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This page was generated on 2021-10-23 15:51:47 -0400 (Sat, 23 Oct 2021).

CHECK results for PCHiCdata on nebbiolo2

To the developers/maintainers of the PCHiCdata package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 270/408HostnameOS / ArchINSTALLBUILDCHECK
PCHiCdata 1.21.1  (landing page)
Paula Freire-Pritchett
Snapshot Date: 2021-10-23 09:30:01 -0400 (Sat, 23 Oct 2021)
git_url: https://git.bioconductor.org/packages/PCHiCdata
git_branch: master
git_last_commit: e7a3a96
git_last_commit_date: 2021-08-11 10:29:24 -0400 (Wed, 11 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: PCHiCdata
Version: 1.21.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PCHiCdata.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PCHiCdata_1.21.1.tar.gz
StartedAt: 2021-10-23 12:34:19 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 12:35:54 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 95.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PCHiCdata.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PCHiCdata.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PCHiCdata_1.21.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/PCHiCdata.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PCHiCdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PCHiCdata’ version ‘1.21.1’
* 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 ‘PCHiCdata’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'PCHiCdata' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.14-data-experiment/meat/PCHiCdata.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 344.9Mb
  sub-directories of 1Mb or more:
    data     156.5Mb
    extdata  188.3Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
  LazyData DB of 156.4 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/PCHiCdata.Rcheck/00check.log’
for details.



Installation output

PCHiCdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL PCHiCdata
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘PCHiCdata’ ...
** using staged installation
** 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 from temporary location
Warning: Package 'PCHiCdata' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package can be loaded from final location
Warning: Package 'PCHiCdata' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package keeps a record of temporary installation path
* DONE (PCHiCdata)

Tests output

PCHiCdata.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(PCHiCdata)
Loading required package: Chicago
Loading required package: data.table

Welcome to CHiCAGO - version 1.21.0
If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").
NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")
Warning message:
Package 'PCHiCdata' is deprecated and will be removed from Bioconductor
  version 3.15 
> 
> test_check("PCHiCdata")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
  5.011   1.121   6.118 

Example timings

PCHiCdata.Rcheck/PCHiCdata-Ex.timings

nameusersystemelapsed
PCHiCdata-package0.0020.0000.002
sGM128781.6960.3842.059
smESC1.4350.4891.901