André Veríssimo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/glmSparseNet |
| Branch: RELEASE_3_9 |
| Last Commit: db841b1 |
| Last Changed Date: 2019-05-10 14:57:45 -0400 (Fri, 10 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:03:22 -0400 (Wed, 16 Oct 2019).
| Package 685/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| glmSparseNet 1.2.0 André Veríssimo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: glmSparseNet |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:glmSparseNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings glmSparseNet_1.2.0.tar.gz |
| StartedAt: 2019-10-16 03:17:14 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:22:56 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 341.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: glmSparseNet.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:glmSparseNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings glmSparseNet_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/glmSparseNet.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘glmSparseNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘glmSparseNet’ version ‘1.2.0’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘glmSparseNet’ 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
* 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 ... NOTE
Namespace in Imports field not imported from: ‘rlang’
All declared Imports should be used.
* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
separate2GroupsCox 5.213 0.066 5.282
geneNames 1.835 0.110 12.687
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/glmSparseNet.Rcheck/00check.log’
for details.
glmSparseNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL glmSparseNet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘glmSparseNet’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** 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 (glmSparseNet)
glmSparseNet.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(glmSparseNet)
Loading required package: Matrix
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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:Matrix':
which
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, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:Matrix':
expand
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: glmnet
Loading required package: foreach
Loaded glmnet 2.0-18
>
> test_check("glmSparseNet")
Loading from cache (not calculating): /tmp/RtmpDlyiel/814a/cache-biomart-H_814affbc9d3ea2eab3ccea0a551ccb2290163bbcf23ee395ed1502576db44e09.RData
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 49 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
36.806 17.156 49.530
glmSparseNet.Rcheck/glmSparseNet-Ex.timings
| name | user | system | elapsed | |
| buildLambda | 0.009 | 0.006 | 0.014 | |
| buildStringNetwork | 0.000 | 0.000 | 0.001 | |
| cv.glmDegree | 0.357 | 0.037 | 0.395 | |
| cv.glmHub | 0.093 | 0.007 | 0.101 | |
| cv.glmOrphan | 0.107 | 0.012 | 0.119 | |
| cv.glmSparseNet | 3.093 | 0.190 | 3.285 | |
| degreeCor | 0.038 | 0.005 | 0.043 | |
| degreeCov | 0.012 | 0.001 | 0.014 | |
| degreeSparsebn | 2.465 | 0.045 | 2.514 | |
| dot-calcPenalty | 1.565 | 0.158 | 1.724 | |
| ensemblGeneNames | 0.001 | 0.000 | 0.000 | |
| geneNames | 1.835 | 0.110 | 12.687 | |
| glmDegree | 0.020 | 0.002 | 0.022 | |
| glmHub | 0.012 | 0.003 | 0.015 | |
| glmOrphan | 0.009 | 0.003 | 0.012 | |
| glmSparseNet | 1.356 | 0.026 | 1.382 | |
| hallmarks | 0.001 | 0.001 | 0.001 | |
| heuristicScale | 0.000 | 0.001 | 0.001 | |
| hubHeuristic | 0.001 | 0.000 | 0.001 | |
| networkCorParallel | 0.059 | 0.005 | 0.063 | |
| networkCovParallel | 0.019 | 0.001 | 0.021 | |
| networkOptions | 0.000 | 0.000 | 0.001 | |
| orphanHeuristic | 0 | 0 | 0 | |
| protein2EnsemblGeneNames | 0.071 | 0.001 | 0.470 | |
| separate2GroupsCox | 5.213 | 0.066 | 5.282 | |
| string.network.700.cache | 1.645 | 0.626 | 2.271 | |
| stringDBhomoSapiens | 0.000 | 0.000 | 0.001 | |