From a182cc616f7e3149b566c2731b603f18ece25352 Mon Sep 17 00:00:00 2001 From: naja Date: Wed, 25 Aug 2021 17:45:40 +0200 Subject: [PATCH] Fix URLs --- R/epmc_db.r | 27 +++++++++++---------------- R/epmc_db_count.r | 26 ++++++++++---------------- cran-comments.md | 2 +- man/epmc_db.Rd | 26 ++++++++++---------------- man/epmc_db_count.Rd | 26 ++++++++++---------------- 5 files changed, 42 insertions(+), 65 deletions(-) diff --git a/R/epmc_db.r b/R/epmc_db.r index db5e781..5243680 100644 --- a/R/epmc_db.r +++ b/R/epmc_db.r @@ -4,32 +4,27 @@ #' Europe PMC RESTful Web Service. #' #' @inheritParams epmc_refs +#' #' @param db character, specify database: #' \describe{ -#' \item{'ARXPR'}{Array Express, a database of functional genomics experiments -#' \url{https://www.ebi.ac.uk/arrayexpress/}} +#' \item{'ARXPR'}{Array Express, a database of functional genomics experiments} #' \item{'CHEBI'}{a database and ontology of chemical entities of biological -#' interest \url{https://www.ebi.ac.uk/chebi/}} -#' \item{'CHEMBL'}{a database of bioactive drug-like small molecules -#' \url{https://www.ebi.ac.uk/chembldb/}} +#' interest} +#' \item{'CHEMBL'}{a database of bioactive drug-like small molecules} #' \item{'EMBL'}{now ENA, provides a comprehensive record of the world's -#' nucleotide sequencing information \url{https://www.ebi.ac.uk/ena/browser}} +#' nucleotide sequencing information} #' \item{'INTACT'}{provides a freely available, open -#' source database system and analysis tools for molecular interaction data -#' \url{https://www.ebi.ac.uk/intact/}} +#' source database system and analysis tools for molecular interaction data} #' \item{'INTERPRO'}{provides functional analysis of proteins by classifying -#' them into families and predicting domains and important sites -#' \url{https://www.ebi.ac.uk/interpro/}} +#' them into families and predicting domains and important sites} #' \item{'OMIM'}{a comprehensive and authoritative compendium of human genes and -#' genetic phenotypes \url{https://www.omim.org/about}} +#' genetic phenotypes} #' \item{'PDB'}{European resource for the collection, #' organisation and dissemination of data on biological macromolecular -#' structures \url{https://www.ebi.ac.uk/pdbe/}} +#' structures} #' \item{'UNIPROT'}{comprehensive and freely accessible -#' resource of protein sequence and functional information -#' \url{https://www.uniprot.org/}} -#' \item{'PRIDE'}{PRIDE Archive - proteomics data repository -#' \url{https://www.ebi.ac.uk/pride/archive/}}} +#' resource of protein sequence and functional information} +#' \item{'PRIDE'}{PRIDE Archive - proteomics data repository}} #' #' @return Cross-references as data.frame #' @examples diff --git a/R/epmc_db_count.r b/R/epmc_db_count.r index ffc3dca..661f189 100644 --- a/R/epmc_db_count.r +++ b/R/epmc_db_count.r @@ -6,30 +6,24 @@ #' @details Europe PMC supports cross-references between literature and the #' following databases: #' \describe{ -#' \item{'ARXPR'}{Array Express, a database of functional genomics experiments -#' \url{https://www.ebi.ac.uk/arrayexpress/}} +#' \item{'ARXPR'}{Array Express, a database of functional genomics experiments} #' \item{'CHEBI'}{a database and ontology of chemical entities of biological -#' interest \url{https://www.ebi.ac.uk/chebi/}} -#' \item{'CHEMBL'}{a database of bioactive drug-like small molecules -#' \url{https://www.ebi.ac.uk/chembldb/}} +#' interest} +#' \item{'CHEMBL'}{a database of bioactive drug-like small molecules} #' \item{'EMBL'}{now ENA, provides a comprehensive record of the world's -#' nucleotide sequencing information \url{https://www.ebi.ac.uk/ena/browser}} +#' nucleotide sequencing information} #' \item{'INTACT'}{provides a freely available, open -#' source database system and analysis tools for molecular interaction data -#' \url{https://www.ebi.ac.uk/intact/}} +#' source database system and analysis tools for molecular interaction data} #' \item{'INTERPRO'}{provides functional analysis of proteins by classifying -#' them into families and predicting domains and important sites -#' \url{https://www.ebi.ac.uk/interpro/}} +#' them into families and predicting domains and important sites} #' \item{'OMIM'}{a comprehensive and authoritative compendium of human genes and -#' genetic phenotypes \url{https://www.omim.org/about}} +#' genetic phenotypes} #' \item{'PDB'}{European resource for the collection, #' organisation and dissemination of data on biological macromolecular -#' structures \url{https://www.ebi.ac.uk/pdbe/}} +#' structures} #' \item{'UNIPROT'}{comprehensive and freely accessible -#' resource of protein sequence and functional information -#' \url{https://www.uniprot.org/}} -#' \item{'PRIDE'}{PRIDE Archive - proteomics data repository -#' \url{https://www.ebi.ac.uk/pride/archive/}}} +#' resource of protein sequence and functional information} +#' \item{'PRIDE'}{PRIDE Archive - proteomics data repository}} #' #' @param ext_id character, publication identifier #' @param data_src character, data source, by default Pubmed/MedLine index will diff --git a/cran-comments.md b/cran-comments.md index 05a17b4..e06393e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -23,7 +23,7 @@ Status: OK --- -This submission implements the most recent API changes. This will fix current R checks problems. +This submission implements the most recent API changes. This will fix current R checks problems. It will also prevent warnings and errors on CRAN when internet resource should fail. Thanks! diff --git a/man/epmc_db.Rd b/man/epmc_db.Rd index f9231d3..bcc3c5e 100644 --- a/man/epmc_db.Rd +++ b/man/epmc_db.Rd @@ -37,30 +37,24 @@ epmc_db( \item{db}{character, specify database: \describe{ -\item{'ARXPR'}{Array Express, a database of functional genomics experiments - \url{https://www.ebi.ac.uk/arrayexpress/}} +\item{'ARXPR'}{Array Express, a database of functional genomics experiments} \item{'CHEBI'}{a database and ontology of chemical entities of biological - interest \url{https://www.ebi.ac.uk/chebi/}} - \item{'CHEMBL'}{a database of bioactive drug-like small molecules - \url{https://www.ebi.ac.uk/chembldb/}} + interest} + \item{'CHEMBL'}{a database of bioactive drug-like small molecules} \item{'EMBL'}{now ENA, provides a comprehensive record of the world's - nucleotide sequencing information \url{https://www.ebi.ac.uk/ena/browser}} + nucleotide sequencing information} \item{'INTACT'}{provides a freely available, open - source database system and analysis tools for molecular interaction data - \url{https://www.ebi.ac.uk/intact/}} + source database system and analysis tools for molecular interaction data} \item{'INTERPRO'}{provides functional analysis of proteins by classifying - them into families and predicting domains and important sites - \url{https://www.ebi.ac.uk/interpro/}} + them into families and predicting domains and important sites} \item{'OMIM'}{a comprehensive and authoritative compendium of human genes and - genetic phenotypes \url{https://www.ncbi.nlm.nih.gov/omim}} + genetic phenotypes} \item{'PDB'}{European resource for the collection, organisation and dissemination of data on biological macromolecular - structures \url{https://www.ebi.ac.uk/pdbe/}} + structures} \item{'UNIPROT'}{comprehensive and freely accessible - resource of protein sequence and functional information - \url{https://www.uniprot.org/}} - \item{'PRIDE'}{PRIDE Archive - proteomics data repository - \url{https://www.ebi.ac.uk/pride/archive/}}}} + resource of protein sequence and functional information} + \item{'PRIDE'}{PRIDE Archive - proteomics data repository}}} \item{limit}{integer, number of results. By default, this function returns 100 records.} diff --git a/man/epmc_db_count.Rd b/man/epmc_db_count.Rd index 64a9bb3..a0f486e 100644 --- a/man/epmc_db_count.Rd +++ b/man/epmc_db_count.Rd @@ -23,30 +23,24 @@ publication. Europe PMC supports cross-references between literature and the following databases: \describe{ - \item{'ARXPR'}{Array Express, a database of functional genomics experiments - \url{https://www.ebi.ac.uk/arrayexpress/}} + \item{'ARXPR'}{Array Express, a database of functional genomics experiments} \item{'CHEBI'}{a database and ontology of chemical entities of biological - interest \url{https://www.ebi.ac.uk/chebi/}} - \item{'CHEMBL'}{a database of bioactive drug-like small molecules - \url{https://www.ebi.ac.uk/chembldb/}} + interest} + \item{'CHEMBL'}{a database of bioactive drug-like small molecules} \item{'EMBL'}{now ENA, provides a comprehensive record of the world's - nucleotide sequencing information \url{https://www.ebi.ac.uk/ena/browser}} + nucleotide sequencing information} \item{'INTACT'}{provides a freely available, open - source database system and analysis tools for molecular interaction data - \url{https://www.ebi.ac.uk/intact/}} + source database system and analysis tools for molecular interaction data} \item{'INTERPRO'}{provides functional analysis of proteins by classifying - them into families and predicting domains and important sites - \url{https://www.ebi.ac.uk/interpro/}} + them into families and predicting domains and important sites} \item{'OMIM'}{a comprehensive and authoritative compendium of human genes and - genetic phenotypes \url{https://www.ncbi.nlm.nih.gov/omim}} + genetic phenotypes} \item{'PDB'}{European resource for the collection, organisation and dissemination of data on biological macromolecular - structures \url{https://www.ebi.ac.uk/pdbe/}} + structures} \item{'UNIPROT'}{comprehensive and freely accessible - resource of protein sequence and functional information - \url{https://www.uniprot.org/}} - \item{'PRIDE'}{PRIDE Archive - proteomics data repository - \url{https://www.ebi.ac.uk/pride/archive/}}} + resource of protein sequence and functional information} + \item{'PRIDE'}{PRIDE Archive - proteomics data repository}} } \examples{ \dontrun{