* using log directory ‘/Users/ripley/R/packages/tests-devel/searchAnalyzeR.Rcheck’
* using R Under development (unstable) (2026-11-03 r90835)
* using platform: aarch64-apple-darwin27.2.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.4.1.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Golden Gate 27.2
* using session charset: UTF-8
* current time: 2026-11-05 09:15:02 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘searchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘searchAnalyzeR’ version ‘0.1.0’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘searchAnalyzeR’ 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 use of S3 registration ... 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 installed files from ‘inst/doc’ ... 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 ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Comparing_Search_Strategies_with_searchAnalyzeR.Rmd’ using rmarkdown

Quitting from Comparing_Search_Strategies_with_searchAnalyzeR.Rmd:130-150 [execute_searches]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! HTTP failure: 500
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> 
<html>
<head>
<title>NCBI/eutils201 - 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 : / / e x t - h t t p - e u t i l s . l i n k e r d . n c b i . n l m . n i h . g o v / e n t r e z / e u t i l s / e s e a r c h . f c g i ? d b = p u b m e d & a m p ; t e r m =  2 8  2 0  2 2 c o v i d - 1 9  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 c o r o n a v i r u s  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 s a r s - c o v - 2  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 p a n d e m i c  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 c o v i d  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0  2 9  2 0 A N D  2 0  2 8  2 2 2 0 2 0  2 F 0 1  2 F 0 1  2 2  5 B D a t e  2 0 -  2 0 P u b l i c a t i o n  5 D  2 0  3 A  2 0  2 2 2 0 2 4  2 F 1 2  2 F 3 1  2 2  5 B D a t e  2 0 -  2 0 P u b l i c a t i o n  5 D  2 9  2 0 A N D  2 0 E n g l i s h  2 0  5 B L a n g u a g e  5 D & a m p ; r e t m o d e = x m l & a m p ; u s e h i s t o r y = y & a m p ; r e t m a x = 2 0 0 & 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 ; t o o l = r e n t r e z </div>

<div class="diags">Client: 130.14.22.147</div>

<div class="diags">Server: eutils201</div>

<div class="diags">Time: Thu Nov  5 04:15:43 EST 2026</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. └─searchAnalyzeR::search_pubmed(...)
 2.   └─rentrez::entrez_search(...)
 3.     └─rentrez:::make_entrez_query(...)
 4.       └─rentrez:::entrez_check(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Comparing_Search_Strategies_with_searchAnalyzeR.Rmd' failed with diagnostics:
HTTP failure: 500
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> 
<html>
<head>
<title>NCBI/eutils201 - 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 : / / e x t - h t t p - e u t i l s . l i n k e r d . n c b i . n l m . n i h . g o v / e n t r e z / e u t i l s / e s e a r c h . f c g i ? d b = p u b m e d & a m p ; t e r m =  2 8  2 0  2 2 c o v i d - 1 9  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 c o r o n a v i r u s  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 s a r s - c o v - 2  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 p a n d e m i c  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 c o v i d  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0  2 9  2 0 A N D  2 0  2 8  2 2 2 0 2 0  2 F 0 1  2 F 0 1  2 2  5 B D a t e  2 0 -  2 0 P u b l i c a t i o n  5 D  2 0  3 A  2 0  2 2 2 0 2 4  2 F 1 2  2 F 3 1  2 2  5 B D a t e  2 0 -  2 0 P u b l i c a t i o n  5 D  2 9  2 0 A N D  2 0 E n g l i s h  2 0  5 B L a n g u a g e  5 D & a m p ; r e t m o d e = x m l & a m p ; u s e h i s t o r y = y & a m p ; r e t m a x = 2 0 0 & 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 ; t o o l = r e n t r e z </div>

<div class="diags">Client: 130.14.22.147</div>

<div class="diags">Server: eutils201</div>

<div class="diags">Time: Thu Nov  5 04:15:43 EST 2026</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>

--- failed re-building ‘Comparing_Search_Strategies_with_searchAnalyzeR.Rmd’

--- re-building ‘Real_PubMed_Search_Analysis_with_searchAnalyzeR.Rmd’ using rmarkdown

Quitting from Real_PubMed_Search_Analysis_with_searchAnalyzeR.Rmd:106-117 [execute-search]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! HTTP failure: 500
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> 
<html>
<head>
<title>NCBI/eutils201 - 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 : / / e x t - h t t p - e u t i l s . l i n k e r d . n c b i . n l m . n i h . g o v / e n t r e z / e u t i l s / e s e a r c h . f c g i ? d b = p u b m e d & a m p ; t e r m =  2 8  2 0  2 2 l o n g  2 0 c o v i d  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 p o s t - c o v i d  2 0 s y n d r o m e  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 c o v i d - 1 9  2 0 s e q u e l a e  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 p o s t - a c u t e  2 0 c o v i d - 1 9  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 p e r s i s t e n t  2 0 c o v i d  2 0 s y m p t o m s  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0  2 9  2 0 A N D  2 0  2 8  2 2 2 0 2 0  2 F 0 1  2 F 0 1  2 2  5 B D a t e  2 0 -  2 0 P u b l i c a t i o n  5 D  2 0  3 A  2 0  2 2 2 0 2 4  2 F 1 2  2 F 3 1  2 2  5 B D a t e  2 0 -  2 0 P u b l i c a t i o n  5 D  2 9  2 0 A N D  2 0 E n g l i s h  2 0  5 B L a n g u a g e  5 D & a m p ; r e t m o d e = x m l & a m p ; u s e h i s t o r y = y & a m p ; r e t m a x = 1 5 0 & 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 ; t o o l = r e n t r e z </div>

<div class="diags">Client: 130.14.19.0</div>

<div class="diags">Server: eutils201</div>

<div class="diags">Time: Thu Nov  5 04:15:45 EST 2026</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. └─searchAnalyzeR::search_pubmed(...)
 2.   └─rentrez::entrez_search(...)
 3.     └─rentrez:::make_entrez_query(...)
 4.       └─rentrez:::entrez_check(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Real_PubMed_Search_Analysis_with_searchAnalyzeR.Rmd' failed with diagnostics:
HTTP failure: 500
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> 
<html>
<head>
<title>NCBI/eutils201 - 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 : / / e x t - h t t p - e u t i l s . l i n k e r d . n c b i . n l m . n i h . g o v / e n t r e z / e u t i l s / e s e a r c h . f c g i ? d b = p u b m e d & a m p ; t e r m =  2 8  2 0  2 2 l o n g  2 0 c o v i d  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 p o s t - c o v i d  2 0 s y n d r o m e  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 c o v i d - 1 9  2 0 s e q u e l a e  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 p o s t - a c u t e  2 0 c o v i d - 1 9  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0 O R  2 0  2 2 p e r s i s t e n t  2 0 c o v i d  2 0 s y m p t o m s  2 2  5 B T i t l e  2 F A b s t r a c t  5 D  2 0  2 9  2 0 A N D  2 0  2 8  2 2 2 0 2 0  2 F 0 1  2 F 0 1  2 2  5 B D a t e  2 0 -  2 0 P u b l i c a t i o n  5 D  2 0  3 A  2 0  2 2 2 0 2 4  2 F 1 2  2 F 3 1  2 2  5 B D a t e  2 0 -  2 0 P u b l i c a t i o n  5 D  2 9  2 0 A N D  2 0 E n g l i s h  2 0  5 B L a n g u a g e  5 D & a m p ; r e t m o d e = x m l & a m p ; u s e h i s t o r y = y & a m p ; r e t m a x = 1 5 0 & 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 ; t o o l = r e n t r e z </div>

<div class="diags">Client: 130.14.19.0</div>

<div class="diags">Server: eutils201</div>

<div class="diags">Time: Thu Nov  5 04:15:45 EST 2026</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>

--- failed re-building ‘Real_PubMed_Search_Analysis_with_searchAnalyzeR.Rmd’

SUMMARY: processing the following files failed:
  ‘Comparing_Search_Strategies_with_searchAnalyzeR.Rmd’
  ‘Real_PubMed_Search_Analysis_with_searchAnalyzeR.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/searchAnalyzeR.Rcheck/00check.log’
for details.

       48.44 real        37.27 user         8.91 sys