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CHECK report for miRSM on machv2

This page was generated on 2020-10-17 11:58:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE miRSM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1098/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRSM 1.6.4
Junpeng Zhang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/miRSM
Branch: RELEASE_3_11
Last Commit: 4113eb9
Last Changed Date: 2020-09-22 22:13:01 -0400 (Tue, 22 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: miRSM
Version: 1.6.4
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_1.6.4.tar.gz
StartedAt: 2020-10-17 03:07:51 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:14:21 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 389.7 seconds
RetCode: 0
Status:  OK 
CheckDir: miRSM.Rcheck
Warnings: 0

Command output

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### Running 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_1.6.4.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/miRSM.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.6.4’
* 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
* 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-3.11-bioc/meat/miRSM.Rcheck/00check.log’
for details.



Installation output

miRSM.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL miRSM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘miRSM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c complex.c -o complex.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang -mmacosx-version-min=10.13 -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/4.0/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)

Tests output

miRSM.Rcheck/tests/test_miRSM.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)

+----------------------------+                                          
|............................|                                          
|............................|                                          
|..............########......|  #######    #    ######    ###      #    
|..............########......|  #         # #   #     #    #      # #   
|.....####.....########......|  #        #   #  #     #    #     #   #  
|.....####.....########......|  #####   #     # ######     #    #     # 
|.....####...................|  #       ####### #     #    #    ####### 
|.....####...........###.....|  #       #     # #     #    #    #     # 
|....................###.....|  #       #     # ######    ###   #     # 
|....................###.....|                                          
|............................|                                          
+----------------------------+                                          

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 2.34.0


> 
> # 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 
 16.699   0.860  17.536 

Example timings

miRSM.Rcheck/miRSM-Ex.timings

nameusersystemelapsed
cor_binary0.2250.0140.239
miRSM0.2600.0060.267
module_CEA3.5270.0653.594
module_Coexpress2.9110.0842.997
module_FA0.0010.0000.000
module_GFA3.6040.1703.775
module_NMF3.7890.0763.867
module_ProNet0.1800.0020.182
module_Validate2.3000.0952.397
module_WGCNA1.4930.0191.511
module_biclust0.4260.0040.432
module_clust0.1330.0020.135
module_igraph0.1320.0020.135
module_miRdistribute2.2770.0662.347
module_miRsponge2.2660.0282.306
module_miRtarget2.2750.0652.344
share_miRs2.2250.0602.286