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CHECK report for miRLAB on malbec2

This page was generated on 2019-10-16 12:07:08 -0400 (Wed, 16 Oct 2019).

Package 1011/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRLAB 1.14.3
Thuc Duy Le
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/miRLAB
Branch: RELEASE_3_9
Last Commit: 0f05df0
Last Changed Date: 2019-07-14 20:41:43 -0400 (Sun, 14 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: miRLAB
Version: 1.14.3
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:miRLAB.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings miRLAB_1.14.3.tar.gz
StartedAt: 2019-10-16 03:13:58 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:19:05 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 306.3 seconds
RetCode: 0
Status:  OK 
CheckDir: miRLAB.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:miRLAB.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings miRLAB_1.14.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/miRLAB.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miRLAB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRLAB’ version ‘1.14.3’
* 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 ‘miRLAB’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK


Installation output

miRLAB.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL miRLAB
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘miRLAB’ ...
** using staged installation
** R
** inst
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miRLAB)

Tests output

miRLAB.Rcheck/tests/runTests.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-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.

> BiocGenerics:::testPackage("miRLAB")
Loading required package: amap


RUNIT TEST PROTOCOL -- Wed Oct 16 03:19:01 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
miRLAB RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 16.516   0.681  17.224 

Example timings

miRLAB.Rcheck/miRLAB-Ex.timings

nameusersystemelapsed
Borda0.0940.0000.105
BordaTopk0.0600.0030.064
Dcov0.0150.0040.018
Elastic0.0450.0000.045
Extopk0.0070.0000.007
GOBPenrichment0.0010.0000.001
Hoeffding0.020.000.02
IDA0.0380.0000.038
ImputeNormData0.0040.0040.008
KEGGenrichment000
Kendall0.0070.0000.007
Lasso0.0340.0000.034
MI0.1690.0000.169
Pearson0.0050.0000.005
ProMISe0.0060.0040.010
RDC0.070.000.07
Read0.0020.0000.002
ReadExtResult000
Spearman0.0070.0000.007
Standardise000
ValidateAll000
Validation0.0140.0000.015
ValidationT000
Zscore0.0120.0000.012
bRank0.0110.0000.011
convert0.0230.0000.023
filterAndCompare0.0000.0000.001
readHeader0.0010.0040.005