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CHECK report for srnadiff on malbec2

This page was generated on 2020-10-17 11:55:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE srnadiff PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1730/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
srnadiff 1.8.2
Zytnicki Matthias
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/srnadiff
Branch: RELEASE_3_11
Last Commit: 3eb715d
Last Changed Date: 2020-10-13 05:48:40 -0400 (Tue, 13 Oct 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  TIMEOUT  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: srnadiff
Version: 1.8.2
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings srnadiff_1.8.2.tar.gz
StartedAt: 2020-10-17 05:48:50 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:57:48 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 538.0 seconds
RetCode: 0
Status:  OK 
CheckDir: srnadiff.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings srnadiff_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/srnadiff.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘srnadiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘srnadiff’ version ‘1.8.2’
* 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 ‘srnadiff’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.9Mb
    libs      3.3Mb
* 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 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 (user + system) or elapsed time > 5s
                            user system elapsed
plotRegions               13.410  0.824  13.104
parameters                11.899  1.324  11.034
countMatrix               11.773  1.449  11.847
srnadiffDefaultParameters  7.766  0.807   7.223
srnadiff                   5.725  0.757   5.290
regions                    5.706  0.654   5.268
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/srnadiff.Rcheck/00check.log’
for details.



Installation output

srnadiff.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL srnadiff
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘srnadiff’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_hmm.cpp -o rcpp_hmm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_ir.cpp -o rcpp_ir.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_main.cpp -o rcpp_main.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpp_utils.cpp -o rcpp_utils.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c srnadiff_init.c -o srnadiff_init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o srnadiff.so RcppExports.o rcpp_hmm.o rcpp_ir.o rcpp_main.o rcpp_utils.o srnadiff_init.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-srnadiff/00new/srnadiff/libs
** 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
** 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 (srnadiff)

Tests output

srnadiff.Rcheck/tests/testthat.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-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(srnadiff)
> 
> test_check("srnadiff")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 30 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 97.310   8.405  98.427 

Example timings

srnadiff.Rcheck/srnadiff-Ex.timings

nameusersystemelapsed
annotReg0.1460.0000.165
bamFiles0.1890.0000.190
chromosomeSizes0.0130.0000.012
countMatrix11.773 1.44911.847
coverages0.0810.0000.082
normFactors0.0170.0030.020
parameters11.899 1.32411.034
plotRegions13.410 0.82413.104
readAnnotation1.1610.0041.177
regions5.7060.6545.268
sampleInfo0.0140.0000.013
srnadiff5.7250.7575.290
srnadiffDefaultParameters7.7660.8077.223
srnadiffExample0.0220.0000.022
srnadiffExp2.1330.0442.177