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CHECK report for BiocFileCache on malbec1

This page was generated on 2020-08-06 11:40:38 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiocFileCache PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 151/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocFileCache 1.13.1
Lori Shepherd
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocFileCache
Branch: master
Last Commit: c130b26
Last Changed Date: 2020-08-04 14:41:56 -0400 (Tue, 04 Aug 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocFileCache
Version: 1.13.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiocFileCache.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiocFileCache_1.13.1.tar.gz
StartedAt: 2020-08-06 02:45:51 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 02:47:22 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 91.4 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocFileCache.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiocFileCache.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiocFileCache_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiocFileCache.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocFileCache/DESCRIPTION’ ... OK
* this is package ‘BiocFileCache’ version ‘1.13.1’
* 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 ‘BiocFileCache’ 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
.get_all_web_rids: no visible binding for global variable ‘rtype’
.sql_clean_cache: no visible binding for global variable ‘rid’
.sql_clean_cache: no visible binding for global variable ‘access_time’
.sql_get_field: no visible binding for global variable ‘rid’
.sql_get_resource_table: no visible binding for global variable ‘rid’
.sql_get_resource_table: no visible binding for global variable ‘id’
Undefined global functions or variables:
  access_time id rid rtype
* 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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
BiocFileCache-class 4.996  0.032   5.104
* 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/BiocFileCache.Rcheck/00check.log’
for details.



Installation output

BiocFileCache.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BiocFileCache’ ...
** 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 (BiocFileCache)

Tests output

BiocFileCache.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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(BiocFileCache)
Loading required package: dbplyr
> 
> test_check("BiocFileCache")
  adding: BiocFileCacheExport/ (stored 0%)
  adding: BiocFileCacheExport/51b71a07ceec_file51b77d7f170b (stored 0%)
  adding: BiocFileCacheExport/BiocFileCache.sqlite (deflated 96%)
  adding: BiocFileCacheExport/file51b77d7f170b (stored 0%)
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 254 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 41.648   0.352  43.501 

Example timings

BiocFileCache.Rcheck/BiocFileCache-Ex.timings

nameusersystemelapsed
BiocFileCache-class4.9960.0325.104
makeCachedActiveBinding0.0040.0000.001