From a1a91be11bd6ba183541008cd038e328b4c33868 Mon Sep 17 00:00:00 2001 From: Daniel Osorio Date: Wed, 13 Dec 2023 11:58:59 -0600 Subject: [PATCH] CRAN version 2.4.6 --- .Rbuildignore | 1 + DESCRIPTION | 4 ++-- NEWS.md | 4 ++++ R/RcppExports.R | 2 +- R/aacomp.R | 20 ++++++++++---------- R/massShift.R | 13 +++++++------ inst/CITATION | 23 +++++++++++------------ man/aaComp.Rd | 22 +++++++++++----------- man/massShift.Rd | 13 +++++++------ man/mw.Rd | 3 +++ src/RcppExports.cpp | 9 +++++++-- src/init.c | 2 +- 12 files changed, 65 insertions(+), 51 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index b2a8151..9f4f63a 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,4 @@ .travis.yml ^.*\.Rproj$ ^\.Rproj\.user$ +NEWS.md diff --git a/DESCRIPTION b/DESCRIPTION index 570db1f..54f33af 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: Peptides -Version: 2.4.4 +Version: 2.4.6 Title: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences Authors@R: c(person("Daniel","Osorio", email="daniecos@uio.no",role=c("aut","cre"), comment = c(ORCID = "0000-0003-4424-8422")), @@ -17,5 +17,5 @@ Description: Includes functions to calculate several physicochemical properties License: GPL-2 LinkingTo: Rcpp Imports: Rcpp -RoxygenNote: 7.1.1 +RoxygenNote: 7.2.3 Encoding: UTF-8 diff --git a/NEWS.md b/NEWS.md index f580e68..58328ff 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,10 @@ NEWS ==== **Peptides v.2.4.4** +* A warning related with Rcpp was solved + +**Peptides v.2.4.4** + * An error in the mz function related with the aminoacid composition of the peptides used as input was solved **Peptides v.2.4.2** diff --git a/R/RcppExports.R b/R/RcppExports.R index c6a9e12..6a366c4 100644 --- a/R/RcppExports.R +++ b/R/RcppExports.R @@ -11,5 +11,5 @@ absoluteCharge <- function(seq, pH = 7, pKscale = "Lehninger") { # Register entry points for exported C++ functions methods::setLoadAction(function(ns) { - .Call('_Peptides_RcppExport_registerCCallable', PACKAGE = 'Peptides') + .Call(`_Peptides_RcppExport_registerCCallable`) }) diff --git a/R/aacomp.R b/R/aacomp.R index b807fc9..076b8ed 100755 --- a/R/aacomp.R +++ b/R/aacomp.R @@ -6,17 +6,17 @@ #' Some amino acids possess side chains with specific properties that allow grouping them in different ways. #' The \code{aaComp} function classifies amino acids based on their size, side chains, hydrophobicity, charge and their response to pH 7. #' @param seq An amino-acid sequence -#' @return The output is a matrix with the number and percentage of amino acids of a particular class +#' @return The output is a matrix with the number and percentage of amino acids of a particular class: #' \itemize{ -#' \item{Tiny }{(A + C + G + S + T)} -#' \item{Small }{(A + B + C + D + G + N + P + S + T + V)} -#' \item{Aliphatic }{(A + I + L + V)} -#' \item{Aromatic }{(F + H + W + Y)} -#' \item{Non-polar }{(A + C + F + G + I + L + M + P + V + W + Y)} -#' \item{Polar }{(D + E + H + K + N + Q + R + S + T + Z)} -#' \item{Charged }{(B + D + E + H + K + R + Z)} -#' \item{Basic }{(H + K + R)} -#' \item{Acidic }{(B + D + E + Z)} +#' \item Tiny (A + C + G + S + T) +#' \item Small (A + B + C + D + G + N + P + S + T + V) +#' \item Aliphatic (A + I + L + V) +#' \item Aromatic (F + H + W + Y) +#' \item Non-polar (A + C + F + G + I + L + M + P + V + W + Y) +#' \item Polar (D + E + H + K + N + Q + R + S + T + Z) +#' \item Charged (B + D + E + H + K + R + Z) +#' \item Basic (H + K + R) +#' \item Acidic (B + D + E + Z) #' } #' @note This function was originally written by Alan Bleasby (ajb@ebi.ac.uk) for the EMBOSS package. #' Further information: http://emboss.sourceforge.net/apps/cvs/emboss/apps/pepstats.html diff --git a/R/massShift.R b/R/massShift.R index 7b7308f..74f13dc 100644 --- a/R/massShift.R +++ b/R/massShift.R @@ -8,20 +8,21 @@ #' Use the amino acid one letter code as names and the mass shift in Dalton as values. #' N-terminal and C-terminal modifications can be defined by using "Nterm =" and "Cterm =", respectively. #' @source For the predefined heavy isotope labels, compare: +#' #' \itemize{ -#' \item{silac_13c}{ +#' \item silac_13c #' \href{http://www.unimod.org/modifications_view.php?editid1=188}{Unimod 188} -#' } -#' \item{silac_13c15n}{ +#' +#' \item silac_13c15n #' \href{http://www.unimod.org/modifications_view.php?editid1=259}{Unimod 259} and #' \href{http://www.unimod.org/modifications_view.php?editid1=267}{Unimod 267} -#' } -#' \item{15n}{ +#' +#' \item 15n #' \href{http://www.unimod.org/modifications_view.php?editid1=994}{Unimod 994}, #' \href{http://www.unimod.org/modifications_view.php?editid1=995}{Unimod 995}, #' \href{http://www.unimod.org/modifications_view.php?editid1=996}{Unimod 996} and #' \href{http://www.unimod.org/modifications_view.php?editid1=897}{Unimod 897} -#' } +#' #' } #' @examples #' massShift("EGVNDNECEGFFSAR", label = "silac_13c") diff --git a/inst/CITATION b/inst/CITATION index 140959d..799dfa2 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,12 +1,11 @@ -citHeader("To cite Peptides in publications, please use:") -citEntry(entry = "article", - author = personList(c(person(given = "Daniel", family = "Osorio"),person(given = "Paola", family = "Rondon-Villarreal"),person(given = "Rodrigo", family = "Torres"))), - title = "Peptides: A Package for Data Mining of Antimicrobial Peptides", - journal = "The R Journal", - year = "2015", - issn = "2073-4859", - volume = "7", - number = "1", - pages = "4-14", - textVersion = "Osorio, D., Rondon-Villarreal, P. & Torres, R. Peptides: A package for data mining of antimicrobial peptides. The R Journal. 7(1), 4-14 (2015)." -) \ No newline at end of file +bibentry( + bibtype = "Article", + title = "Peptides: a package for data mining of antimicrobial peptides", + author = "Daniel Osorio and Paola Rondón-Villarreal and Rodrigo Torres", + journal = "The R Journal", + year = 2015, + volume = 7, + number = 1, + pages = "4-14", + doi = "10.32614/RJ-2015-001" +) diff --git a/man/aaComp.Rd b/man/aaComp.Rd index 0b076bf..95e1584 100644 --- a/man/aaComp.Rd +++ b/man/aaComp.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/aacomp.R +% Please edit documentation in R/aaComp.R \name{aaComp} \alias{aaComp} \title{Compute the amino acid composition of a protein sequence} @@ -10,17 +10,17 @@ aaComp(seq) \item{seq}{An amino-acid sequence} } \value{ -The output is a matrix with the number and percentage of amino acids of a particular class +The output is a matrix with the number and percentage of amino acids of a particular class: \itemize{ -\item{Tiny }{(A + C + G + S + T)} -\item{Small }{(A + B + C + D + G + N + P + S + T + V)} -\item{Aliphatic }{(A + I + L + V)} -\item{Aromatic }{(F + H + W + Y)} -\item{Non-polar }{(A + C + F + G + I + L + M + P + V + W + Y)} -\item{Polar }{(D + E + H + K + N + Q + R + S + T + Z)} -\item{Charged }{(B + D + E + H + K + R + Z)} -\item{Basic }{(H + K + R)} -\item{Acidic }{(B + D + E + Z)} +\item Tiny (A + C + G + S + T) +\item Small (A + B + C + D + G + N + P + S + T + V) +\item Aliphatic (A + I + L + V) +\item Aromatic (F + H + W + Y) +\item Non-polar (A + C + F + G + I + L + M + P + V + W + Y) +\item Polar (D + E + H + K + N + Q + R + S + T + Z) +\item Charged (B + D + E + H + K + R + Z) +\item Basic (H + K + R) +\item Acidic (B + D + E + Z) } } \description{ diff --git a/man/massShift.Rd b/man/massShift.Rd index cf52412..c873f90 100644 --- a/man/massShift.Rd +++ b/man/massShift.Rd @@ -5,20 +5,21 @@ \title{Calculate the mass difference of modified peptides.} \source{ For the predefined heavy isotope labels, compare: + \itemize{ - \item{silac_13c}{ + \item silac_13c \href{http://www.unimod.org/modifications_view.php?editid1=188}{Unimod 188} - } - \item{silac_13c15n}{ + + \item silac_13c15n \href{http://www.unimod.org/modifications_view.php?editid1=259}{Unimod 259} and \href{http://www.unimod.org/modifications_view.php?editid1=267}{Unimod 267} - } - \item{15n}{ + + \item 15n \href{http://www.unimod.org/modifications_view.php?editid1=994}{Unimod 994}, \href{http://www.unimod.org/modifications_view.php?editid1=995}{Unimod 995}, \href{http://www.unimod.org/modifications_view.php?editid1=996}{Unimod 996} and \href{http://www.unimod.org/modifications_view.php?editid1=897}{Unimod 897} - } + } } \usage{ diff --git a/man/mw.Rd b/man/mw.Rd index 3bef76a..d2b617e 100644 --- a/man/mw.Rd +++ b/man/mw.Rd @@ -41,6 +41,9 @@ The molecular weight is the sum of the masses of each atom constituting a molecu mw(seq = "QWGRRCCGWGPGRRYCVRWC",monoisotopic = FALSE) # [1] 2485.911 +mw(seq = "QWGRRCCGWGPGRRYCVRWC",monoisotopic = FALSE, avgScale = "mascot") +# [1] 2485.899 + mw(seq = "QWGRRCCGWGPGRRYCVRWC",monoisotopic = TRUE) # [1] 2484.12 diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index 28656dc..46d8591 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -8,6 +8,11 @@ using namespace Rcpp; +#ifdef RCPP_USE_GLOBAL_ROSTREAM +Rcpp::Rostream& Rcpp::Rcout = Rcpp::Rcpp_cout_get(); +Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(); +#endif + // chargeList Rcpp::List chargeList(std::vector< std::string > seq, NumericVector pH, std::string pKscale); static SEXP _Peptides_chargeList_try(SEXP seqSEXP, SEXP pHSEXP, SEXP pKscaleSEXP) { @@ -39,7 +44,7 @@ RcppExport SEXP _Peptides_chargeList(SEXP seqSEXP, SEXP pHSEXP, SEXP pKscaleSEXP if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s",CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -75,7 +80,7 @@ RcppExport SEXP _Peptides_absoluteCharge(SEXP seqSEXP, SEXP pHSEXP, SEXP pKscale if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s",CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; diff --git a/src/init.c b/src/init.c index 60530f4..4682b6b 100644 --- a/src/init.c +++ b/src/init.c @@ -10,7 +10,7 @@ /* .Call calls */ extern SEXP _Peptides_absoluteCharge(SEXP, SEXP, SEXP); extern SEXP _Peptides_chargeList(SEXP, SEXP, SEXP); -extern SEXP _Peptides_RcppExport_registerCCallable(); +extern SEXP _Peptides_RcppExport_registerCCallable(void); static const R_CallMethodDef CallEntries[] = { {"_Peptides_absoluteCharge", (DL_FUNC) &_Peptides_absoluteCharge, 3},