Mark A. van de Wiel
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/GRridge |
| Branch: RELEASE_3_6 |
| Last Commit: 1b5e901 |
| Last Changed Date: 2017-10-30 12:41:23 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:15:41 -0400 (Thu, 12 Apr 2018).
| Package 621/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GRridge 1.2.0 Mark A. van de Wiel
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: GRridge |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GRridge_1.2.0.tar.gz |
| StartedAt: 2018-04-12 00:07:17 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:13:39 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 382.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GRridge.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GRridge_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GRridge.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘penalized’ ‘Iso’ ‘survival’ ‘GSEABase’ ‘BiocGenerics’ ‘Biobase’
‘annotate’ ‘graph’
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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
See ‘/home/biocbuild/bbs-3.6-bioc/meat/GRridge.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 8.5Mb
* 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 loading without being on the library search path ... 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 ... OK
* 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 1.9Mb 1.2Mb xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predict.grridge 160.056 0.344 160.497
grridgeCV 68.116 0.216 68.378
* 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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/GRridge.Rcheck/00check.log’
for details.
GRridge.Rcheck/00install.out
* installing *source* package ‘GRridge’ ... ** R ** data ** inst ** preparing package for lazy loading Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’ Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’ Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’ Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’ Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’ Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’ Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’ Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’ Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’ Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’ Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’ Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’ Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’ Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’ Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’ * DONE (GRridge)
GRridge.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: GSEABase
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, cbind, colMeans, colSums, colnames, 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: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Warning messages:
1: replacing previous import 'stats::xtabs' by 'BiocGenerics::xtabs' when loading 'GRridge'
2: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when loading 'GRridge'
3: replacing previous import 'stats::mad' by 'BiocGenerics::mad' when loading 'GRridge'
4: replacing previous import 'stats::IQR' by 'BiocGenerics::IQR' when loading 'GRridge'
5: replacing previous import 'GSEABase::intersect' by 'BiocGenerics::intersect' when loading 'GRridge'
6: replacing previous import 'penalized::as.data.frame' by 'BiocGenerics::as.data.frame' when loading 'GRridge'
7: replacing previous import 'GSEABase::setdiff' by 'BiocGenerics::setdiff' when loading 'GRridge'
8: replacing previous import 'stats::var' by 'BiocGenerics::var' when loading 'GRridge'
>
> 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
4.792 0.072 4.866
GRridge.Rcheck/GRridge-Ex.timings
| name | user | system | elapsed | |
| CreatePartition | 0.128 | 0.000 | 0.128 | |
| PartitionsSelection | 0.004 | 0.000 | 0.002 | |
| auc | 0.352 | 0.004 | 0.355 | |
| dataFarkas | 0.312 | 0.004 | 0.314 | |
| dataVerlaat | 0.036 | 0.004 | 0.038 | |
| dataWurdinger | 2.224 | 0.036 | 2.260 | |
| grridge | 0.116 | 0.000 | 0.117 | |
| grridgeCV | 68.116 | 0.216 | 68.378 | |
| hello | 0.000 | 0.000 | 0.001 | |
| matchGeneSets | 1.156 | 0.004 | 1.159 | |
| mergeGroups | 1.412 | 0.000 | 1.409 | |
| predict.grridge | 160.056 | 0.344 | 160.497 | |
| roc | 1.444 | 0.004 | 1.449 | |