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CHECK report for marr on malbec1

This page was generated on 2021-05-06 12:28:08 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the marr package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1000/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
marr 1.00.03  (landing page)
Tusharkanti Ghosh
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/marr
Branch: RELEASE_3_12
Last Commit: a59d771
Last Changed Date: 2021-04-27 21:18:02 -0400 (Tue, 27 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: marr
Version: 1.00.03
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:marr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings marr_1.00.03.tar.gz
StartedAt: 2021-05-06 03:04:17 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:07:36 -0400 (Thu, 06 May 2021)
EllapsedTime: 199.5 seconds
RetCode: 0
Status:   OK  
CheckDir: marr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:marr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings marr_1.00.03.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/marr.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘marr’ version ‘1.00.03’
* 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 ‘marr’ 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 ‘testthat.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-3.12-bioc/meat/marr.Rcheck/00check.log’
for details.



Installation output

marr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL marr
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘marr’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c marrUtility.cpp -o marrUtility.o
marrUtility.cpp: In function ‘Rcpp::NumericVector getSS(Rcpp::NumericVector)’:
marrUtility.cpp:75:7: warning: variable ‘i’ set but not used [-Wunused-but-set-variable]
   int i=0;
       ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o marr.so RcppExports.o marrUtility.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-marr/00new/marr/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 (marr)

Tests output

marr.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(marr)
> 
> test_check("marr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 32.272   0.388  32.708 

Example timings

marr.Rcheck/marr-Ex.timings

nameusersystemelapsed
Marr-class0.6640.0120.678
Marr4.5160.0124.535
MarrAlpha0.1360.0000.137
MarrData0.1360.0040.143
MarrFeatureVars0.1360.0000.137
MarrFeatures0.1400.0000.141
MarrFeaturesfiltered0.1440.0000.144
MarrFilterData0.1880.0040.192
MarrPFeatures0.1760.0000.176
MarrPSamplepairs0.2320.0000.230
MarrPlotFeatures0.4920.0000.492
MarrPlotSamplepairs0.2760.0000.275
MarrProc0.1360.0000.139
MarrSamplepairs0.1440.0000.145
MarrSamplepairsfiltered0.1400.0000.142
msprepCOPD0.0200.0000.022