CRAN version 2.4.6

dosorio · Dec 13, 2023 · a1a91be · a1a91be
1 parent f36996a
commit a1a91be
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,4 @@
 .travis.yml
 ^.*\.Rproj$
 ^\.Rproj\.user$
+NEWS.md
diff --git 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="[email protected]",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
@@ -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
@@ -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
@@ -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 ([email protected]) 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
@@ -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
@@ -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)."
-)
+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
diff --git a/man/massShift.Rd b/man/massShift.Rd
diff --git a/man/mw.Rd b/man/mw.Rd
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -8,6 +8,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& 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
@@ -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},