Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-11 12:05:55 -0400 (Mon, 11 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4323
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4136
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for BiocFileCache on tokay2


To the developers/maintainers of the BiocFileCache package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocFileCache.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 158/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocFileCache 2.2.1  (landing page)
Lori Shepherd
Snapshot Date: 2022-04-10 01:55:06 -0400 (Sun, 10 Apr 2022)
git_url: https://git.bioconductor.org/packages/BiocFileCache
git_branch: RELEASE_3_14
git_last_commit: cc91212
git_last_commit_date: 2022-01-20 09:21:33 -0400 (Thu, 20 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiocFileCache
Version: 2.2.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocFileCache.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocFileCache_2.2.1.tar.gz
StartedAt: 2022-04-10 16:22:18 -0400 (Sun, 10 Apr 2022)
EndedAt: 2022-04-10 16:26:09 -0400 (Sun, 10 Apr 2022)
EllapsedTime: 230.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocFileCache.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocFileCache.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocFileCache_2.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BiocFileCache.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocFileCache/DESCRIPTION' ... OK
* this is package 'BiocFileCache' version '2.2.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
BiocFileCache-class 6.53    0.2    6.87
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
BiocFileCache-class 8.59   0.11    9.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/BiocFileCache.Rcheck/00check.log'
for details.



Installation output

BiocFileCache.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BiocFileCache_2.2.1.tar.gz && rm -rf BiocFileCache.buildbin-libdir && mkdir BiocFileCache.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocFileCache.buildbin-libdir BiocFileCache_2.2.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BiocFileCache_2.2.1.zip && rm BiocFileCache_2.2.1.tar.gz BiocFileCache_2.2.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 50074  100 50074    0     0   314k      0 --:--:-- --:--:-- --:--:--  317k

install for i386

* installing *source* package 'BiocFileCache' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocFileCache'
    finding HTML links ... done
    BFCOption                               html  
    BiocFileCache-class                     html  
    makeBiocFileCacheFromDataFrame          html  
    makeCachedActiveBinding                 html  
** 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

install for x64

* installing *source* package 'BiocFileCache' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocFileCache' as BiocFileCache_2.2.1.zip
* DONE (BiocFileCache)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BiocFileCache' successfully unpacked and MD5 sums checked

Tests output

BiocFileCache.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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/13dc54de23bd_file13dc231f58b9 (stored 0%)
  adding: BiocFileCacheExport/BiocFileCache.sqlite (deflated 96%)
  adding: BiocFileCacheExport/file13dc231f58b9 (stored 0%)
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 254 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 254 ]
> 
> proc.time()
   user  system elapsed 
  57.56    1.51   65.25 

BiocFileCache.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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/20ec719d32be_file20ec76632a0f (stored 0%)
  adding: BiocFileCacheExport/BiocFileCache.sqlite (deflated 96%)
  adding: BiocFileCacheExport/file20ec76632a0f (stored 0%)
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 254 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 254 ]
> 
> proc.time()
   user  system elapsed 
  62.32    1.51   73.37 

Example timings

BiocFileCache.Rcheck/examples_i386/BiocFileCache-Ex.timings

nameusersystemelapsed
BFCOption000
BiocFileCache-class6.530.206.87
makeCachedActiveBinding0.010.000.02

BiocFileCache.Rcheck/examples_x64/BiocFileCache-Ex.timings

nameusersystemelapsed
BFCOption000
BiocFileCache-class8.590.119.06
makeCachedActiveBinding000