CODEWITHSUNDEEP
rpubmedpubmed-api
Başak Uysal
Başak Uysal

Reputation: 21

Rismed R package fails to run EUtilsGet function

I'm using the Rismed package to make s search query for the word "hsv".

search_topic_hsv <- "HSV"
search_query_hsv <- EUtilsSummary(search_topic_hsv, retmax= 27000, mindate= 1970, maxdate= 2022)

summary(search_query_hsv)   #returns to 26149

records_hsv <- EUtilsGet(search_query_hsv)

EutilsGet functions gives this error:

Error in readLines(collapse(EUtilsFetch, "&retmode=xml"), warn = FALSE,  : 
  cannot read from connection
In addition: Warning message:
In readLines(collapse(EUtilsFetch, "&retmode=xml"), warn = FALSE,  :
  URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=35245365,35243667,35243023,35241838,35240194,35239848,35230726,35229412,35228129,35225980,35225036,35223260,35217873,35216177,35215908,35215799,35214758,35214644,35212944,35208817,35208572,35206263,35205731,35204477,35201702,35202955,35202734,35202567,35201013,35200997,35200729,35200645,35199176,35199165,35198914,35198826,35197947,35197285,35196784,35193038,35187895,35187000,35186664,35185822,35182142,35180012,35179120,35178081,35176987,35175220,35172828,35168095,35167501,35167411,35165387,35164537,35163675,35163086,35161988,35157734,35155582,35154980,35154946,35154584,35150885,35146210,35145504,35144835,35144523,35143960,35142052,35141364,35141210,35141072,35130299,35126336,35121324,35120255,35119473,35119328,35115776,35114961,35114414,35112018,35111489,35110532,35107381,35106980,35106191,35105326,35105322,35103749,35102178,35101046,35100650,35100323,35099587,35097177,35087520,35085968,35083659,35082770,350825 [... truncated]

is this a pubmed connection related issue or package related issue?

packageVersion("RISmed") [1] ‘2.3.0’

Thanks in advance.

Upvotes: 2

Views: 197

Answers (1)

song
song

Reputation: 1

records_hsv <- EUtilsGet(search_query_hsv)

you can try to resolve this trouble by change '<-' to '='.

Upvotes: 0

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