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CHECK report for DominoEffect on malbec1

This page was generated on 2019-04-16 11:53:19 -0400 (Tue, 16 Apr 2019).

Package 428/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DominoEffect 1.2.1
Marija Buljan
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/DominoEffect
Branch: RELEASE_3_8
Last Commit: f16db7f
Last Changed Date: 2019-02-22 09:30:08 -0400 (Fri, 22 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DominoEffect
Version: 1.2.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DominoEffect.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DominoEffect_1.2.1.tar.gz
StartedAt: 2019-04-15 23:34:35 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:40:34 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 359.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DominoEffect.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DominoEffect.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DominoEffect_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DominoEffect.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DominoEffect/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DominoEffect’ version ‘1.2.1’
* 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 ‘DominoEffect’ 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 ... NOTE
import_txdb: no visible binding for global variable ‘TXTYPE’
Undefined global functions or variables:
  TXTYPE
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
DominoEffect     3.456  0.164  18.324
GPo_of_hotspots  3.364  0.060  17.346
map_to_func_elem 2.792  0.072  19.235
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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-3.8-bioc/meat/DominoEffect.Rcheck/00check.log’
for details.



Installation output

DominoEffect.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DominoEffect
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘DominoEffect’ ...
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (DominoEffect)

Tests output

DominoEffect.Rcheck/tests/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> library(testthat)
> test_check("DominoEffect")
Loading required package: DominoEffect
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain' length 1421 bytes
==================================================
downloaded 1421 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes

trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain' length 655 bytes
==================================================
downloaded 655 bytes

================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes

================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain' length 1421 bytes
==================================================
downloaded 1421 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes

trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain' length 655 bytes
==================================================
downloaded 655 bytes

================================================================================
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 15 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 26.572   0.828  78.478 

Example timings

DominoEffect.Rcheck/DominoEffect-Ex.timings

nameusersystemelapsed
DominoEffect 3.456 0.16418.324
GPo_of_hotspots 3.364 0.06017.346
align_to_unip0.2600.0000.262
calculate_boundary000
identify_hotspots1.4840.0001.487
import_txdb000
map_to_func_elem 2.792 0.07219.235