prepare cran submission 1.3.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gslnls
 Type: Package
 Title: GSL Multi-Start Nonlinear Least-Squares Fitting
-Version: 1.3.0
-Date: 2024-04-24
+Version: 1.3.1
+Date: 2024-04-25
 Authors@R: person("Joris", "Chau", email = "[email protected]", role = c("aut", "cre"))
 Description: An R interface to nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
 BugReports: https://github.com/JorisChau/gslnls/issues

NEWS.md

@@ -1,3 +1,7 @@
+# gslnls 1.3.1
+
+* Minor edits configure.ac to fix cran check results
+
 # gslnls 1.3.0
 
 * Missing starting values/ranges allowed in `gsl_nls()`

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# {gslnls}: GSL Nonlinear Least-Squares Fitting in R
+# {gslnls}: GSL Multi-Start Nonlinear Least-Squares Fitting in R
 
 <!-- badges: start -->
 
@@ -1047,7 +1047,7 @@ system.time({
   )
 })
 #>    user  system elapsed 
-#>  34.454   0.108  34.564
+#>  33.720   0.084  33.812
 
 cat("Residual sum-of-squares:", deviance(ex4_fit_lm), "\n")
 #> Residual sum-of-squares: 0.004778845
@@ -1069,7 +1069,7 @@ system.time({
   )
 })
 #>    user  system elapsed 
-#>   1.362   0.384   1.747
+#>   1.214   0.312   1.527
 
 cat("Residual sum-of-squares:", deviance(ex4_fit_cgst), "\n")
 #> Residual sum-of-squares: 0.004778845
@@ -1114,8 +1114,8 @@ bench::mark(
 #> # A tibble: 4 × 6
 #>   expression       min   median `itr/sec` mem_alloc `gc/sec`
 #>   <bch:expr>  <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
-#> 1 Dense LM       6.33s    6.39s     0.157     1.8GB    6.61 
-#> 2 Dense CGST     1.29s    1.36s     0.726    1.02GB   16.4  
+#> 1 Dense LM       6.33s    6.39s     0.157     1.8GB    6.61  
+#> 2 Dense CGST     1.29s    1.36s     0.726    1.02GB    16.4  
 #> 3 Sparse LM      4.87s    4.91s     0.203   33.19MB    0.122
 #> 4 Sparse CGST 166.09ms 176.09ms     4.66    23.04MB    3.73
 ```
@@ -1215,7 +1215,7 @@ solutions and a vector of suggested starting values for the parameters:
 #> 
 #> $fn
 #> y ~ b1/(1 + exp(b2 - b3 * x))
-#> <environment: 0x559c59502090>
+#> <environment: 0x55b96bf04da0>
 #> 
 #> $start
 #>    b1    b2    b3 

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for gslnls 1.3.0.
+# Generated by GNU Autoconf 2.71 for gslnls 1.3.1.
 #
 # Report bugs to <https://github.com/JorisChau/gslnls/issues/>.
 #
@@ -610,8 +610,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='gslnls'
 PACKAGE_TARNAME='gslnls'
-PACKAGE_VERSION='1.3.0'
-PACKAGE_STRING='gslnls 1.3.0'
+PACKAGE_VERSION='1.3.1'
+PACKAGE_STRING='gslnls 1.3.1'
 PACKAGE_BUGREPORT='https://github.com/JorisChau/gslnls/issues/'
 PACKAGE_URL=''
 
@@ -1231,7 +1231,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures gslnls 1.3.0 to adapt to many kinds of systems.
+\`configure' configures gslnls 1.3.1 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1293,7 +1293,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of gslnls 1.3.0:";;
+     short | recursive ) echo "Configuration of gslnls 1.3.1:";;
    esac
   cat <<\_ACEOF
 
@@ -1375,7 +1375,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-gslnls configure 1.3.0
+gslnls configure 1.3.1
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1533,7 +1533,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by gslnls $as_me 1.3.0, which was
+It was created by gslnls $as_me 1.3.1, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -3463,19 +3463,18 @@ fi
 
 
 if test -n "${GSL_CONFIG}"; then
-    # Use gsl-config for header and linker arguments (without BLAS which we get from R)
+    # Use gsl-config for header and linker arguments
     GSL_CFLAGS=`${GSL_CONFIG} --cflags`
-    GSL_LIBS=`${GSL_CONFIG} --libs-without-cblas`
+    GSL_LIBS=`${GSL_CONFIG} --libs`
     CFLAGS="$CFLAGS $GSL_CFLAGS"
 else
     echo "------------------------- LIBGSL ERROR ------------------------------"
     echo "Configuration failed because libgsl was not found. Try installing:"
     echo " * deb: libgsl-dev (Debian, Ubuntu, etc)"
     echo " * rpm: gsl-devel (Fedora, CentOS, RHEL)"
     echo " * csw: gsl_dev (Solaris)"
-    echo "If libgsl is already installed, check that 'pkg-config' is in your"
-    echo "PATH and PKG_CONFIG_PATH contains a libgsl .pc file. If pkg-config"
-    echo "is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:"
+    echo "If libgsl is installed, check that 'gsl-config' is in your PATH. If"
+    echo "gsl-config is unavailable, set INCLUDE_DIR and LIB_DIR manually via:"
     echo "R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'"
     echo "--------------------------------------------------------------------"
   exit 1;
@@ -4067,7 +4066,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by gslnls $as_me 1.3.0, which was
+This file was extended by gslnls $as_me 1.3.1, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -4122,7 +4121,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-gslnls config.status 1.3.0
+gslnls config.status 1.3.1
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,5 +1,5 @@
 
-AC_INIT([gslnls],[1.3.0],[https://github.com/JorisChau/gslnls/issues/])
+AC_INIT([gslnls],[1.3.1],[https://github.com/JorisChau/gslnls/issues/])
 
 : ${R_HOME=`R RHOME`}
 if test -z "${R_HOME}"; then
@@ -18,19 +18,18 @@ AC_PROG_FC
 AC_PATH_PROG([GSL_CONFIG], [gsl-config])
 
 if test -n "${GSL_CONFIG}"; then
-    # Use gsl-config for header and linker arguments (without BLAS which we get from R)
+    # Use gsl-config for header and linker arguments
     GSL_CFLAGS=`${GSL_CONFIG} --cflags`
-    GSL_LIBS=`${GSL_CONFIG} --libs-without-cblas`
+    GSL_LIBS=`${GSL_CONFIG} --libs`
     CFLAGS="$CFLAGS $GSL_CFLAGS"
 else
     echo "------------------------- LIBGSL ERROR ------------------------------"
     echo "Configuration failed because libgsl was not found. Try installing:"
     echo " * deb: libgsl-dev (Debian, Ubuntu, etc)"
     echo " * rpm: gsl-devel (Fedora, CentOS, RHEL)"
     echo " * csw: gsl_dev (Solaris)"
-    echo "If libgsl is already installed, check that 'pkg-config' is in your"
-    echo "PATH and PKG_CONFIG_PATH contains a libgsl .pc file. If pkg-config"
-    echo "is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:"
+    echo "If libgsl is installed, check that 'gsl-config' is in your PATH. If"
+    echo "gsl-config is unavailable, set INCLUDE_DIR and LIB_DIR manually via:"
     echo "R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'"
     echo "--------------------------------------------------------------------"
   exit 1;

cran-comments.md

@@ -1,7 +1,11 @@
-## CRAN package version 1.3.0
+## CRAN package version 1.3.1
 
 * System requirements: GSL (>= 2.2)
 
+## Comments
+
+* Edited configure.ac + configure to fix cran check errors (fedora builds)
+
 ## Test environments
 
 * ubuntu gcc R-oldrel, R-release, R-next, R-devel (rhub, gh-actions)