Fix URLs

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

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

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!