From 884f5b90f3fcd0de2a80c2f64fb7e5bddf78a0ff Mon Sep 17 00:00:00 2001 From: stitam Date: Wed, 30 Sep 2020 14:39:01 +0200 Subject: [PATCH 1/9] Add startup message --- R/zzz.R | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 R/zzz.R diff --git a/R/zzz.R b/R/zzz.R new file mode 100644 index 00000000..8a992f94 --- /dev/null +++ b/R/zzz.R @@ -0,0 +1,4 @@ +.onAttach <- function(libname, pkgname) { + packageStartupMessage("Help us improve the package") + packageStartupMessage("Fill out our 2020 survey at https://forms.gle/V7dfGGn73dkesn5L6") +} \ No newline at end of file From 93ff82508356ca240f6da06ab802f93d829237e0 Mon Sep 17 00:00:00 2001 From: stitam Date: Wed, 30 Sep 2020 23:43:33 +0200 Subject: [PATCH 2/9] Remove authors from function documentation --- R/alanwood.R | 2 -- R/chebi.R | 4 ---- R/chemspider.R | 16 ---------------- R/cir.R | 2 -- R/cts.R | 4 ---- R/etox.R | 6 ------ R/flavornet.R | 1 - R/pan.R | 1 - R/pubchem.R | 7 ------- R/srs.R | 1 - R/utils.R | 8 -------- R/wikidata.R | 3 --- 12 files changed, 55 deletions(-) diff --git a/R/alanwood.R b/R/alanwood.R index 62906932..3fb8e5aa 100644 --- a/R/alanwood.R +++ b/R/alanwood.R @@ -20,7 +20,6 @@ #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' \dontrun{ @@ -176,7 +175,6 @@ aw_query <- function(query, from = c("name", "cas"), verbose = TRUE, #' @param force_build logical; force building a new index? #' @return a data.frame #' @seealso \code{\link{aw_query}}, \code{\link{tempdir}} -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @source \url{http://www.alanwood.net/pesticides} #' @noRd build_aw_idx <- function(verbose = TRUE, force_build = FALSE) { diff --git a/R/chebi.R b/R/chebi.R index ae64c58d..20c30eaf 100644 --- a/R/chebi.R +++ b/R/chebi.R @@ -55,7 +55,6 @@ #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Andreas Scharmüller, \email{andschar@@protonmail.com} #' @export #' @examples #' \donttest{ @@ -230,7 +229,6 @@ get_chebiid <- function(query, #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Andreas Scharmüller, \email{andschar@@protonmail.com} #' @export #' @examples #' \donttest{ @@ -354,7 +352,6 @@ chebi_comp_entity <- function(chebiid, verbose = TRUE, ...) { #' @param x list; a list to bind into a data.frame #' @return a data.frame #' @seealso \code{\link{chebi_comp_entity}} -#' @author Andreas Scharmüller, \email{andschar@@protonmail.com} #' @noRd #' l2df <- function(x) { @@ -373,7 +370,6 @@ l2df <- function(x) { #' https://stackoverflow.com/questions/17308551/do-callrbind-list-for-uneven-number-of-column #' @param x list; a list to bind into a data.frame #' @seealso \code{\link{l2df}} -#' @author Andreas Scharmüller, \email{andschar@@protonmail.com} #' @noRd #' rbind_named_fill <- function(x) { diff --git a/R/chemspider.R b/R/chemspider.R index a45241c1..e8caeaca 100644 --- a/R/chemspider.R +++ b/R/chemspider.R @@ -44,7 +44,6 @@ cs_check_key <- function() { #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions #' can be found at \url{https://developer.rsc.org/terms}. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @export #' @examples #' \dontrun{ @@ -101,7 +100,6 @@ cs_datasources <- function(apikey = NULL) { #' The controls that are available for a given function are indicated within the #' documentation of the function. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @seealso \code{\link{get_csid}} #' @export #' @examples @@ -161,8 +159,6 @@ cs_control <- function(datasources = vector(), #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @importFrom httr POST add_headers http_status #' @importFrom jsonlite toJSON #' @importFrom tibble enframe @@ -243,7 +239,6 @@ get_csid <- function(query, #' for an API key. #' Please respect the Terms & conditions \url{https://developer.rsc.org/terms}. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @noRd cs_query_csid <- function(postres, headers) { query_id <- jsonlite::fromJSON(rawToChar(postres$content))$queryId @@ -315,7 +310,6 @@ cs_query_csid <- function(postres, headers) { #' for an API key. Please respect the Terms & conditions #' \url{https://developer.rsc.org/terms}. #' @references https://developer.rsc.org/compounds-v1/apis -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @note This is a low level function and is not exported. #' @examples #' \dontrun{ @@ -364,7 +358,6 @@ cs_name_csid <- function(name, apikey = NULL, control = cs_control()) { #' for an API key. Please respect the Terms & conditions #' \url{https://developer.rsc.org/terms}. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @note This is a low level function and is not exported. #' @examples #' \dontrun{ @@ -409,7 +402,6 @@ cs_formula_csid <- function(formula, apikey = NULL, control = cs_control()) { #' for an API key. Please respect the Terms & conditions #' \url{https://developer.rsc.org/terms}. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @note This is a low level function and is not exported. #' @examples #' \dontrun{ @@ -451,7 +443,6 @@ cs_smiles_csid <- function(smiles, apikey = NULL) { #' for an API key. Please respect the Terms & conditions #' \url{https://developer.rsc.org/terms}. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @note This is a low level function and is not exported. #' @examples #' \dontrun{ @@ -495,7 +486,6 @@ cs_inchi_csid <- function(inchi, apikey = NULL) { #' for an API key. Please respect the Terms & conditions #' \url{https://developer.rsc.org/terms}. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @note This is a low level function and is not exported. #' @examples #' \dontrun{ @@ -550,7 +540,6 @@ cs_inchikey_csid <- function(inchikey, apikey = NULL) { #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions #' can be found at \url{https://developer.rsc.org/terms}. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @seealso This is a low level function and is not exported. See #' \code{\link{cs_convert}} for the top level function. #' @seealso \code{\link{parse_mol}} @@ -618,8 +607,6 @@ cs_convert_multiple <- function(input, from, to, apikey = NULL) { #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @export #' @examples #' \dontrun{ @@ -710,7 +697,6 @@ cs_convert <- function(query, from, to, apikey = NULL) { #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions #' can be found at \url{https://developer.rsc.org/terms}. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @export #' @examples #' \dontrun{ @@ -772,7 +758,6 @@ cs_compinfo <- function(csid, fields, apikey = NULL) { #' for a security token. #' Please respect the Terms & conditions #' \url{https://www.rsc.org/help-legal/legal/terms-conditions/}. -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @seealso \code{\link{get_csid}} to retrieve ChemSpider IDs, #' \code{\link{cs_compinfo}} for extended compound information. #' @note use \code{\link{cs_compinfo}} to retrieve standard inchikey. @@ -850,7 +835,6 @@ use 'cs_commpinfo()' instead.") #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions #' can be found at \url{https://developer.rsc.org/terms}. #' @references \url{https://developer.rsc.org/compounds-v1/apis} -#' @author Tamas Stirling, \email{stirling.tamas@@gmail.com} #' @seealso \code{\link{get_csid}}, \code{\link{cs_check_key}} #' @importFrom httr GET add_headers message_for_status content #' @importFrom jsonlite fromJSON diff --git a/R/cir.R b/R/cir.R index fb26d368..b3c2456e 100644 --- a/R/cir.R +++ b/R/cir.R @@ -96,7 +96,6 @@ #' \url{http://cactus.nci.nih.gov/blog/?p=1386}, \cr #' \url{http://cactus.nci.nih.gov/blog/?p=1456}, \cr #' -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' #' @examples #' \donttest{ @@ -234,7 +233,6 @@ cir_query <- function(identifier, representation = "smiles", #' \url{http://cactus.nci.nih.gov/blog/?p=1386}, \cr #' \url{http://cactus.nci.nih.gov/blog/?p=1456}, \cr #' -#' @author Andreas Scharmueller, \email{andschar@@protonmail.com} #' #' @examples #' \donttest{ diff --git a/R/cts.R b/R/cts.R index 26fb6e50..54444244 100644 --- a/R/cts.R +++ b/R/cts.R @@ -10,7 +10,6 @@ #' @param inchikey deprecated #' @return a list of lists (for each supplied inchikey): #' a list of 7. inchikey, inchicode, molweight, exactmass, formula, synonyms and externalIds -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' #' @references Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service #' -- a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648. @@ -97,7 +96,6 @@ cts_compinfo <- function(query, from = "inchikey", verbose = TRUE, inchikey){ #' @param verbose logical; should a verbose output be printed on the console? #' @param ... currently not used. #' @return a list of character vectors or if \code{choices} is used, then a single named vector. -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @details See also \url{http://cts.fiehnlab.ucdavis.edu/} #' for possible values of from and to. #' @@ -205,7 +203,6 @@ cts_convert <- function(query, #' @import jsonlite #' @param verbose logical; should a verbose output be printed on the console? #' @return a character vector. -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @details See also \url{http://cts.fiehnlab.ucdavis.edu/services} #' #' @seealso \code{\link{cts_convert}} @@ -242,7 +239,6 @@ cts_from <- function(verbose = TRUE){ #' @import jsonlite #' @param verbose logical; should a verbose output be printed on the console? #' @return a character vector. -#' @author Eduard Szoecs, \email{eduardszoecs@@gmail.com} #' @details See also \url{http://cts.fiehnlab.ucdavis.edu/services} #' #' @seealso \code{\link{cts_convert}} diff --git a/R/etox.R b/R/etox.R index b5592046..8fa6971f 100644 --- a/R/etox.R +++ b/R/etox.R @@ -27,9 +27,6 @@ #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} -#' @author Andreas Scharmüller, \email{andschar@@protonmail.com} #' @export #' @examples #' \dontrun{ @@ -159,7 +156,6 @@ get_etoxid <- function(query, #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' \dontrun{ @@ -286,7 +282,6 @@ etox_basic <- function(id, verbose = TRUE) { #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' \dontrun{ @@ -386,7 +381,6 @@ etox_targets <- function(id, verbose = TRUE) { #' @seealso \code{\link{get_etoxid}} to retrieve ETOX IDs, \code{\link{etox_basic}} for basic information, #' \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results #' -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' \dontrun{ diff --git a/R/flavornet.R b/R/flavornet.R index 273f844c..f9198f93 100644 --- a/R/flavornet.R +++ b/R/flavornet.R @@ -13,7 +13,6 @@ #' #' @return A named character vector containing flavor percepts or NA's in the case of CAS numbers that are not found #' -#' @author Eric Scott, \email{eric.scott@@tufts.edu} #' #' @examples #' \dontrun{ diff --git a/R/pan.R b/R/pan.R index 76e7107d..ebd5753e 100644 --- a/R/pan.R +++ b/R/pan.R @@ -49,7 +49,6 @@ #' Fresh Water Guidelines (ug/L); Salt Water Guidelines (ug/L); #' Irrigation Water Guidelines (ug/L); Livestock Water Guidelines (ug/L); #' Chemical Name; matching synonym; source URL -#' @author Eduard Szoecs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' \dontrun{ diff --git a/R/pubchem.R b/R/pubchem.R index 02e2321e..a7ae5b9b 100644 --- a/R/pubchem.R +++ b/R/pubchem.R @@ -72,8 +72,6 @@ #' \url{https://pubchemdocs.ncbi.nlm.nih.gov/programmatic-access}, and the data #' usage policies of the indicidual data sources #' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}. -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @import httr #' @importFrom purrr map map2 #' @importFrom jsonlite fromJSON @@ -277,7 +275,6 @@ get_cid <- #' @param ... currently not used. #' #' @return a data.frame -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @seealso \code{\link{get_cid}}, \code{\link{pc_sect}} #' @references Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public #' Information System for @@ -436,7 +433,6 @@ pc_prop <- function(cid, properties = NULL, verbose = TRUE, ...) { #' \url{https://pubchemdocs.ncbi.nlm.nih.gov/programmatic-access}, and the data #' usage policies of the indicidual data sources #' \url{https://pubchem.ncbi.nlm.nih.gov/sources/}. -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' \donttest{ @@ -541,7 +537,6 @@ pc_synonyms <- function(query, #' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic #' access to chemical annotations integrated in PubChem. J Cheminform 11, 56 #' (2019). https://doi.org/10.1186/s13321-019-0375-2. -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @seealso \code{\link{get_cid}}, \code{\link{pc_prop}} #' @examples #' # might fail if API is not available @@ -594,7 +589,6 @@ pc_sect <- function(id, #' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic #' access to chemical annotations integrated in PubChem. J Cheminform 11, 56 #' (2019). https://doi.org/10.1186/s13321-019-0375-2. -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @examples #' # might fail if API is not available #' \donttest{ @@ -674,7 +668,6 @@ pc_page <- function(id, #' @references Kim, S., Thiessen, P.A., Cheng, T. et al. PUG-View: programmatic #' access to chemical annotations integrated in PubChem. J Cheminform 11, 56 #' (2019). https://doi.org/10.1186/s13321-019-0375-2. -#' @author Tamás Stirling, \email{stirling.tamas@@gmail.com} #' @examples #' # might fail if API is not available #' \donttest{ diff --git a/R/srs.R b/R/srs.R index d1f4c4a0..fb266b5a 100644 --- a/R/srs.R +++ b/R/srs.R @@ -13,7 +13,6 @@ #' categoryClass, kingdomCode, iupacName, pubChemId, molecularWeight, #' molecularFormula, inchiNotation, smilesNotation, classifications, #' characteristics, synonyms, casNumbers, taxonomicSerialNumbers, relationships -#'@author Gordon Getzinger, \email{gjg3@@duke.edu} #'@export #' #' @examples diff --git a/R/utils.R b/R/utils.R index e40fdd34..8dcb5757 100644 --- a/R/utils.R +++ b/R/utils.R @@ -22,7 +22,6 @@ #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' is.inchikey('BQJCRHHNABKAKU-KBQPJGBKSA-N') @@ -53,7 +52,6 @@ is.inchikey = function(x, type = c('format', 'chemspider'), verbose = TRUE) { #' @return a logical #' #' @seealso \code{\link{is.inchikey}} for a pure-R implementation. -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' \donttest{ @@ -118,7 +116,6 @@ is.inchikey_cs <- function(x, verbose = TRUE){ #' @return a logical #' #' @seealso \code{\link{is.inchikey}} for a pure-R implementation. -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' \donttest{ @@ -194,7 +191,6 @@ is.inchikey_format = function(x, verbose = TRUE) { #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical #' Information from the Web. Journal of Statistical Software, 93(13). #' . -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' #' @export #' @examples @@ -275,8 +271,6 @@ is.cas <- function(x, verbose = TRUE) { #' #' @note This function can handle only one SMILES string. #' -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} -#' #' @references Egon Willighagen (2015). How to test SMILES strings in #' Supplementary Information. #' \url{https://chem-bla-ics.blogspot.nl/2015/10/how-to-test-smiles-strings-in.html} @@ -339,7 +333,6 @@ extr_num <- function(x) { #' 1 = first atom, 2 = second atom, t = bond type, s = stereo type, x = not #' used, r = bond typology, c = reacting center status. #' -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @references Grabner, M., Varmuza, K., & Dehmer, M. (2012). RMol: #' a toolset for transforming SD/Molfile structure information into R objects. #' Source Code for Biology and Medicine, 7, 12. @@ -383,7 +376,6 @@ parse_mol <- function(string) { #' @return character vector of valid CAS numbers #' @seealso \code{\link{is.cas}} #' @export -#' @author Eric Scott, \email{scottericr@@gmail.com} #' @examples #' x = c(58082, 123456, "hexenol") #' as.cas(x) diff --git a/R/wikidata.R b/R/wikidata.R index 8f3012d0..ed00bf1d 100644 --- a/R/wikidata.R +++ b/R/wikidata.R @@ -17,8 +17,6 @@ #' #' @note Only matches in labels are returned. #' -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} -#' #' @import jsonlite httr #' @importFrom stats rgamma #' @importFrom utils URLencode URLdecode @@ -144,7 +142,6 @@ get_wdid <- #' Mitraka, Elvira, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, et al. 2015 #' Wikidata: A Platform for Data Integration and Dissemination for the Life Sciences and beyond. bioRxiv: 031971. #' -#' @author Eduard Szöcs, \email{eduardszoecs@@gmail.com} #' @export #' @examples #' \dontrun{ From 2f9b3a0a69e73cea60f4f0e93a7b2b777915d1d5 Mon Sep 17 00:00:00 2001 From: stitam Date: Wed, 30 Sep 2020 23:52:21 +0200 Subject: [PATCH 3/9] Remove contributors and PRs from NEWS.md --- NEWS.md | 63 ++++++++++++++++++++++++++++----------------------------- 1 file changed, 31 insertions(+), 32 deletions(-) diff --git a/NEWS.md b/NEWS.md index 30e8c735..0778f573 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,10 @@ # webchem (development version) -# webchem 1.0.0.9010 +# webchem 1.1.0. ## NEW FEATURES -* Download images of substances from Chemical Identifier Resolver (CIR) with `cir_img()` [contributed by @andschar]. +* Download images of substances from Chemical Identifier Resolver (CIR) with `cir_img()`. * Download images of substances from ChemSpider with `cs_img()` * `find_db()` checks if a query gets a hit in most databases integrated in webchem. Useful for deciding which of several databases to focus on given a set of chemicals. @@ -29,7 +29,7 @@ * get_cid() now can search by registry IDs (e.g. CAS RN), and can handle more complex requests like searching for similar compounds. * Retrieve chemical data from PubChem content pages with pc_sect(). -* get_etoxid() now can search by CAS, EC, GSBL and RTECS numbers. Added `from = ` argument. [PR #241, added by @andschar] +* get_etoxid() now can search by CAS, EC, GSBL and RTECS numbers. Added `from = ` argument. * nist_ri() now can search by name, InChI, InChIKey, or CAS. The `cas` argument is deprecated. Use `query` instead with `from = "cas"` ## MINOR IMPROVEMENTS @@ -43,10 +43,10 @@ * nist_ri() returned malformed tables or errored if there was only one entry for a query * get_csid() now returns all csids when queried from formula -* get_csid() returned an error when query was NA [PR #226, fixed by stitam] -* get_chebiid() and chebi_comp_entity() fixed for invalid queries [PR #225, fixed by stitam] -* get_cid() returned the PubChem ID of sodium when the query was NA [PR #223, fixed by stitam] -* aw_query() returned a list for successful queries, NA for unsuccessful queries [PR #222, fixed by stitam] +* get_csid() returned an error when query was NA +* get_chebiid() and chebi_comp_entity() fixed for invalid queries +* get_cid() returned the PubChem ID of sodium when the query was NA +* aw_query() returned a list for successful queries, NA for unsuccessful queries ## DEPRECATED FUNCTIONS @@ -57,10 +57,10 @@ ## NEW FEATURES -* Retrieve data from ChEBI (https://www.ebi.ac.uk/chebi/) webservice with get_chebiid() and chebi_comp_entity(). ChEBI comprises a rich data base on chemicals with bilogical interest [contributed by @andschar]. -* Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri() [PR #154, contributed by @Aariq] -* Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query() [PR #179] -* "first" argument in cts_convert() and cir_query() and "interactive" argument in pc_synonyms() deprecated. Use "choices" instead to return either a list of all results, only the first result, or an interactive menu to choose a result to return. [contributed by @Aariq] +* Retrieve data from ChEBI (https://www.ebi.ac.uk/chebi/) webservice with get_chebiid() and chebi_comp_entity(). ChEBI comprises a rich data base on chemicals with bilogical interest. +* Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri() +* Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query() +* "first" argument in cts_convert() and cir_query() and "interactive" argument in pc_synonyms() deprecated. Use "choices" instead to return either a list of all results, only the first result, or an interactive menu to choose a result to return. * ChemSpider functions now look for an API token stored in .Renviron or .Rprofile by default so you can keep them hidden more easily. ## MINOR IMPROVEMENTS @@ -70,14 +70,14 @@ ## BUG FIXES -* cs_prop() failed with duplicated return values [issue #148, reported and fixed by @stanstrup] -* pp_query() failed when compound present, but no properties [issue #151, reported and fixed by @stanstrup] -* ci_query() failed when missing table [issue #196, reported and fixed by @gjgetzinger] -* get_csid() failed because of a major change in the ChemSpider API [issue #149, PR #165, contributed by @stitam] -* multiple functions failed because of a major change in the ChemSpider API [issue #149, contributed by @stitam] -* cir_query() mistook NA for sodium [issue #158, reported and fixed by @Aariq] -* fixed functions that communicate with the ChemSpider API [issue #149, issue #160, fixed by @stitam] -* get_etoxid() printed incorrect results for certain match types [issue #201, fixed by @stitam] +* cs_prop() failed with duplicated return values +* pp_query() failed when compound present, but no properties +* ci_query() failed when missing table +* get_csid() failed because of a major change in the ChemSpider API +* multiple functions failed because of a major change in the ChemSpider API +* cir_query() mistook NA for sodium +* fixed functions that communicate with the ChemSpider API +* get_etoxid() printed incorrect results for certain match types ## DEPRECATED FUNCTIONS @@ -97,13 +97,13 @@ ## BUG FIXES -* extr_num() did not work properly with decimal numbers [issue #136, reported and fixed by @stanstrup] -* cs_prop() failed when epi-suite data was not available [issue #139, reported and fixed by @stanstrup] -* cs_prop() failed with invalid html [issue #138, reported and fixed by @stanstrup] -* cs_prop() gave incorrect answer, if entries were not available [issue #142, reported and fixed by @stanstrup] -* cs_prop() did not parse scientific number correctly [issue #143, reported by @stanstrup, fixed by @EDiLD] -* is.smiles() failed because of changes in rcdk [PR #140, reported and fixed by @allaway] -* cir_query() failed with identifiers containing spaces (e.g. 'acetic acid') [issue #146, reported by Lars Nielsen] +* extr_num() did not work properly with decimal numbers +* cs_prop() failed when epi-suite data was not available +* cs_prop() failed with invalid html +* cs_prop() gave incorrect answer, if entries were not available +* cs_prop() did not parse scientific number correctly +* is.smiles() failed because of changes in rcdk +* cir_query() failed with identifiers containing spaces (e.g. 'acetic acid') * several other functions failed with identifiers containing spaces & returned wrong distance. ## DEPRECATED FUNCTIONS @@ -119,13 +119,12 @@ ## MINOR IMPROVEMENTS * cs_prop() now also return experimental data for Boiling and Melting Points. -* pc_synonyms gained an argument 'interactive' to enter an interactive mode for - selecting synonyms [issue #129, requested by @Aariq] +* pc_synonyms gained an argument 'interactive' to enter an interactive mode for selecting synonyms * cts_convert now returns NA if no matches are found. ## BUG FIXES -* cs_prop() failed with some CSIDs [isse #127, reported by @Aariq] +* cs_prop() failed with some CSIDs * wd_ident() failed if multiple entries where found. Now returns the first hit only. * ci_query() did not return fully cleaned smiles and inchi @@ -139,7 +138,7 @@ ## NEW FEATURES -* fn_percept() extracts flavor percepts using CAS numbers from www.flavornet.org. Flavornet is a database of 738 compounds with human-detectible odors. [contributed by @Aariq] +* fn_percept() extracts flavor percepts using CAS numbers from www.flavornet.org. Flavornet is a database of 738 compounds with human-detectible odors. ## MINOR IMPROVEMENTS @@ -163,7 +162,7 @@ ## BUG FIXES * pc_prop() returned to many rows if last cid supplied was NA -* Switched to https for NCBI, chemspider & chemid (Issue #120, reported by @jranke) +* Switched to https for NCBI, chemspider & chemid * get_wdid() failed if non-ascii characters where returned by wikipedia * rcdk:parse.smiles() now returns NA if a SMILES string could not be parsed. => broke is.smiles @@ -332,7 +331,7 @@ The new ppdb_parse() parses only a html, but does not interact with the database ## BUG FIXES -* Correct the spelling of Alan Wood and rename function allanwood() to alanwood() [contribution of @jranke] +* Correct the spelling of Alan Wood and rename function allanwood() to alanwood() From 7b5b25e0b8cf5f569ccd1d1c9ac6983dd9ecdbcf Mon Sep 17 00:00:00 2001 From: stitam Date: Wed, 30 Sep 2020 23:59:15 +0200 Subject: [PATCH 4/9] If bullet is more than a function name, it ends with full stop --- NEWS.md | 152 ++++++++++++++++++++++++++++---------------------------- 1 file changed, 76 insertions(+), 76 deletions(-) diff --git a/NEWS.md b/NEWS.md index 0778f573..4bb8e968 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,17 +5,17 @@ ## NEW FEATURES * Download images of substances from Chemical Identifier Resolver (CIR) with `cir_img()`. -* Download images of substances from ChemSpider with `cs_img()` +* Download images of substances from ChemSpider with `cs_img()`. * `find_db()` checks if a query gets a hit in most databases integrated in webchem. Useful for deciding which of several databases to focus on given a set of chemicals. ## MINOR IMPROVEMENTS * Most functions now use httr::RETRY() to access webservices. * Verbose messages are now harmonized. -* The `"type"` argument in `ci_query()` and `aw_query()` has been changed to `"from"` for consistency with other functions -* `fn_percept()` and `cts_compinfo()` now have `"query"` and `"from"` arguments for consistency with other functions -* Possible values for `"from"` have been made more consistent across functions -* `pc_synonyms()`, `cts_convert()`, `cir_query()` have been changed to use the `match` argument instead of `choices` for consistency with other functions +* The `"type"` argument in `ci_query()` and `aw_query()` has been changed to `"from"` for consistency with other functions. +* `fn_percept()` and `cts_compinfo()` now have `"query"` and `"from"` arguments for consistency with other functions. +* Possible values for `"from"` have been made more consistent across functions. +* `pc_synonyms()`, `cts_convert()`, `cir_query()` have been changed to use the `match` argument instead of `choices` for consistency with other functions. * `get_etoxid()` output changed slightly so that the matched chemical name string no longer includes the etoxid in parentheses. * `is.cas()` is now vectorized. @@ -30,23 +30,23 @@ * get_cid() now can search by registry IDs (e.g. CAS RN), and can handle more complex requests like searching for similar compounds. * Retrieve chemical data from PubChem content pages with pc_sect(). * get_etoxid() now can search by CAS, EC, GSBL and RTECS numbers. Added `from = ` argument. -* nist_ri() now can search by name, InChI, InChIKey, or CAS. The `cas` argument is deprecated. Use `query` instead with `from = "cas"` +* nist_ri() now can search by name, InChI, InChIKey, or CAS. The `cas` argument is deprecated. Use `query` instead with `from = "cas"`. ## MINOR IMPROVEMENTS -* all `get_*()` functions now output tibbles with a column for the query and a column for the retrieved ID -* changes to arguments in `get_*()` functions to make them more consistent +* all `get_*()` functions now output tibbles with a column for the query and a column for the retrieved ID. +* changes to arguments in `get_*()` functions to make them more consistent. * aw_idx.rda is no longer included in the package as a data set. Instead, it is built by build_aw_idx() to tempdir(). ## BUG FIXES -* nist_ri() returned malformed tables or errored if there was only one entry for a query -* get_csid() now returns all csids when queried from formula -* get_csid() returned an error when query was NA -* get_chebiid() and chebi_comp_entity() fixed for invalid queries -* get_cid() returned the PubChem ID of sodium when the query was NA -* aw_query() returned a list for successful queries, NA for unsuccessful queries +* nist_ri() returned malformed tables or errored if there was only one entry for a query. +* get_csid() now returns all csids when queried from formula. +* get_csid() returned an error when query was NA. +* get_chebiid() and chebi_comp_entity() fixed for invalid queries. +* get_cid() returned the PubChem ID of sodium when the query was NA. +* aw_query() returned a list for successful queries, NA for unsuccessful queries. ## DEPRECATED FUNCTIONS @@ -58,8 +58,8 @@ ## NEW FEATURES * Retrieve data from ChEBI (https://www.ebi.ac.uk/chebi/) webservice with get_chebiid() and chebi_comp_entity(). ChEBI comprises a rich data base on chemicals with bilogical interest. -* Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri() -* Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query() +* Retrieve retention indices from NIST (https://webbook.nist.gov) with nist_ri(). +* Get record details from US EPA Substance Registry Services (https://cdxnodengn.epa.gov/cdx-srs-rest/) with srs_query(). * "first" argument in cts_convert() and cir_query() and "interactive" argument in pc_synonyms() deprecated. Use "choices" instead to return either a list of all results, only the first result, or an interactive menu to choose a result to return. * ChemSpider functions now look for an API token stored in .Renviron or .Rprofile by default so you can keep them hidden more easily. @@ -70,14 +70,14 @@ ## BUG FIXES -* cs_prop() failed with duplicated return values -* pp_query() failed when compound present, but no properties -* ci_query() failed when missing table -* get_csid() failed because of a major change in the ChemSpider API -* multiple functions failed because of a major change in the ChemSpider API -* cir_query() mistook NA for sodium -* fixed functions that communicate with the ChemSpider API -* get_etoxid() printed incorrect results for certain match types +* cs_prop() failed with duplicated return values. +* pp_query() failed when compound present, but no properties. +* ci_query() failed when missing table. +* get_csid() failed because of a major change in the ChemSpider API. +* multiple functions failed because of a major change in the ChemSpider API. +* cir_query() mistook NA for sodium. +* fixed functions that communicate with the ChemSpider API. +* get_etoxid() printed incorrect results for certain match types. ## DEPRECATED FUNCTIONS @@ -97,13 +97,13 @@ ## BUG FIXES -* extr_num() did not work properly with decimal numbers -* cs_prop() failed when epi-suite data was not available -* cs_prop() failed with invalid html -* cs_prop() gave incorrect answer, if entries were not available -* cs_prop() did not parse scientific number correctly -* is.smiles() failed because of changes in rcdk -* cir_query() failed with identifiers containing spaces (e.g. 'acetic acid') +* extr_num() did not work properly with decimal numbers. +* cs_prop() failed when epi-suite data was not available. +* cs_prop() failed with invalid html. +* cs_prop() gave incorrect answer, if entries were not available. +* cs_prop() did not parse scientific number correctly. +* is.smiles() failed because of changes in rcdk. +* cir_query() failed with identifiers containing spaces (e.g. 'acetic acid'). * several other functions failed with identifiers containing spaces & returned wrong distance. ## DEPRECATED FUNCTIONS @@ -119,14 +119,14 @@ ## MINOR IMPROVEMENTS * cs_prop() now also return experimental data for Boiling and Melting Points. -* pc_synonyms gained an argument 'interactive' to enter an interactive mode for selecting synonyms +* pc_synonyms gained an argument 'interactive' to enter an interactive mode for selecting synonyms. * cts_convert now returns NA if no matches are found. ## BUG FIXES -* cs_prop() failed with some CSIDs +* cs_prop() failed with some CSIDs. * wd_ident() failed if multiple entries where found. Now returns the first hit only. -* ci_query() did not return fully cleaned smiles and inchi +* ci_query() did not return fully cleaned smiles and inchi. ## DEPRECATED FUNCTIONS @@ -154,16 +154,16 @@ ## NEW FEATURES -* added ping_pubchem() to check whether pubchem is up & running -* added cs_web_ping () to check whether the chemspider webpage is functional +* added ping_pubchem() to check whether pubchem is up & running. +* added cs_web_ping () to check whether the chemspider webpage is functional. ## MINOR IMPROVEMENTS -* updated allan wood index +* updated allan wood index. ## BUG FIXES -* pc_prop() returned to many rows if last cid supplied was NA -* Switched to https for NCBI, chemspider & chemid -* get_wdid() failed if non-ascii characters where returned by wikipedia +* pc_prop() returned to many rows if last cid supplied was NA. +* Switched to https for NCBI, chemspider & chemid. +* get_wdid() failed if non-ascii characters where returned by wikipedia. * rcdk:parse.smiles() now returns NA if a SMILES string could not be parsed. => broke is.smiles @@ -184,14 +184,14 @@ ## MINOR IMPROVEMENTS -* rewrite of pubchem functions using PUG-REST -* chemspider: better use of NA in input (=return NA) -* more robust matching in get_etoxid +* rewrite of pubchem functions using PUG-REST. +* chemspider: better use of NA in input (=return NA). +* more robust matching in get_etoxid. ## BUG FIXES -* pan_query() did not return numeric values -* get_cid() failed with multiple results +* pan_query() did not return numeric values. +* get_cid() failed with multiple results. ## DEPRECATED FUNCTIONS @@ -199,7 +199,7 @@ ## DEFUNCT FUNCTIONS * ppdb_query() has been removed due to copyright issues. -The new ppdb_parse() parses only a html, but does not interact with the database +The new ppdb_parse() parses only a html, but does not interact with the database. * pan() * alanwood() * get_cid() @@ -217,16 +217,16 @@ The new ppdb_parse() parses only a html, but does not interact with the database * get_wdid() and wd_indent() to retrieve information from wikidata. * get_etoxid() can handle multi inputs (interactive mode, best match, first match, NA and all matches). * ci_query() can handle multi inputs (interactive mode, best match, first match and NA). -* cs_prop() queries predcitions (ACD and EPiSuite) from ChemSpider +* cs_prop() queries predictions (ACD and EPiSuite) from ChemSpider. ## MINOR IMPROVEMENTS * webchem uses exclusively xml2 (instead of XML). -* All function return source_url for (micro-)attribution of sources +* All function return source_url for (micro-)attribution of sources. * cs_compinfo(): names of returned list changed. * cs_extcompinfo(): - - names of returned list changed - - result is numeric where appropriate + - names of returned list changed. + - result is numeric where appropriate. * cir(): result is numeric where appropriate. * unified naming scheme of functions. * is.inchikey_cs() has been integrated into is.inchikey(). @@ -245,12 +245,12 @@ The new ppdb_parse() parses only a html, but does not interact with the database ## DEPRECATED FUNCTIONS -* pan_query() replaces pan() -* aw_query() replaces alanwood() -* get_pcid() replaces get_cid() -* pc_compinfo() replaces cid_compinfo() -* ci_query() replaces chemid() -* pp_query() replaces physprop() +* pan_query() replaces pan(). +* aw_query() replaces alanwood(). +* get_pcid() replaces get_cid(). +* pc_compinfo() replaces cid_compinfo(). +* ci_query() replaces chemid(). +* pp_query() replaces physprop(). ## DEFUNCT FUNCTIONS @@ -269,24 +269,24 @@ The new ppdb_parse() parses only a html, but does not interact with the database * is.inchikey() and is.cas() to check if a string is valid inchikey or CAS registry number. * parse_mol(): A simple molfile parser. * Functions to work with ChemSpider InChI API: - + cs_csid_mol() : convert csid to mol - + cs_inchikey_csid() : convert inchikey to csid - + cs_inchikey_inchi() : convert inchikey to inchi - + cs_inchikey_mol() : convert inchikey to Molfile - + cs_inchi_csid() : convert inchi to csid - + cs_inchi_inchikey : convert inchi to inchikey - + cs_inchi_mol() : convert inchi to molfile - + cs_inchi_smiles() : convert inchi to smiles - + cs_smiles_inchi() : convert smiles to inchi - + These are all wrapped into cs_convert() - + is.inchikey_cs() : Check via ChemSpider if inchikey is valid + + cs_csid_mol() : convert csid to mol. + + cs_inchikey_csid() : convert inchikey to csid. + + cs_inchikey_inchi() : convert inchikey to inchi. + + cs_inchikey_mol() : convert inchikey to Molfile. + + cs_inchi_csid() : convert inchi to csid. + + cs_inchi_inchikey : convert inchi to inchikey. + + cs_inchi_mol() : convert inchi to molfile. + + cs_inchi_smiles() : convert inchi to smiles. + + cs_smiles_inchi() : convert smiles to inchi. + + These are all wrapped into cs_convert(). + + is.inchikey_cs() : Check via ChemSpider if inchikey is valid. * webchem has now a zenodo doi, please cite if you use it. ## MINOR IMPROVEMENTS * cts_compinfo() checks if input is a inchikey (via exported function is.inchikey()). -* cts_compinfo() is now more robust and verbose, if problems are encountered +* cts_compinfo() is now more robust and verbose, if problems are encountered. * alanwood() returns separate inchi and ichikeys in case of isomers. * alanwood() returns also subactvity (e.g. $Fluazinam$activity [1] "fungicides" and $Fluazinam$subactivity [1] "pyridine fungicides"). * physprop() also returns boiling and melting points. Moreover, values are now numeric. @@ -294,17 +294,17 @@ The new ppdb_parse() parses only a html, but does not interact with the database ## BUG FIXES -* alanwood() returns only results for first match in case of multiple links found +* alanwood() returns only results for first match in case of multiple links found. * physprop() stopped working after change of SRC to https, fixed now. -* changed etox_* functions to https +* changed etox_* functions to https. ## DEPRECATED FUNCTIONS * ppdb() replaces ppdb_query() and accepts individual index as created by ppdb_buildidx(). * cir() replaces cir_query(). -* cs_compinfo() replaces csid_compinfo() -* cs_extcompinfo() replaces csid_extcompinfo() +* cs_compinfo() replaces csid_compinfo(). +* cs_extcompinfo() replaces csid_extcompinfo(). ## DEFUNCT FUNCTIONS @@ -322,16 +322,16 @@ The new ppdb_parse() parses only a html, but does not interact with the database * Query SRC PHYSPROP Database with physprop(). * Query the ETOX ID with get_etoxid(); query basic information with etox_basic(); quality targets with etox_targets() and test results with etox_tests(). -* Query PPDB with ppdb_query() +* Query PPDB with ppdb_query(). ## MINOR IMPROVEMENTS -* added exceptions/checks to tests -* improved robustness of cir_query() +* added exceptions/checks to tests. +* improved robustness of cir_query(). ## BUG FIXES -* Correct the spelling of Alan Wood and rename function allanwood() to alanwood() +* Correct the spelling of Alan Wood and rename function allanwood() to alanwood(). From 54ac62f9c2a295c22e769f900b5d1395fef142c8 Mon Sep 17 00:00:00 2001 From: stitam Date: Thu, 1 Oct 2020 09:13:06 +0200 Subject: [PATCH 5/9] Fix typo in fn_percept() --- R/flavornet.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/flavornet.R b/R/flavornet.R index f9198f93..41f98766 100644 --- a/R/flavornet.R +++ b/R/flavornet.R @@ -1,7 +1,7 @@ #' Retrieve flavor percepts from www.flavornet.org #' #' Retreive flavor percepts from \url{http://www.flavornet.org}. Flavornet is a database of 738 compounds with odors -#' perceptible to humans detected using gas chromatography ofactometry (GCO). +#' perceptible to humans detected using gas chromatography olfactometry (GCO). #' #' @import xml2 #' @importFrom stats rgamma From b4436f0c9ccdb76752f5d270e1724886e5f0cea9 Mon Sep 17 00:00:00 2001 From: stitam Date: Thu, 1 Oct 2020 09:28:23 +0200 Subject: [PATCH 6/9] Update codemeta.json --- .Rbuildignore | 1 + codemeta.json | 113 +++++++++++++++++++++++++++++++++++++++++++++++--- 2 files changed, 109 insertions(+), 5 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 5846b589..47aa47de 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -25,3 +25,4 @@ README_cache ^\.github$ codemeta.json +^codemeta\.json$ diff --git a/codemeta.json b/codemeta.json index 27c1af15..9c258b15 100644 --- a/codemeta.json +++ b/codemeta.json @@ -1,14 +1,20 @@ { - "@context": ["https://doi.org/10.5063/schema/codemeta-2.0", "http://schema.org"], + "@context": [ + "https://doi.org/10.5063/schema/codemeta-2.0", + "http://schema.org" + ], "@type": "SoftwareSourceCode", "identifier": "webchem", "description": "Chemical information from around the web. This package interacts \n with a suite of web services for chemical information. Sources include: Alan\n Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,\n ChEBI, Chemical Translation Service, ChemIDplus, ChemSpider, ETOX,\n Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,\n SRS, Wikidata.", "name": "webchem: Chemical Information from the Web", "codeRepository": "https://github.com/ropensci/webchem", - "relatedLink": ["https://docs.ropensci.org/webchem", "https://CRAN.R-project.org/package=webchem"], + "relatedLink": [ + "https://docs.ropensci.org/webchem", + "https://CRAN.R-project.org/package=webchem" + ], "issueTracker": "https://github.com/ropensci/webchem/issues", "license": "https://spdx.org/licenses/MIT", - "version": "1.0.0", + "version": "1.0.0.9001", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -153,6 +159,18 @@ "url": "https://cran.r-project.org" }, "sameAs": "https://CRAN.R-project.org/package=rmarkdown" + }, + { + "@type": "SoftwareApplication", + "identifier": "plot.matrix", + "name": "plot.matrix", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=plot.matrix" } ], "softwareRequirements": [ @@ -286,9 +304,94 @@ "url": "https://cran.r-project.org" }, "sameAs": "https://CRAN.R-project.org/package=tibble" + }, + { + "@type": "SoftwareApplication", + "identifier": "base64enc", + "name": "base64enc", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=base64enc" + }, + { + "@type": "SoftwareApplication", + "identifier": "rlang", + "name": "rlang", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=rlang" } ], "readme": "https://github.com/ropensci/webchem/blob/master/README.md", - "fileSize": "349.763KB", - "keywords": ["rstats", "ropensci", "chemical-information", "webscraping", "cas-number", "chemspider", "identifier", "r", "r-package"] + "fileSize": "0KB", + "keywords": [ + "rstats", + "ropensci", + "chemical-information", + "webscraping", + "cas-number", + "chemspider", + "identifier", + "r", + "r-package" + ], + "releaseNotes": "https://github.com/ropensci/webchem/blob/master/NEWS.md", + "contIntegration": "https://codecov.io/gh/ropensci/webchem/branch/master", + "citation": [ + { + "@type": "ScholarlyArticle", + "datePublished": "2020", + "author": [ + { + "@type": "Person", + "givenName": "Eduard", + "familyName": "Sz\\\"ocs" + }, + { + "@type": "Person", + "givenName": "Tam\\'as", + "familyName": "Stirling", + "email": "stirling.tamas@gmail.com" + }, + { + "@type": "Person", + "givenName": ["Eric", "R."], + "familyName": "Scott" + }, + { + "@type": "Person", + "givenName": "Andreas", + "familyName": "Scharm\\\"uller" + }, + { + "@type": "Person", + "givenName": ["Ralf", "B."], + "familyName": "Sch\\\"afer" + } + ], + "name": "{webchem}: An {R} Package to Retrieve Chemical Information from the {W}eb", + "identifier": "10.18637/jss.v093.i13", + "pagination": "1--17", + "@id": "https://doi.org/10.18637/jss.v093.i13", + "sameAs": "https://doi.org/10.18637/jss.v093.i13", + "isPartOf": { + "@type": "PublicationIssue", + "issueNumber": "13", + "datePublished": "2020", + "isPartOf": { + "@type": ["PublicationVolume", "Periodical"], + "volumeNumber": "93", + "name": "Journal of Statistical Software" + } + } + } + ] } From f0383958d70028856fac64304476e6390c9666dd Mon Sep 17 00:00:00 2001 From: stitam Date: Thu, 1 Oct 2020 09:32:46 +0200 Subject: [PATCH 7/9] Update DESCRIPTION --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 07e10f74..27dd6a6e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,8 +7,8 @@ Description: Chemical information from around the web. This package interacts Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem, SRS, Wikidata. Type: Package -Version: 1.0.0.9001 -Date: 2020-05-27 +Version: 1.1.0 +Date: 2020-10-01 License: MIT + file LICENSE URL: https://docs.ropensci.org/webchem, https://github.com/ropensci/webchem BugReports: https://github.com/ropensci/webchem/issues From 12f771ae3298c0167c1c6c1785c21e1804f0bf55 Mon Sep 17 00:00:00 2001 From: stitam Date: Thu, 1 Oct 2020 09:33:21 +0200 Subject: [PATCH 8/9] Regenerate function documentation --- man/as.cas.Rd | 3 --- man/aw_query.Rd | 3 --- man/chebi_comp_entity.Rd | 3 --- man/cir_img.Rd | 3 --- man/cir_query.Rd | 3 --- man/cs_compinfo.Rd | 3 --- man/cs_control.Rd | 3 --- man/cs_convert.Rd | 5 ----- man/cs_datasources.Rd | 3 --- man/cs_extcompinfo.Rd | 3 --- man/cs_img.Rd | 3 --- man/cts_compinfo.Rd | 3 --- man/cts_convert.Rd | 3 --- man/cts_from.Rd | 3 --- man/cts_to.Rd | 3 --- man/etox_basic.Rd | 3 --- man/etox_targets.Rd | 3 --- man/etox_tests.Rd | 3 --- man/fn_percept.Rd | 5 +---- man/get_chebiid.Rd | 3 --- man/get_cid.Rd | 5 ----- man/get_csid.Rd | 5 ----- man/get_etoxid.Rd | 7 ------- man/get_wdid.Rd | 3 --- man/is.cas.Rd | 3 --- man/is.inchikey.Rd | 3 --- man/is.inchikey_cs.Rd | 3 --- man/is.inchikey_format.Rd | 3 --- man/is.smiles.Rd | 3 --- man/pan_query.Rd | 3 --- man/parse_mol.Rd | 3 --- man/pc_prop.Rd | 3 --- man/pc_sect.Rd | 3 --- man/pc_synonyms.Rd | 3 --- man/srs_query.Rd | 3 --- man/wd_ident.Rd | 3 --- 36 files changed, 1 insertion(+), 119 deletions(-) diff --git a/man/as.cas.Rd b/man/as.cas.Rd index 271ac816..7bd349fe 100644 --- a/man/as.cas.Rd +++ b/man/as.cas.Rd @@ -26,6 +26,3 @@ as.cas(x) \seealso{ \code{\link{is.cas}} } -\author{ -Eric Scott, \email{scottericr@gmail.com} -} diff --git a/man/aw_query.Rd b/man/aw_query.Rd index ffe8e3a9..bbfde4ea 100644 --- a/man/aw_query.Rd +++ b/man/aw_query.Rd @@ -49,6 +49,3 @@ Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). . } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/chebi_comp_entity.Rd b/man/chebi_comp_entity.Rd index 3ba02fea..db6c0e5e 100644 --- a/man/chebi_comp_entity.Rd +++ b/man/chebi_comp_entity.Rd @@ -64,6 +64,3 @@ Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). . } -\author{ -Andreas Scharmüller, \email{andschar@protonmail.com} -} diff --git a/man/cir_img.Rd b/man/cir_img.Rd index c2f79c6a..a63b10ab 100644 --- a/man/cir_img.Rd +++ b/man/cir_img.Rd @@ -131,6 +131,3 @@ Group at NCI/NIH! \cr \url{http://cactus.nci.nih.gov/blog/?p=1386}, \cr \url{http://cactus.nci.nih.gov/blog/?p=1456}, \cr } -\author{ -Andreas Scharmueller, \email{andschar@protonmail.com} -} diff --git a/man/cir_query.Rd b/man/cir_query.Rd index 84ec244b..6380d41c 100644 --- a/man/cir_query.Rd +++ b/man/cir_query.Rd @@ -134,6 +134,3 @@ Group at NCI/NIH! \cr \url{http://cactus.nci.nih.gov/blog/?p=1386}, \cr \url{http://cactus.nci.nih.gov/blog/?p=1456}, \cr } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/cs_compinfo.Rd b/man/cs_compinfo.Rd index 63d13df7..cfe19791 100644 --- a/man/cs_compinfo.Rd +++ b/man/cs_compinfo.Rd @@ -44,6 +44,3 @@ cs_compinfo(171:182, "SMILES") \references{ \url{https://developer.rsc.org/compounds-v1/apis} } -\author{ -Tamás Stirling, \email{stirling.tamas@gmail.com} -} diff --git a/man/cs_control.Rd b/man/cs_control.Rd index df05be5f..9c7f09f8 100644 --- a/man/cs_control.Rd +++ b/man/cs_control.Rd @@ -70,6 +70,3 @@ cs_control(order_direction = "descending") \seealso{ \code{\link{get_csid}} } -\author{ -Tamás Stirling, \email{stirling.tamas@gmail.com} -} diff --git a/man/cs_convert.Rd b/man/cs_convert.Rd index 7f14c160..82af34f7 100644 --- a/man/cs_convert.Rd +++ b/man/cs_convert.Rd @@ -64,8 +64,3 @@ Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). . } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} - -Tamás Stirling, \email{stirling.tamas@gmail.com} -} diff --git a/man/cs_datasources.Rd b/man/cs_datasources.Rd index 1de3ee9d..b16bf42d 100644 --- a/man/cs_datasources.Rd +++ b/man/cs_datasources.Rd @@ -32,6 +32,3 @@ cs_datasources() \references{ \url{https://developer.rsc.org/compounds-v1/apis} } -\author{ -Tamás Stirling, \email{stirling.tamas@gmail.com} -} diff --git a/man/cs_extcompinfo.Rd b/man/cs_extcompinfo.Rd index 64c78b3b..d6af0b93 100644 --- a/man/cs_extcompinfo.Rd +++ b/man/cs_extcompinfo.Rd @@ -47,6 +47,3 @@ cs_compinfo(csids) \code{\link{get_csid}} to retrieve ChemSpider IDs, \code{\link{cs_compinfo}} for extended compound information. } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/cs_img.Rd b/man/cs_img.Rd index 664be128..3e7100f0 100644 --- a/man/cs_img.Rd +++ b/man/cs_img.Rd @@ -41,6 +41,3 @@ cs_img(c(582, 682), dir = tempdir()) \seealso{ \code{\link{get_csid}}, \code{\link{cs_check_key}} } -\author{ -Tamas Stirling, \email{stirling.tamas@gmail.com} -} diff --git a/man/cts_compinfo.Rd b/man/cts_compinfo.Rd index cf6ffb06..0ab6af30 100644 --- a/man/cts_compinfo.Rd +++ b/man/cts_compinfo.Rd @@ -43,6 +43,3 @@ sapply(out2, function(y) y$molweight) Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service -- a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648. } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/cts_convert.Rd b/man/cts_convert.Rd index 30351ab7..5d7c95a3 100644 --- a/man/cts_convert.Rd +++ b/man/cts_convert.Rd @@ -61,6 +61,3 @@ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Che \code{\link{cts_from}} for possible values in the 'from' argument and \code{\link{cts_to}} for possible values in the 'to' argument. } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/cts_from.Rd b/man/cts_from.Rd index 6ba8414c..2605a8f8 100644 --- a/man/cts_from.Rd +++ b/man/cts_from.Rd @@ -30,6 +30,3 @@ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Che \seealso{ \code{\link{cts_convert}} } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/cts_to.Rd b/man/cts_to.Rd index ed7509c7..2f1c8812 100644 --- a/man/cts_to.Rd +++ b/man/cts_to.Rd @@ -30,6 +30,3 @@ Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Che \seealso{ \code{\link{cts_convert}} } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} diff --git a/man/etox_basic.Rd b/man/etox_basic.Rd index 9856a35d..ae705126 100644 --- a/man/etox_basic.Rd +++ b/man/etox_basic.Rd @@ -49,6 +49,3 @@ Information from the Web. Journal of Statistical Software, 93(13). \code{\link{etox_basic}} for basic information, \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/etox_targets.Rd b/man/etox_targets.Rd index a43db07f..cf92ed36 100644 --- a/man/etox_targets.Rd +++ b/man/etox_targets.Rd @@ -44,6 +44,3 @@ Information from the Web. Journal of Statistical Software, 93(13). \code{\link{etox_basic}} for basic information, \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/etox_tests.Rd b/man/etox_tests.Rd index e3fde969..809c635b 100644 --- a/man/etox_tests.Rd +++ b/man/etox_tests.Rd @@ -35,6 +35,3 @@ etox_tests( c("20179", "9051")) \code{\link{get_etoxid}} to retrieve ETOX IDs, \code{\link{etox_basic}} for basic information, \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/fn_percept.Rd b/man/fn_percept.Rd index 423cec11..858096eb 100644 --- a/man/fn_percept.Rd +++ b/man/fn_percept.Rd @@ -22,7 +22,7 @@ A named character vector containing flavor percepts or NA's in the case of CAS n } \description{ Retreive flavor percepts from \url{http://www.flavornet.org}. Flavornet is a database of 738 compounds with odors -perceptible to humans detected using gas chromatography ofactometry (GCO). +perceptible to humans detected using gas chromatography olfactometry (GCO). } \examples{ \dontrun{ @@ -33,6 +33,3 @@ CASs <- c("75-07-0", "64-17-5", "109-66-0", "78-94-4", "78-93-3") fn_percept(CASs) } } -\author{ -Eric Scott, \email{eric.scott@tufts.edu} -} diff --git a/man/get_chebiid.Rd b/man/get_chebiid.Rd index 80b717be..b5ced240 100644 --- a/man/get_chebiid.Rd +++ b/man/get_chebiid.Rd @@ -93,6 +93,3 @@ Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller, Information from the Web. Journal of Statistical Software, 93(13). . } -\author{ -Andreas Scharmüller, \email{andschar@protonmail.com} -} diff --git a/man/get_cid.Rd b/man/get_cid.Rd index 31cd9145..6f684629 100644 --- a/man/get_cid.Rd +++ b/man/get_cid.Rd @@ -148,8 +148,3 @@ Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). . } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} - -Tamás Stirling, \email{stirling.tamas@gmail.com} -} diff --git a/man/get_csid.Rd b/man/get_csid.Rd index e114b01d..fb0959f7 100644 --- a/man/get_csid.Rd +++ b/man/get_csid.Rd @@ -71,8 +71,3 @@ Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). . } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} - -Tamás Stirling, \email{stirling.tamas@gmail.com} -} diff --git a/man/get_etoxid.Rd b/man/get_etoxid.Rd index 654809c3..0ac3a264 100644 --- a/man/get_etoxid.Rd +++ b/man/get_etoxid.Rd @@ -61,10 +61,3 @@ Information from the Web. Journal of Statistical Software, 93(13). \code{\link{etox_targets}} for quality targets and \code{\link{etox_tests}} for test results. } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} - -Tamás Stirling, \email{stirling.tamas@gmail.com} - -Andreas Scharmüller, \email{andschar@protonmail.com} -} diff --git a/man/get_wdid.Rd b/man/get_wdid.Rd index 51a5c3f3..480e04b6 100644 --- a/man/get_wdid.Rd +++ b/man/get_wdid.Rd @@ -46,6 +46,3 @@ comps <- c('Triclosan', 'Glyphosate') get_wdid(comps) } } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/is.cas.Rd b/man/is.cas.Rd index 4c31282c..ed53dc47 100644 --- a/man/is.cas.Rd +++ b/man/is.cas.Rd @@ -41,6 +41,3 @@ Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). . } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/is.inchikey.Rd b/man/is.inchikey.Rd index 4e6007eb..2aaf6d5c 100644 --- a/man/is.inchikey.Rd +++ b/man/is.inchikey.Rd @@ -47,6 +47,3 @@ Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(13). . } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/is.inchikey_cs.Rd b/man/is.inchikey_cs.Rd index b00527ab..2266329b 100644 --- a/man/is.inchikey_cs.Rd +++ b/man/is.inchikey_cs.Rd @@ -32,6 +32,3 @@ is.inchikey_cs('BQJCRHHNABKAKU-KBQPJGBKSB-N') \seealso{ \code{\link{is.inchikey}} for a pure-R implementation. } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/is.inchikey_format.Rd b/man/is.inchikey_format.Rd index b977d35f..c96645a7 100644 --- a/man/is.inchikey_format.Rd +++ b/man/is.inchikey_format.Rd @@ -38,6 +38,3 @@ is.inchikey_format('BQJCRHHNABKAKU-KBQPJGBKSB-N') \seealso{ \code{\link{is.inchikey}} for a pure-R implementation. } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/is.smiles.Rd b/man/is.smiles.Rd index cf96e4bd..c8daf312 100644 --- a/man/is.smiles.Rd +++ b/man/is.smiles.Rd @@ -34,6 +34,3 @@ Egon Willighagen (2015). How to test SMILES strings in Supplementary Information. \url{https://chem-bla-ics.blogspot.nl/2015/10/how-to-test-smiles-strings-in.html} } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/pan_query.Rd b/man/pan_query.Rd index 102d5f06..a68d166d 100644 --- a/man/pan_query.Rd +++ b/man/pan_query.Rd @@ -84,6 +84,3 @@ Retrieve information from the PAN database (\url{http://www.pesticideinfo.org/}) sapply(out, function(y) y$`Acute Toxicity Summary`) } } -\author{ -Eduard Szoecs, \email{eduardszoecs@gmail.com} -} diff --git a/man/parse_mol.Rd b/man/parse_mol.Rd index 918d2b18..e8f8bdee 100644 --- a/man/parse_mol.Rd +++ b/man/parse_mol.Rd @@ -35,6 +35,3 @@ a toolset for transforming SD/Molfile structure information into R objects. Source Code for Biology and Medicine, 7, 12. \url{http://doi.org/10.1186/1751-0473-7-12} } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/pc_prop.Rd b/man/pc_prop.Rd index d851bff9..4fbb60ee 100644 --- a/man/pc_prop.Rd +++ b/man/pc_prop.Rd @@ -70,6 +70,3 @@ Information from the Web. Journal of Statistical Software, 93(13). \seealso{ \code{\link{get_cid}}, \code{\link{pc_sect}} } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/pc_sect.Rd b/man/pc_sect.Rd index bbeaf546..7c4d6536 100644 --- a/man/pc_sect.Rd +++ b/man/pc_sect.Rd @@ -73,6 +73,3 @@ access to chemical annotations integrated in PubChem. J Cheminform 11, 56 \seealso{ \code{\link{get_cid}}, \code{\link{pc_prop}} } -\author{ -Tamás Stirling, \email{stirling.tamas@gmail.com} -} diff --git a/man/pc_synonyms.Rd b/man/pc_synonyms.Rd index f863f87d..63e3ab05 100644 --- a/man/pc_synonyms.Rd +++ b/man/pc_synonyms.Rd @@ -72,6 +72,3 @@ Kim, S., Thiessen, P. A., Bolton, E. E., & Bryant, S. H. (2015). PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic acids research, gkv396. } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} diff --git a/man/srs_query.Rd b/man/srs_query.Rd index c43e9884..86132b8a 100644 --- a/man/srs_query.Rd +++ b/man/srs_query.Rd @@ -42,6 +42,3 @@ casrn <- c('50-00-0', '67-64-1') srs_query(query = casrn, from = 'cas') } } -\author{ -Gordon Getzinger, \email{gjg3@duke.edu} -} diff --git a/man/wd_ident.Rd b/man/wd_ident.Rd index ed2fd062..dc78e71f 100644 --- a/man/wd_ident.Rd +++ b/man/wd_ident.Rd @@ -38,6 +38,3 @@ Wikidata: A Platform for Data Integration and Dissemination for the Life Science \seealso{ \code{\link{get_wdid}} } -\author{ -Eduard Szöcs, \email{eduardszoecs@gmail.com} -} From 5e380aa1971c7d2c2785f793e24232e2cc00245e Mon Sep 17 00:00:00 2001 From: stitam Date: Thu, 1 Oct 2020 12:30:27 +0200 Subject: [PATCH 9/9] Update codemeta.json --- codemeta.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/codemeta.json b/codemeta.json index 9c258b15..a13c7144 100644 --- a/codemeta.json +++ b/codemeta.json @@ -14,7 +14,7 @@ ], "issueTracker": "https://github.com/ropensci/webchem/issues", "license": "https://spdx.org/licenses/MIT", - "version": "1.0.0.9001", + "version": "1.1.0", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R",