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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings animalcules_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/animalcules.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘animalcules’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘animalcules-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_taxonomy
> ### Title: Find the taxonomy for unlimited tids
> ### Aliases: find_taxonomy
>
> ### ** Examples
>
> taxonLevels <- find_taxonomy(tids = 1200)
Error: HTTP failure: 400
Error: CEFetchPApplication::proxy_stream(): <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html>
<head>
<title>NCBI/portal105 - WWW Error 500 Diagnostic</title>
<style type="text/css">
h1.error {color: red; font-size: 40pt}
div.diags {text-indent: 0.5in }
</style>
</head>
<body>
<h1>Server Error</h1>
<p>Your request could not be processed due to a problem on
our Web server. This could be a transient problem, please
try the query again. If it doesn't clear up within a
reasonable period of time, e-mail a short description of your
query and th
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Error: CEFetchPApplication::proxy_stream(): <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html>
<head>
<title>NCBI/portal106 - WWW Error 500 Diagnostic</title>
<style type="text/css">
h1.error {color: red; font-size: 40pt}
div.diags {text-indent: 0.5in }
</style>
</head>
<body>
<h1>Server Error</h1>
<p>Your request could not be processed due to a problem on
our Web server. This could be a transient problem, please
try the query again. If it doesn't clear up within a
reasonable period of time, e-mail a short description of your
query and the diagnostic information shown below to:</p>
<p>
pubmed@nlm.nih.gov - for problems with PubMed<br/>
webadmin@ncbi.nlm.nih.gov - for problems with other services<br/>
</p>
<p>Thank you for your assistance. We will try to fix the
problem as soon as possible.
</p>
<hr/>
<p>
Diagnostic Information:</p>
<div class="diags">Error: 500</div>
<div class="diags">URL: h t t p : / / 1 3 0 . 1 4 . 2 2 . 5 8 / p o r t a l / p o r t a l . f c g i ? p l = E m a i l & a m p ; M o d e = e f e t c h & a m p ; p d e b u g o u t p u t = o f f & a m p ; d b = t a x o n o m y & a m p ; e m a i l = d a v i d . w i n t e r 4 0 g m a i l . c o m & a m p ; f o r m a t = x m l & a m p ; V i e w = x m l & a m p ; t o o l = r e n t r e z & a m p ; p a r t = h e a d e r & a m p ; n c b i _ s i d = 7 C E 5 B E 3 F C B C E 0 4 3 0 _ 8 D 2 7 S I D & a m p ; n c b i _ p h i d = 3 2 2 C 8 2 C 6 2 6 5 7 7 8 B 5 0 0 0 0 7 2 C 8 C 6 7 A 7 C E A . 1 . 1 . 1 </div>
<div class="diags">Client: 130.14.22.13</div>
<div class="diags">Server: portal106</div>
<div class="diags">Time: Wed Feb 5 18:06:48 EST 2025</div>
<p>
NOTE: The above is an internal URL which may differ from the one you used to address the page.</p>
<hr/>
<p>Rev. 01/04/08</p>
</body>
</html>
Backtrace:
▆
1. └─animalcules::find_taxonomy(1200) at test-examples.R:286:3
2. └─animalcules::find_taxonomy_300(tids)
3. └─rentrez::entrez_fetch(db = "taxonomy", id = tids, rettype = "xml")
4. ├─base::do.call(make_entrez_query, args)
5. └─rentrez (local) ``(...)
6. └─rentrez:::entrez_check(response)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 37 ]
Error: Test failures
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
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/animalcules.Rcheck/00check.log’
for details.