Mark A. van de Wiel
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/GRridge |
| Branch: RELEASE_3_7 |
| Last Commit: ac3cf01 |
| Last Changed Date: 2018-04-30 10:35:44 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:57:29 -0400 (Wed, 17 Oct 2018).
| Package 653/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GRridge 1.4.0 Mark A. van de Wiel
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: GRridge |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GRridge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GRridge_1.4.0.tar.gz |
| StartedAt: 2018-10-16 21:52:44 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:54:41 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 116.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GRridge.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GRridge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GRridge_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GRridge.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRridge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRridge’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘penalized’ ‘Iso’ ‘survival’ ‘graph’ ‘glmnet’ ‘mvtnorm’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GRridge’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 8.6Mb
* 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
.grridgeCVlin: no visible binding for global variable ‘dataunpensam’
.grridgelin: no visible binding for global variable ‘datapred’
predict.grridge: no visible binding for global variable ‘samout’
Undefined global functions or variables:
datapred dataunpensam samout
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
dataFarkas.rda 3.4Mb 2.5Mb bzip2
dataWurdinger.rda 2.0Mb 1.2Mb xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/GRridge.Rcheck/00check.log’
for details.
GRridge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GRridge ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘GRridge’ ... ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GRridge)
GRridge.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("GRridge")
Loading required package: penalized
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
Loading required package: Iso
Iso 0.0-17
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:penalized':
as.data.frame
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16
Loading required package: mvtnorm
Attaching package: 'GRridge'
The following object is masked from 'package:glmnet':
auc
>
> testthat::test_check("GRridge")
[1] "Summary of group sizes:"
VarIn VarOut
50 50
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
2.417 0.214 2.617
GRridge.Rcheck/GRridge-Ex.timings
| name | user | system | elapsed | |
| CreatePartition | 0.145 | 0.006 | 0.153 | |
| PartitionsSelection | 0.005 | 0.001 | 0.007 | |
| auc | 0.143 | 0.014 | 0.160 | |
| dataFarkas | 0.107 | 0.011 | 0.119 | |
| dataVerlaat | 0.043 | 0.005 | 0.047 | |
| dataWurdinger | 3.570 | 0.148 | 3.756 | |
| grridge | 0.120 | 0.005 | 0.126 | |
| grridgeCV | 0.118 | 0.016 | 0.135 | |
| hello | 0.001 | 0.000 | 0.002 | |
| matchGeneSets | 3.229 | 0.081 | 3.363 | |
| mergeGroups | 2.826 | 0.035 | 2.895 | |
| predict.grridge | 0.002 | 0.000 | 0.003 | |
| roc | 4.083 | 0.063 | 4.199 | |