Carlos Ruiz-Arenas
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MultiDataSet |
| Branch: RELEASE_3_10 |
| Last Commit: 157af5f |
| Last Changed Date: 2019-10-29 13:09:38 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:11:21 -0400 (Wed, 15 Apr 2020).
| Package 1113/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MultiDataSet 1.14.0 Carlos Ruiz-Arenas
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MultiDataSet |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MultiDataSet_1.14.0.tar.gz |
| StartedAt: 2020-04-15 03:48:34 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:52:02 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 208.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MultiDataSet.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MultiDataSet_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MultiDataSet.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiDataSet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiDataSet’ version ‘1.14.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MultiDataSet’ 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
Unexported objects imported by ':::' calls:
‘Biobase:::assayDataEnvLock’ ‘Biobase:::assayDataStorageMode’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
downloadGEO : <anonymous>: no visible global function definition for
‘methylationSet’
lambdaClayton: no visible global function definition for ‘qnorm’
lambdaClayton: no visible global function definition for ‘qchisq’
qq_plot: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
methylationSet qbeta qchisq qnorm
Consider adding
importFrom("stats", "qbeta", "qchisq", "qnorm")
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 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
add_methy 17.416 0.668 19.316
* 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 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/MultiDataSet.Rcheck/00check.log’
for details.
MultiDataSet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MultiDataSet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘MultiDataSet’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for ‘add_methy’ with signature ‘"MultiDataSet","GenomicRatioSet"’: no definition for class “GenomicRatioSet” ** 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 (MultiDataSet)
MultiDataSet.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(MultiDataSet)
Loading required package: Biobase
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 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("MultiDataSet")
Object of class 'MultiDataSet'
. assayData: 1 elements
. rnaseq: 3 features, 2 samples
. featureData:
. rnaseq: 3 rows, 5 cols (chromosome, ..., status)
. rowRanges:
. rnaseq: NO
. phenoData:
. rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
. assayData: 1 elements
. rnaseq: 3 features, 2 samples
. featureData:
. rnaseq: 3 rows, 5 cols (chromosome, ..., status)
. rowRanges:
. rnaseq: YES
. phenoData:
. rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
. assayData: 1 elements
. rnaseq: 3 features, 2 samples
. featureData:
. rnaseq: 3 rows, 5 cols (chromosome, ..., status)
. rowRanges:
. rnaseq: NO
. phenoData:
. rnaseq: 2 samples, 2 cols (id, sex)
Object of class 'ResultSet'
. created with: test
. sva:
. #results: 1 ( error: 1 )
. featureData: 0
Object of class 'ResultSet'
. created with: association
. via: a and b
. sva:
. #results: 1 ( error: 1 )
. featureData: 10 probes x 2 variables
Object of class 'ResultSet'
. created with: crossomics
. sva:
. method: met ( metpac )
. #results: 2 ( error: 1 )
. featureData: 2
. pac: 10x2
. cot: 10x2
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 178 | SKIPPED: 0 | WARNINGS: 27 | FAILED: 0 ]
>
> proc.time()
user system elapsed
35.032 0.852 36.136
MultiDataSet.Rcheck/MultiDataSet-Ex.timings
| name | user | system | elapsed | |
| MultiDataSet-class | 0.004 | 0.000 | 0.001 | |
| ResultSet-class | 0.000 | 0.000 | 0.001 | |
| add_eset | 0.092 | 0.004 | 0.096 | |
| add_genexp | 0.176 | 0.000 | 0.178 | |
| add_methy | 17.416 | 0.668 | 19.316 | |
| add_rnaseq-methods | 0.116 | 0.004 | 0.121 | |
| add_rse | 1.424 | 0.008 | 1.431 | |
| add_se | 0.048 | 0.000 | 0.045 | |
| add_snps | 0.068 | 0.000 | 0.070 | |
| add_table | 0.012 | 0.000 | 0.015 | |
| chrNumToChar | 0.004 | 0.000 | 0.000 | |
| commonIds | 0.160 | 0.000 | 0.163 | |
| commonSamples | 0.176 | 0.000 | 0.179 | |
| getAssociation-methods | 0.020 | 0.008 | 0.031 | |
| lambdaClayton | 0.000 | 0.000 | 0.001 | |
| opt-methods | 0.000 | 0.000 | 0.001 | |
| qq_plot | 0.332 | 0.016 | 0.350 | |
| rowRangesElements | 0.100 | 0.004 | 0.105 | |
| volcano_plot | 0.172 | 0.012 | 0.187 | |