- using R Under development (unstable) (2026-08-10 r90389 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.3.0
GNU Fortran (GCC) 14.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
* current time: 2026-08-12 00:08:27 UTC
- 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 hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'searchAnalyzeR' can be installed ... OK
See the install log for details.
- 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 ... [2s] OK
- checking whether the package can be loaded with stated dependencies ... [2s] OK
- checking whether the package can be unloaded cleanly ... [2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s] OK
- checking loading without being on the library search path ... [2s] 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 ... [13s] OK
- checking Rd files ... [2s] 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 ... [8s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [15s] OK
Running 'testthat.R' [15s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [41s] 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: 400
<?xml version="1.0" ?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2025//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_250101.dtd">
<PubmedArticleSet> }
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margin-bottom:0;
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color:#212121;
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padding:0;
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.usa-banner .usa-banner-header{
padding-top:0.55rem;
padding-bottom:0.55rem;
font-size:0.75rem;
font-weight:400;
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.usa-banner .usa-banner-header{
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.usa-banner .usa-banner-inner{
max-width:1040px;
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padding-right:1.5rem;
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.usa-banner .usa-banner-inner::after{
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padding-left:3rem;
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-ms-flex-align:center;
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border-bottom:1px solid #aeb0b5;
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padding-right:3rem;
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@media screen and (min-width: 481px){
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.usa-banner p{
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text-align:left;
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padding-top:0;
padding-left:4.0rem;
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display:block;
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.usa-banner .usa-banner-button:hover{
background-color:transparent;
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@media screen and (min-width: 481px){
.usa-banner .usa-accordion-button.usa-banner-button{
padding-top:0;
padding-left:0;
display:inline;
height:auto;
margin-left:3px;
position:relative;
vertical-align:middle;
width:auto;
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background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-down-primary.png");
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-down-primary.svg");
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background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-down-primary-hover.png");
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.usa-banner .usa-banner-button[aria-expanded=true]::after{
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background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/close.svg");
background-size:100%;
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.usa-banner .usa-banner-button[aria-expanded=true]{
height:initial;
padding:0;
position:relative;
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.usa-banner .usa-banner-button[aria-expanded=true]::after{
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-up-primary.png");
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-up-primary.svg");
background-size:100%;
content:'';
display:inline-block;
height:0.7rem;
width:0.7rem;
margin-left:0;
}
.usa-banner .usa-banner-button[aria-expanded=true]:hover::after{
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-up-primary-hover.png");
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-up-primary-hover.svg");
}
.usa-banner .usa-banner-button[aria-expanded=true]::after{
background-position-y:1px;
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}
.usa-banner .usa-banner-button[aria-expanded=true]::after{
position:absolute;
right:1.0rem;
top:1.15rem;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-button[aria-expanded=true]::after{
position:static;
}
}
.usa-banner .usa-banner-button[aria-expanded=true] .usa-banner-button-text{
display:none;
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@media screen and (min-width: 481px){
.usa-banner .usa-banner-button[aria-expanded=true] .usa-banner-button-text{
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marg
---
Backtrace:
▆
1. └─searchAnalyzeR::search_pubmed(...)
2. └─rentrez::entrez_fetch(...)
3. ├─base::do.call(make_entrez_query, args)
4. └─rentrez (local) `<fn>`(...)
5. └─rentrez:::entrez_check(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Comparing_Search_Strategies_with_searchAnalyzeR.Rmd' failed with diagnostics:
HTTP failure: 400
<?xml version="1.0" ?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2025//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_250101.dtd">
<PubmedArticleSet> }
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font-size:1.3rem;
padding-bottom:0;
}
}
.usa-banner .usa-accordion, .usa-banner .usa-accordion-bordered{
margin-top:0;
margin-bottom:0;
list-style-type:none;
padding-left:0;
color:#212121;
margin:0;
padding:0;
width:100%;
}
.usa-banner .usa-banner-header{
padding-top:0.55rem;
padding-bottom:0.55rem;
font-size:0.75rem;
font-weight:400;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-header{
padding-top:0;
padding-bottom:0;
}
}
.usa-banner .usa-banner-inner{
max-width:1040px;
margin-left:auto;
margin-right:auto;
padding-right:1.5rem;
padding-left:1.5rem;
}
.usa-banner .usa-banner-inner::after{
clear:both;
content:"";
display:block;
}
@media screen and (min-width: 951px){
.usa-banner .usa-banner-inner{
padding-right:3rem;
padding-left:3rem;
}
}
.usa-banner .usa-banner-header-expanded{
-ms-flex-align:center;
align-items:center;
border-bottom:1px solid #aeb0b5;
display:-ms-flexbox;
display:flex;
font-size:0.75rem;
min-height:0rem;
padding-right:3rem;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-header-expanded{
border-bottom:none;
display:block;
font-size:0.75rem;
font-weight:400;
min-height:0;
padding-right:0;
}
}
.usa-banner .usa-banner-header-expanded > .usa-banner-inner{
margin-left:0;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-header-expanded > .usa-banner-inner{
margin-left:auto;
}
}
.usa-banner .usa-section > :first-child,
.usa-banner .usa-grid > :first-child,
.usa-banner .usa-grid-full > :first-child{
margin-top:0;
}
.usa-banner .usa-section > :last-child,
.usa-banner .usa-grid > :last-child,
.usa-banner .usa-grid-full > :last-child{
margin-bottom:0;
}
.usa-banner img{
border:0;
}
.usa-banner img{
max-width:100%;
}
.usa-banner .usa-banner-header img{
float:left;
margin-right:1rem;
margin-top:1px;
width:1.5rem;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-header img{
margin-right:0.7rem;
width:1.3rem;
}
}
.usa-banner .usa-banner-header-expanded img{
margin-right:1rem;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-header-expanded img{
margin-right:0.7rem;
}
}
.usa-banner p{
line-height:1.5;
/*margin-bottom:1em;
margin-top:1em;*/
}
.usa-banner .usa-banner-header p{
margin-top:0;
margin-bottom:0;
display:inline;
overflow:hidden;
vertical-align:middle;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-header p{
margin-top:2px;
margin-bottom:2px;
display:inline-block;
}
}
.usa-banner .usa-banner-header-expanded p{
line-height:1.3;
vertical-align:top;
font-size: 0.95rem;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-header-expanded p{
line-height:1.5;
vertical-align:middle;
font-size: 0.75rem;
}
}
.usa-banner .usa-accordion-button.usa-banner-button{
background-color:transparent;
border:0;
border-radius:0;
font-weight:400;
margin:0;
padding:0;
text-align:left;
-webkit-font-smoothing:auto;
padding-top:0;
padding-left:4.0rem;
background-position-x:right;
color:#0071bc;
display:block;
font-size:0.7rem;
height:4.3rem;
left:0;
position:absolute;
text-decoration:underline;
top:0;
width:100%;
}
.usa-banner .usa-banner-button:hover{
background-color:transparent;
}
@media screen and (min-width: 481px){
.usa-banner .usa-accordion-button.usa-banner-button{
padding-top:0;
padding-left:0;
display:inline;
height:auto;
margin-left:3px;
position:relative;
vertical-align:middle;
width:auto;
}
}
.usa-banner .usa-accordion-button.usa-banner-button:hover{
color:#205493;
text-decoration:underline;
}
.usa-banner .usa-accordion-button.usa-banner-button[aria-expanded=false]{
background-image:none;
}
.usa-banner .usa-banner-button[aria-expanded=false]::after{
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-down-primary.png");
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-down-primary.svg");
background-size:100%;
content:'';
display:inline-block;
height:0.7rem;
width:0.7rem;
margin-left:0;
}
.usa-banner .usa-banner-button[aria-expanded=false]:hover::after{
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-down-primary-hover.png");
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-down-primary-hover.svg");
}
.usa-banner .usa-banner-button[aria-expanded=false]::after{
background-position-y:1px;
}
.usa-banner .usa-banner-button[aria-expanded=true]{
background-image:none;
height:3.1rem;
}
.usa-banner .usa-banner-button[aria-expanded=true]::after{
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/close.png");
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/close.svg");
background-size:100%;
content:'';
display:inline-block;
height:0.9rem;
width:0.9rem;
margin-left:0;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-button[aria-expanded=true]{
height:initial;
padding:0;
position:relative;
}
.usa-banner .usa-banner-button[aria-expanded=true]::after{
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-up-primary.png");
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-up-primary.svg");
background-size:100%;
content:'';
display:inline-block;
height:0.7rem;
width:0.7rem;
margin-left:0;
}
.usa-banner .usa-banner-button[aria-expanded=true]:hover::after{
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-up-primary-hover.png");
background-image:url("https://www.ncbi.nlm.nih.gov/style-guide/static/django_uswds/uswds/img/angle-arrow-up-primary-hover.svg");
}
.usa-banner .usa-banner-button[aria-expanded=true]::after{
background-position-y:1px;
}
}
.usa-banner .usa-banner-button[aria-expanded=true]::after{
position:absolute;
right:1.0rem;
top:1.15rem;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-button[aria-expanded=true]::after{
position:static;
}
}
.usa-banner .usa-banner-button[aria-expanded=true] .usa-banner-button-text{
display:none;
}
@media screen and (min-width: 481px){
.usa-banner .usa-banner-button[aria-expanded=true] .usa-banner-button-text{
display:inline;
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.usa-banner .usa-accordion-button{
background-color:transparent;
border:0;
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font-weight:400;
marg
--- failed re-building 'Comparing_Search_Strategies_with_searchAnalyzeR.Rmd'
--- re-building 'Real_PubMed_Search_Analysis_with_searchAnalyzeR.Rmd' using rmarkdown
--- finished re-building 'Real_PubMed_Search_Analysis_with_searchAnalyzeR.Rmd'
SUMMARY: processing the following file failed:
'Comparing_Search_Strategies_with_searchAnalyzeR.Rmd'
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [22s] OK
- checking HTML version of manual ... [5s] OK
- DONE
Status: 1 ERROR