | 0.00 | 0.03 | |