Junpeng Zhang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/miRSM |
| Branch: RELEASE_3_9 |
| Last Commit: 06c25e5 |
| Last Changed Date: 2019-09-10 23:02:58 -0400 (Tue, 10 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:03:10 -0400 (Wed, 16 Oct 2019).
| Package 1016/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| miRSM 1.2.2 Junpeng Zhang
| 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: miRSM |
| Version: 1.2.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:miRSM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings miRSM_1.2.2.tar.gz |
| StartedAt: 2019-10-16 04:42:35 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:51:21 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 525.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miRSM.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:miRSM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings miRSM_1.2.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/miRSM.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 ‘miRSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRSM’ version ‘1.2.2’
* 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 6.900 1.027 7.917
module_Validate 6.261 0.934 7.186
module_miRtarget 6.027 0.798 6.817
module_Coexpress 5.867 0.927 6.786
module_miRsponge 5.965 0.808 6.765
share_miRs 5.836 0.823 6.650
module_miRdistribute 5.835 0.776 6.603
module_NMF 6.291 0.239 6.527
module_GFA 5.017 0.232 5.242
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/miRSM.Rcheck/00check.log’
for details.
miRSM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL miRSM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘miRSM’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c complex.c -o complex.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o miRSM.so complex.o registerDynamicSymbol.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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 3.6.1 (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(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 2.30.0
>
> # 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
21.118 1.922 22.971
miRSM.Rcheck/miRSM-Ex.timings
| name | user | system | elapsed | |
| cor_binary | 0.474 | 0.034 | 0.509 | |
| miRSM | 1.476 | 0.051 | 1.525 | |
| module_CEA | 6.900 | 1.027 | 7.917 | |
| module_Coexpress | 5.867 | 0.927 | 6.786 | |
| module_FA | 0.001 | 0.001 | 0.001 | |
| module_GFA | 5.017 | 0.232 | 5.242 | |
| module_NMF | 6.291 | 0.239 | 6.527 | |
| module_ProNet | 0.248 | 0.013 | 0.261 | |
| module_Validate | 6.261 | 0.934 | 7.186 | |
| module_WGCNA | 1.958 | 0.057 | 2.013 | |
| module_biclust | 0.586 | 0.016 | 0.603 | |
| module_clust | 0.152 | 0.011 | 0.163 | |
| module_igraph | 0.130 | 0.009 | 0.139 | |
| module_miRdistribute | 5.835 | 0.776 | 6.603 | |
| module_miRsponge | 5.965 | 0.808 | 6.765 | |
| module_miRtarget | 6.027 | 0.798 | 6.817 | |
| share_miRs | 5.836 | 0.823 | 6.650 | |