Justin Silverman
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/philr |
| Branch: RELEASE_3_7 |
| Last Commit: af0f51f |
| Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:42:48 -0400 (Wed, 17 Oct 2018).
| Package 1090/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| philr 1.6.0 Justin Silverman
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: philr |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:philr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings philr_1.6.0.tar.gz |
| StartedAt: 2018-10-17 03:57:54 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:59:17 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 84.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: philr.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:philr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings philr_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/philr.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'philr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'philr' 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 whether package 'philr' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpimNrBI/R.INSTALL14f46e9f2af2/philr/man/buildilrBasep.Rd:33: file link 'gsi.buildilrBase' in package 'compositions' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/philr.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
name.balance: no visible global function definition for 'as'
vote.annotation: no visible global function definition for 'is'
Undefined global functions or variables:
as is
Consider adding
importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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-3.7-bioc/meat/philr.Rcheck/00check.log'
for details.
philr.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/philr_1.6.0.tar.gz && rm -rf philr.buildbin-libdir && mkdir philr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=philr.buildbin-libdir philr_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL philr_1.6.0.zip && rm philr_1.6.0.tar.gz philr_1.6.0.zip
###
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install for i386
* installing *source* package 'philr' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'philr'
finding HTML links ... done
annotate_balance html
buildilrBasep html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpimNrBI/R.INSTALL14f46e9f2af2/philr/man/buildilrBasep.Rd:33: file link 'gsi.buildilrBase' in package 'compositions' does not exist and so has been treated as a topic
calculate.blw html
convert_to_long html
g.colMeans html
g.rowMeans html
mean_dist_to_tips html
miniclo html
name.balance html
name_nodenumber_conversion html
named_rtree html
philr html
philrInv html
phylo2sbp html
shift html
weighted_clr html
weighted_ilr html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'philr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'philr' as philr_1.6.0.zip
* DONE (philr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'philr' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
philr.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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)
> library(philr)
>
> test_check("philr")
== testthat results ===========================================================
OK: 34 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
2.01 0.29 2.29
|
philr.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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)
> library(philr)
>
> test_check("philr")
== testthat results ===========================================================
OK: 34 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
2.31 0.14 2.43
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philr.Rcheck/examples_i386/philr-Ex.timings
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philr.Rcheck/examples_x64/philr-Ex.timings
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