Paul J. McMurdie
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/biomformat |
| Branch: RELEASE_3_8 |
| Last Commit: e67c6f4 |
| Last Changed Date: 2019-01-04 13:20:43 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:08 -0400 (Sat, 13 Apr 2019).
| Package 151/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| biomformat 1.10.1 Paul J. McMurdie
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: biomformat |
| Version: 1.10.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomformat.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings biomformat_1.10.1.tar.gz |
| StartedAt: 2019-04-13 00:48:59 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 00:50:59 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 119.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biomformat.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomformat.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings biomformat_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/biomformat.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.10.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/ncol-methods.Rd:6: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/ncol-methods.Rd:19: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/ncol-methods.Rd:31: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/rownames-methods.Rd:6: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/rownames-methods.Rd:19: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/rownames-methods.Rd:31: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-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 ... 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 ...
** 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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/biomformat.Rcheck/00check.log'
for details.
biomformat.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/biomformat_1.10.1.tar.gz && rm -rf biomformat.buildbin-libdir && mkdir biomformat.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biomformat.buildbin-libdir biomformat_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL biomformat_1.10.1.zip && rm biomformat_1.10.1.tar.gz biomformat_1.10.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'biomformat' ...
** 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
biom_shape-methods html
colnames-methods html
header-methods html
make_biom html
matrix_element_type-methods html
ncol-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/ncol-methods.Rd:6: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/ncol-methods.Rd:19: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/ncol-methods.Rd:31: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
nrow-methods html
observation_metadata-methods html
read_biom html
read_hdf5_biom html
rownames-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/rownames-methods.Rd:6: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/rownames-methods.Rd:19: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp46pjYB/R.INSTALL143826b716b/biomformat/man/rownames-methods.Rd:31: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
sample_metadata-methods html
show-methods html
write_biom html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'biomformat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biomformat' as biomformat_1.10.1.zip
* DONE (biomformat)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'biomformat' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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biomformat.Rcheck/tests_i386/testthat-biomformat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
== testthat results ===========================================================
OK: 136 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
2.18 0.14 2.34
|
biomformat.Rcheck/tests_x64/testthat-biomformat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
== testthat results ===========================================================
OK: 136 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
2.32 0.07 2.39
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biomformat.Rcheck/examples_i386/biomformat-Ex.timings
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biomformat.Rcheck/examples_x64/biomformat-Ex.timings
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