Junpeng Zhang
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/miRSM |
| Branch: RELEASE_3_8 |
| Last Commit: 54b5bd5 |
| Last Changed Date: 2018-10-30 11:42:10 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:44 -0400 (Tue, 16 Apr 2019).
| Package 974/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| miRSM 1.0.0 Junpeng Zhang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: miRSM |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings miRSM_1.0.0.tar.gz |
| StartedAt: 2019-04-16 01:29:36 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:34:11 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 274.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miRSM.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings miRSM_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/miRSM.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘miRSM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘miRSM’ version ‘1.0.0’ * 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 ‘miRSM’ 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 ... 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 ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test_miRSM.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 ‘/home/biocbuild/bbs-3.8-bioc/meat/miRSM.Rcheck/00check.log’ for details.
miRSM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL miRSM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘miRSM’ ... ** libs gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c complex.c -o complex.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o miRSM.so complex.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-bioc/R/library/miRSM/libs ** 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 (miRSM)
miRSM.Rcheck/tests/test_miRSM.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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(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 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: 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
> library(miRSM)
+----------------------------+
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|.....####.....########......| # # # # # # # #
|.....####.....########......| ##### # # ###### # # #
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+----------------------------+
Citation: S. Hochreiter et al.,
FABIA: Factor Analysis for Bicluster Acquisition,
Bioinformatics 26(12):1520-1527, 2010.
BibTex: enter 'toBibtex(citation("fabia"))'
Homepage: http://www.bioinf.jku.at/software/fabia/fabia.html
FABIA Package Version 2.28.0
|---------------------------------------------------------------------------------------------------- |
| |
| Note: The name of the 'miRsponge' package has been changed into 'miRspongeR', please download |
| miRspongeR package and obtain the source from Github: https://github.com/zhangjunpeng411/miRspongeR.|
| |
|-------------------------------------------------------------------------------------------------------|
>
> # Load datasets
> data(BRCASampleData)
>
> # Identify gene co-expression modules using igraph method
> modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)],
+ mRExp[, seq_len(10)])
>
>
> test_that("Test miRSM", {
+ expect_equal(geneIds(module_igraph(ceRExp[, seq_len(10)],
+ mRExp[, seq_len(10)])), geneIds(modulegenes_igraph))
+ })
>
> proc.time()
user system elapsed
12.488 0.372 12.888
miRSM.Rcheck/miRSM-Ex.timings
| name | user | system | elapsed | |
| cor_binary | 0.232 | 0.016 | 0.250 | |
| miRSM | 0.644 | 0.004 | 0.660 | |
| module_FA | 0 | 0 | 0 | |
| module_GFA | 3.256 | 0.020 | 3.279 | |
| module_NMF | 3.272 | 0.232 | 3.517 | |
| module_ProNet | 0.172 | 0.000 | 0.174 | |
| module_WGCNA | 1.712 | 0.004 | 1.721 | |
| module_biclust | 0.444 | 0.000 | 0.442 | |
| module_igraph | 0.120 | 0.000 | 0.122 | |