Junpeng Zhang
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/miRSM |
| Branch: RELEASE_3_10 |
| Last Commit: 5441072 |
| Last Changed Date: 2020-02-01 22:32:45 -0400 (Sat, 01 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:14:38 -0400 (Wed, 15 Apr 2020).
| Package 1060/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| miRSM 1.4.1 Junpeng Zhang
| 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: miRSM |
| Version: 1.4.1 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings miRSM_1.4.1.tar.gz |
| StartedAt: 2020-04-15 05:58:25 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:04:36 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 370.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miRSM.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings miRSM_1.4.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/miRSM.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 ‘miRSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRSM’ version ‘1.4.1’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘org.Hs.eg.db’
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 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
Examples with CPU or elapsed time > 5s
user system elapsed
module_CEA 5.096 0.124 5.221
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/miRSM.Rcheck/00check.log’
for details.
miRSM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL miRSM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘miRSM’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c complex.c -o complex.o gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o miRSM.so complex.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-miRSM/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (miRSM)
miRSM.Rcheck/tests/test_miRSM.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(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, 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: 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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+----------------------------+
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 2.32.0
>
> # 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
14.640 0.572 15.244
miRSM.Rcheck/miRSM-Ex.timings
| name | user | system | elapsed | |
| cor_binary | 0.332 | 0.024 | 0.359 | |
| miRSM | 0.500 | 0.036 | 0.589 | |
| module_CEA | 5.096 | 0.124 | 5.221 | |
| module_Coexpress | 3.528 | 0.016 | 3.548 | |
| module_FA | 0 | 0 | 0 | |
| module_GFA | 3.956 | 0.060 | 4.020 | |
| module_NMF | 4.076 | 0.268 | 4.354 | |
| module_ProNet | 0.164 | 0.000 | 0.163 | |
| module_Validate | 2.572 | 0.008 | 2.579 | |
| module_WGCNA | 1.948 | 0.008 | 1.955 | |
| module_biclust | 0.432 | 0.004 | 0.436 | |
| module_clust | 0.196 | 0.000 | 0.198 | |
| module_igraph | 0.208 | 0.000 | 0.207 | |
| module_miRdistribute | 2.528 | 0.000 | 2.528 | |
| module_miRsponge | 2.684 | 0.004 | 2.685 | |
| module_miRtarget | 2.636 | 0.008 | 2.646 | |
| share_miRs | 2.852 | 0.012 | 2.871 | |