George Weingart
| Snapshot Date: 2020-07-06 15:51:14 -0400 (Mon, 06 Jul 2020) |
| URL: https://git.bioconductor.org/packages/banocc |
| Branch: RELEASE_3_11 |
| Last Commit: 7299cd2 |
| Last Changed Date: 2020-04-27 15:06:53 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-07-07 13:53:41 -0400 (Tue, 07 Jul 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE banocc PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 111/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| banocc 1.12.0 George Weingart
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: banocc |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:banocc.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings banocc_1.12.0.tar.gz |
| StartedAt: 2020-07-07 07:28:31 -0400 (Tue, 07 Jul 2020) |
| EndedAt: 2020-07-07 07:32:45 -0400 (Tue, 07 Jul 2020) |
| EllapsedTime: 254.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: banocc.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:banocc.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings banocc_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/banocc.Rcheck'
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'banocc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'banocc' version '1.12.0'
* 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 'banocc' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpeUN94e/R.INSTALL111c3a962aa4/banocc/man/run_banocc.Rd:56: file link 'sampling' in package 'rstan' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpeUN94e/R.INSTALL111c3a962aa4/banocc/man/run_banocc.Rd:77: file link 'sampling' in package 'rstan' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/banocc.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
calc_snc: no visible global function definition for 'sd'
get_IVs : <anonymous>: no visible global function definition for
'rgamma'
get_banocc_output : <anonymous>: no visible global function definition
for 'cov2cor'
get_posterior_quantiles: no visible binding for global variable
'quantile'
rgbeta: no visible global function definition for 'rbeta'
rgbeta: no visible global function definition for 'rbinom'
Undefined global functions or variables:
cov2cor quantile rbeta rbinom rgamma sd
Consider adding
importFrom("stats", "cov2cor", "quantile", "rbeta", "rbinom", "rgamma",
"sd")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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-3.11-bioc/meat/banocc.Rcheck/00check.log'
for details.
banocc.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/banocc_1.12.0.tar.gz && rm -rf banocc.buildbin-libdir && mkdir banocc.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=banocc.buildbin-libdir banocc_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL banocc_1.12.0.zip && rm banocc_1.12.0.tar.gz banocc_1.12.0.zip
###
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% 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 25.3M 100 25.3M 0 0 70.0M 0 --:--:-- --:--:-- --:--:-- 71.5M
install for i386
* installing *source* package 'banocc' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'banocc'
finding HTML links ... done
banocc html
banocc_model html
compositions_hard_null html
compositions_neg_spike html
compositions_null html
compositions_pos_spike html
counts_hard_null html
counts_neg_spike html
counts_null html
counts_pos_spike html
get_banocc_output html
run_banocc html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpeUN94e/R.INSTALL111c3a962aa4/banocc/man/run_banocc.Rd:56: file link 'sampling' in package 'rstan' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpeUN94e/R.INSTALL111c3a962aa4/banocc/man/run_banocc.Rd:77: file link 'sampling' in package 'rstan' does not exist and so has been treated as a topic
** 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 'banocc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'banocc' as banocc_1.12.0.zip
* DONE (banocc)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'banocc' successfully unpacked and MD5 sums checked
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banocc.Rcheck/tests_i386/testthat.Rout
R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 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(banocc)
Loading required package: rstan
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.19.3, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
For improved execution time, we recommend calling
Sys.setenv(LOCAL_CPPFLAGS = '-march=corei7 -mtune=corei7')
although this causes Stan to throw an error on a few processors.
>
> test_check("banocc")
== testthat results ===========================================================
[ OK: 2616 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
82.01 2.37 84.39
|
banocc.Rcheck/tests_x64/testthat.Rout
R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 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(banocc)
Loading required package: rstan
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.19.3, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
For improved execution time, we recommend calling
Sys.setenv(LOCAL_CPPFLAGS = '-march=corei7 -mtune=corei7')
although this causes Stan to throw an error on a few processors.
>
> test_check("banocc")
== testthat results ===========================================================
[ OK: 2616 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
83.14 2.09 85.23
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banocc.Rcheck/examples_i386/banocc-Ex.timings
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banocc.Rcheck/examples_x64/banocc-Ex.timings
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