Mark A. van de Wiel
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GRridge |
| Branch: master |
| Last Commit: 5e7e4a1 |
| Last Changed Date: 2019-03-07 09:11:20 -0400 (Thu, 07 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:47:07 -0400 (Tue, 09 Apr 2019).
| Package 710/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GRridge 1.7.4 Mark A. van de Wiel
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: GRridge |
| Version: 1.7.4 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GRridge.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GRridge_1.7.4.tar.gz |
| StartedAt: 2019-04-09 01:03:50 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:06:16 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 146.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GRridge.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GRridge.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GRridge_1.7.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GRridge.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.7.4’
* 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 9.1Mb
sub-directories of 1Mb or more:
data 8.8Mb
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
predict.grridge
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.grridgelin: no visible binding for global variable ‘datapred’
predict.grridge: no visible binding for global variable ‘samout’
Undefined global functions or variables:
datapred samout
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘Y’ ‘part5’ ‘simdata’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
dataSimlin 26.494 0.051 26.697
* 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: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/GRridge.Rcheck/00check.log’
for details.
GRridge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GRridge ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘GRridge’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GRridge)
GRridge.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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
2.607 0.118 2.754
GRridge.Rcheck/GRridge-Ex.timings
| name | user | system | elapsed | |
| CreatePartition | 0.112 | 0.000 | 0.113 | |
| PartitionsSelection | 0.000 | 0.000 | 0.001 | |
| auc | 0.152 | 0.016 | 0.169 | |
| dataFarkas | 0.138 | 0.003 | 0.154 | |
| dataSimlin | 26.494 | 0.051 | 26.697 | |
| dataVerlaat | 0.045 | 0.000 | 0.044 | |
| dataWurdinger | 1.594 | 0.028 | 1.630 | |
| grridge | 0.356 | 0.008 | 0.378 | |
| grridgeCV | 0.131 | 0.000 | 0.132 | |
| hello | 0.000 | 0.000 | 0.001 | |
| matchGeneSets | 1.267 | 0.040 | 1.316 | |
| mergeGroups | 1.483 | 0.048 | 1.542 | |
| predict.grridge | 0.001 | 0.000 | 0.000 | |
| roc | 1.303 | 0.004 | 1.312 | |