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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:biocViews.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biocViews_1.74.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biocViews.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biocViews/DESCRIPTION’ ... OK
* this is package ‘biocViews’ version ‘1.74.0’
* 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 ‘biocViews’ 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 code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘tools:::vignetteInfo’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘tools:::.build_news_db_from_package_NEWS_Rd’
  ‘tools:::.build_news_db_from_package_NEWS_md’
  ‘tools:::.build_repository_package_db’
  ‘tools:::.expand_package_description_db_R_fields’
  ‘tools:::.get_standard_repository_db_fields’
  ‘tools:::.news_reader_default’ ‘tools:::.read_description’
  ‘tools:::.split_dependencies’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dump_concept: no visible binding for global variable ‘biocViewsVocab’
getPackageNEWS : getNews: no visible binding for global variable
  ‘Version’
getReverseDepends : <anonymous>: no visible binding for global variable
  ‘Package’
Undefined global functions or variables:
  Package Version biocViewsVocab
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘biocViews-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: recommendPackages
> ### Title: Recommend Packages using existing biocViews.
> ### Aliases: recommendPackages
> 
> ### ** Examples
> 
>     recommendPackages(c("clustering", "classification"))
Warning in readLines(con) :
  URL 'http://bioconductor.org/js/versions.js': status was 'Server returned nothing (no headers, no data)'
Error in readLines(con) : 
  cannot open the connection to 'http://bioconductor.org/js/versions.js'
Calls: recommendPackages -> .getBioCDevelUrl -> readLines
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  ERROR in test_recommendPackages: Error in readLines(con) : 
    cannot open the connection to 'http://bioconductor.org/js/versions.js'
  
  Test files with failing tests
  
     test_biocViews.R 
       test_recommendPackages 
  
  
  Error in BiocGenerics:::testPackage("biocViews") : 
    unit tests failed for package biocViews
  In addition: Warning message:
  In untar(tarball, tpaths, exdir = tmpdir) :
    '/usr/bin/gtar -xf '/home/biocbuild/tmp/RtmpMYlvXH/testing/testrepos/src/contrib/biocViews_1.74.0.tar.gz' -C '/home/biocbuild/tmp/RtmpMYlvXH' 'biocViews/DESCRIPTION' 'biocViews/inst/CITATION'' returned error code 2
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/biocViews.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL biocViews
###
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* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘biocViews’ ...
** using staged installation
** R
** data
** 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 (biocViews)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

> BiocGenerics:::testPackage("biocViews")
Timing stopped at: 0.074 19.55 63.85
Error in readLines(con) : 
  cannot open the connection to 'http://bioconductor.org/js/versions.js'
In addition: Warning message:
In readLines(con) :
  URL 'https://bioconductor.org/js/versions.js': status was 'SSL connect error'
Generate citation for /home/biocbuild/tmp/RtmpMYlvXH/testing/testrepos/src/contrib/biocViews2_1.74.0.tar.gz ... (try to process CITATION file) OK
Generate citation for /home/biocbuild/tmp/RtmpMYlvXH/testing/testrepos/src/contrib/biocViews_1.74.0.tar.gz ... /usr/bin/gtar: biocViews/inst/CITATION: Not found in archive
/usr/bin/gtar: Exiting with failure status due to previous errors
(auto-generate from DESCRIPTION file) OK


RUNIT TEST PROTOCOL -- Tue Jan 21 05:07:09 2025 
*********************************************** 
Number of test functions: 5 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
biocViews RUnit Tests - 5 test functions, 1 error, 0 failures
ERROR in test_recommendPackages: Error in readLines(con) : 
  cannot open the connection to 'http://bioconductor.org/js/versions.js'

Test files with failing tests

   test_biocViews.R 
     test_recommendPackages 


Error in BiocGenerics:::testPackage("biocViews") : 
  unit tests failed for package biocViews
In addition: Warning message:
In untar(tarball, tpaths, exdir = tmpdir) :
  '/usr/bin/gtar -xf '/home/biocbuild/tmp/RtmpMYlvXH/testing/testrepos/src/contrib/biocViews_1.74.0.tar.gz' -C '/home/biocbuild/tmp/RtmpMYlvXH' 'biocViews/DESCRIPTION' 'biocViews/inst/CITATION'' returned error code 2
Execution halted