Nikos Ignatiadis
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/IHW |
| git_branch: RELEASE_3_13 |
| git_last_commit: 1d7e10d |
| git_last_commit_date: 2021-05-19 12:17:40 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:08 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the IHW package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IHW.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 907/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IHW 1.20.0 (landing page) Nikos Ignatiadis
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: IHW |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IHW.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings IHW_1.20.0.tar.gz |
| StartedAt: 2021-10-15 00:37:53 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:39:49 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 115.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IHW.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IHW.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings IHW_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/IHW.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 'IHW/DESCRIPTION' ... OK
* this is package 'IHW' 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'IHW' can be installed ... OK
* 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
filter_pvals_for_optim: no visible global function definition for
'p.adjust'
groups_by_filter: no visible global function definition for 'runif'
ihw.DESeqResults: no visible global function definition for 'mcols'
ihw.DESeqResults: no visible global function definition for 'mcols<-'
ihw.DESeqResults: no visible global function definition for 'metadata'
ihw.DESeqResults: no visible global function definition for
'metadata<-'
ihw.default: no visible global function definition for 'runif'
ihw.default: no visible global function definition for 'p.adjust'
ihw_convex: no visible global function definition for 'gurobi'
ihw_internal: no visible global function definition for 'p.adjust'
ihw_milp: no visible global function definition for 'str'
ihw_milp: no visible global function definition for 'gurobi'
plot_decisionboundary: no visible binding for global variable 'stratum'
plot_decisionboundary: no visible binding for global variable
'covariate'
plot_decisionboundary: no visible binding for global variable 'pvalue'
plot_decisionboundary: no visible binding for global variable 'fold'
rand_cbum: no visible global function definition for 'rbinom'
rand_cbum: no visible global function definition for 'runif'
rand_cbum: no visible global function definition for 'qbeta'
rand_cbum: no visible global function definition for 'pbeta'
thresholds_ihwResult: no visible global function definition for
'na.exclude'
thresholds,ihwResult: no visible global function definition for
'na.exclude'
Undefined global functions or variables:
covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude
p.adjust pbeta pvalue qbeta rbinom runif str stratum
Consider adding
importFrom("stats", "na.exclude", "p.adjust", "pbeta", "qbeta",
"rbinom", "runif")
importFrom("utils", "str")
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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ihw.default 4.31 0.16 7.14
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/IHW.Rcheck/00check.log'
for details.
IHW.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/IHW_1.20.0.tar.gz && rm -rf IHW.buildbin-libdir && mkdir IHW.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IHW.buildbin-libdir IHW_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL IHW_1.20.0.zip && rm IHW_1.20.0.tar.gz IHW_1.20.0.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 36036 100 36036 0 0 302k 0 --:--:-- --:--:-- --:--:-- 306k
install for i386
* installing *source* package 'IHW' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'nrow' from package 'base' in package 'IHW'
** help
*** installing help indices
converting help for package 'IHW'
finding HTML links ... done
get_bh_threshold html
groups_by_filter html
ihw.DESeqResults html
ihw.default html
ihwResult-class html
plot-ihwResult-ANY-method 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 'IHW' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IHW' as IHW_1.20.0.zip
* DONE (IHW)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'IHW' successfully unpacked and MD5 sums checked
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IHW.Rcheck/tests_i386/testthat.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")
> library("IHW")
>
> test_check("IHW")
List of 3
$ solution: num [1:2000] 0 0 0 0 0 0 0 0 0 0 ...
$ objval : num 70
$ status : Named int 0
..- attr(*, "names")= chr "TM_OPTIMAL_SOLUTION_FOUND"
NULL
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
11.62 0.37 11.98
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IHW.Rcheck/tests_x64/testthat.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")
> library("IHW")
>
> test_check("IHW")
List of 3
$ solution: num [1:2000] 0 0 0 0 0 0 0 0 0 0 ...
$ objval : num 70
$ status : Named int 0
..- attr(*, "names")= chr "TM_OPTIMAL_SOLUTION_FOUND"
NULL
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
11.85 0.39 13.68
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IHW.Rcheck/examples_i386/IHW-Ex.timings
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IHW.Rcheck/examples_x64/IHW-Ex.timings
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