leidenbase version 0.1.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: leidenbase
 Type: Package
 Title: R and C wrappers to run the Leiden find_partition function
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: person( 'Brent', 'Ewing', role = c( 'aut', 'cre' ), email = '[email protected]' )
 Description: An R to C interface that runs the Leiden community
     detection algorithm to find a basic partition. It runs the
@@ -20,13 +20,13 @@ Description: An R to C interface that runs the Leiden community
     Scientific Reports (2019),
     DOI: 10.1038/s41598-019-41695-z.
 Requires: R (>= 3.0.0)
-Imports: igraph (>= 1.1.0)
+Imports: igraph (>= 0.8.2)
 License: GNU PUBLIC LICENSE 2 and GNU PUBLIC LICENSE 3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Suggests: testthat
 NeedsCompilation: yes
-Packaged: 2020-07-10 20:45:17 UTC; brent
+Packaged: 2020-10-02 18:40:44 UTC; brent
 Author: Brent Ewing [aut, cre]
 Maintainer: Brent Ewing <[email protected]>

README.md

@@ -21,6 +21,30 @@ Use the devtools::install_github() command
 devtools::install_github('cole-trapnell-lab/leidenbase')
 ```
 
+### Tested conditions
+
+#### Linux Debian 10 Buster
+
+R distribution: Debian packages  
+C/C++ compilers: Debian distribution packages  
+FORTRAN compiler: Debian distribution packages  
+
+#### MacOS 10.15 Catalina
+
+R distribution: CRAN package from https://cran.r-project.org/bin/macosx/R-4.0.2.pkg  
+C/C++ compilers: Apple Xcode 12.0  
+FORTRAN compiler: gfortran 10.2 from https://github.com/fxcoudert/gfortran-for-macOS/releases  
+
+#### MicroSoft Windows 10
+
+R distribution: CRAN package from https://cran.r-project.org/bin/windows/base/R-4.0.2-win.exe  
+C/C++ compilers: CRAN Rtools40 from https://cran.r-project.org/bin/windows/Rtools/rtools40-x86_64.exe  
+FORTRAN compiler: CRAN Rtools40 from https://cran.r-project.org/bin/windows/Rtools/rtools40-x86_64.exe  
+
+#### Suggestions
+
+Try to use compatible C/C++ and FORTRAN compilers. For example, if you install R using a CRAN package, try to use the R compiler tools, and if you use *brew* on MacOS to install R, try to use brew-installed compilers.
+
 ### Leidenbase functions
 
 The R wrapper for running the Leiden algorithm find partition function is  

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for leidenbase 0.1.0.
+# Generated by GNU Autoconf 2.69 for leidenbase 0.1.2.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -577,8 +577,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='leidenbase'
 PACKAGE_TARNAME='leidenbase'
-PACKAGE_VERSION='0.1.0'
-PACKAGE_STRING='leidenbase 0.1.0'
+PACKAGE_VERSION='0.1.2'
+PACKAGE_STRING='leidenbase 0.1.2'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1253,7 +1253,7 @@ 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 leidenbase 0.1.0 to adapt to many kinds of systems.
+\`configure' configures leidenbase 0.1.2 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1315,7 +1315,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of leidenbase 0.1.0:";;
+     short | recursive ) echo "Configuration of leidenbase 0.1.2:";;
    esac
   cat <<\_ACEOF
 
@@ -1405,7 +1405,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-leidenbase configure 0.1.0
+leidenbase configure 0.1.2
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2081,7 +2081,7 @@ 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 leidenbase $as_me 0.1.0, which was
+It was created by leidenbase $as_me 0.1.2, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -4935,7 +4935,7 @@ cat >>$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 leidenbase $as_me 0.1.0, which was
+This file was extended by leidenbase $as_me 0.1.2, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -4988,7 +4988,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-leidenbase config.status 0.1.0
+leidenbase config.status 0.1.2
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -6,7 +6,7 @@ dnl We acknowledge Gabor Csardi's work on the R/C igraph
 dnl distributions and for making the source code publicly 
 dnl and freely available.
 dnl
-AC_INIT([leidenbase], 0.1.0)
+AC_INIT([leidenbase], 0.1.2)
 AC_CONFIG_SRCDIR(src/leidenFindPartition.cpp)
 
 : ${R_HOME=`R RHOME`}

src/Makevars.in

@@ -17,7 +17,7 @@ PKG_CFLAGS=-I. \
         -Icigraph/src/AMD/Include \
         -Icigraph/src/COLAMD/Include   \
 	-Icigraph/src/SuiteSparse_config \
-	@CPPFLAGS@ @CFLAGS@ -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT\
+	@CPPFLAGS@ @CFLAGS@ -DUSING_R -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT\
 	-DPACKAGE_VERSION=\"0.8.2\" -DINTERNAL_ARPACK \
 	-DIGRAPH_THREAD_LOCAL=/**/
 PKG_CXXFLAGS= -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG \
@@ -26,7 +26,7 @@ PKG_CXXFLAGS= -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG \
         -Icigraph/include \
         -Icigraph/src/prpack \
         -Ileidenalg/include \
-        -DPRPACK_IGRAPH_SUPPORT
+        -DUSING_R -DPRPACK_IGRAPH_SUPPORT
 PKG_LIBS=@XML2_LIBS@ @GMP_LIBS@ @GLPK_LIBS@ $(FLIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
 
 all: $(SHLIB)

src/Makevars.win

@@ -17,7 +17,7 @@ PKG_CPPFLAGS=-I. \
         -Icigraph/src/AMD/Include \
         -Icigraph/src/COLAMD/Include   \
         -Icigraph/src/SuiteSparse_config \
-        -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT\
+        -DUSING_R -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT\
         -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK \
         -DIGRAPH_THREAD_LOCAL= \
         -DHAVE_GFORTRAN
@@ -27,7 +27,7 @@ PKG_CXXFLAGS= -DIGRAPH_THREAD_LOCAL= -DNDEBUG \
         -Icigraph/include \
         -Icigraph/src/prpack \
         -Ileidenalg/include \
-        -DPRPACK_IGRAPH_SUPPORT
+        -DUSING_R -DPRPACK_IGRAPH_SUPPORT
 PKG_LIBS= -liconv -lz -lws2_32 -lgfortran -lquadmath $(BLAS_LIBS) $(LAPACK_LIBS)
 
 all: $(SHLIB)

src/cigraph/include/igraph_arpack.h

@@ -222,34 +222,34 @@ __BEGIN_DECLS
 
 typedef struct igraph_arpack_options_t {
     /* INPUT */
-    char bmat[1];         /* I-standard problem, G-generalized */
-    int n;            /* Dimension of the eigenproblem */
-    char which[2];        /* LA, SA, LM, SM, BE */
-    int nev;                 /* Number of eigenvalues to be computed */
-    igraph_real_t tol;        /* Stopping criterion */
-    int ncv;          /* Number of columns in V */
-    int ldv;          /* Leading dimension of V */
-    int ishift;       /* 0-reverse comm., 1-exact with tridiagonal */
-    int mxiter;              /* Maximum number of update iterations to take */
-    int nb;           /* Block size on the recurrence, only 1 works */
-    int mode;     /* The kind of problem to be solved (1-5)
-                   1: A*x=l*x, A symmetric
-                   2: A*x=l*M*x, A symm. M pos. def.
-                   3: K*x = l*M*x, K symm., M pos. semidef.
-                   4: K*x = l*KG*x, K s. pos. semidef. KG s. indef.
-                   5: A*x = l*M*x, A symm., M symm. pos. semidef. */
-    int start;        /* 0: random, 1: use the supplied vector */
-    int lworkl;       /* Size of temporary storage, default is fine */
-    igraph_real_t sigma;          /* The shift for modes 3,4,5 */
-    igraph_real_t sigmai;     /* The imaginary part of shift for rnsolve */
+    char bmat[1];          /* I-standard problem, G-generalized */
+    int n;                 /* Dimension of the eigenproblem */
+    char which[2];         /* LA, SA, LM, SM, BE */
+    int nev;               /* Number of eigenvalues to be computed */
+    igraph_real_t tol;     /* Stopping criterion */
+    int ncv;               /* Number of columns in V */
+    int ldv;               /* Leading dimension of V */
+    int ishift;            /* 0-reverse comm., 1-exact with tridiagonal */
+    int mxiter;            /* Maximum number of update iterations to take */
+    int nb;                /* Block size on the recurrence, only 1 works */
+    int mode;              /* The kind of problem to be solved (1-5)
+                               1: A*x=l*x, A symmetric
+                               2: A*x=l*M*x, A symm. M pos. def.
+                               3: K*x = l*M*x, K symm., M pos. semidef.
+                               4: K*x = l*KG*x, K s. pos. semidef. KG s. indef.
+                               5: A*x = l*M*x, A symm., M symm. pos. semidef. */
+    int start;             /* 0: random, 1: use the supplied vector */
+    int lworkl;            /* Size of temporary storage, default is fine */
+    igraph_real_t sigma;   /* The shift for modes 3,4,5 */
+    igraph_real_t sigmai;  /* The imaginary part of shift for rnsolve */
     /* OUTPUT */
-    int info;     /* What happened, see docs */
-    int ierr;     /* What happened  in the dseupd call */
-    int noiter;       /* The number of iterations taken */
+    int info;              /* What happened, see docs */
+    int ierr;              /* What happened  in the dseupd call */
+    int noiter;            /* The number of iterations taken */
     int nconv;
-    int numop;        /* Number of OP*x operations */
-    int numopb;       /* Number of B*x operations if BMAT='G' */
-    int numreo;       /* Number of steps of re-orthogonalizations */
+    int numop;             /* Number of OP*x operations */
+    int numopb;            /* Number of B*x operations if BMAT='G' */
+    int numreo;            /* Number of steps of re-orthogonalizations */
     /* INTERNAL */
     int iparam[11];
     int ipntr[14];

src/cigraph/include/igraph_vector_pmt.h

@@ -205,6 +205,7 @@ DECLDIR void FUNCTION(igraph_vector, remove_section)(TYPE(igraph_vector) *v,
 /*-----------*/
 
 DECLDIR void FUNCTION(igraph_vector, sort)(TYPE(igraph_vector) *v);
+DECLDIR void FUNCTION(igraph_vector, reverse_sort)(TYPE(igraph_vector) *v);
 DECLDIR long int FUNCTION(igraph_vector, qsort_ind)(TYPE(igraph_vector) *v,
         igraph_vector_t *inds, igraph_bool_t descending);
 

src/cigraph/include/igraph_version.h

@@ -34,7 +34,7 @@ __BEGIN_DECLS
 #define IGRAPH_VERSION_PATCH @PACKAGE_VERSION_PATCH@
 #define IGRAPH_VERSION_PRERELEASE "@PACKAGE_VERSION_PRERELEASE@"
 
-int igraph_version(const char **version_string,
+DECLDIR int igraph_version(const char **version_string,
                    int *major,
                    int *minor,
                    int *subminor);

src/cigraph/src/adjlist.c

@@ -360,21 +360,27 @@ int igraph_adjlist_simplify(igraph_adjlist_t *al) {
 
 int igraph_adjlist_remove_duplicate(const igraph_t *graph,
                                     igraph_adjlist_t *al) {
-    long int i;
-    long int n = al->length;
+    long int i, j, l, n, p;
+    igraph_vector_int_t *v;
+
     IGRAPH_UNUSED(graph);
+
+    n = al->length;
     for (i = 0; i < n; i++) {
-        igraph_vector_int_t *v = &al->adjs[i];
-        long int j, p = 1, l = igraph_vector_int_size(v);
-        for (j = 1; j < l; j++) {
-            long int e = (long int) VECTOR(*v)[j];
-            /* Non-loop edges, and one end of loop edges are fine. */
-            /* We use here, that the vector is sorted and we also keep it sorted */
-            if (e != i || VECTOR(*v)[j - 1] != e) {
-                VECTOR(*v)[p++] = e;
+        v = &al->adjs[i];
+        l = igraph_vector_int_size(v);
+        if (l > 0) {
+            p = 1;
+            for (j = 1; j < l; j++) {
+                long int e = (long int) VECTOR(*v)[j];
+                /* Non-loop edges, and one end of loop edges are fine. */
+                /* We assume that the vector is sorted and we also keep it sorted */
+                if (e != i || VECTOR(*v)[j - 1] != e) {
+                    VECTOR(*v)[p++] = e;
+                }
             }
+            igraph_vector_int_resize(v, p);
         }
-        igraph_vector_int_resize(v, p);
     }
 
     return 0;
@@ -501,21 +507,25 @@ void igraph_adjedgelist_destroy(igraph_inclist_t *il) {
 
 int igraph_inclist_remove_duplicate(const igraph_t *graph,
                                     igraph_inclist_t *al) {
-    long int i;
-    long int n = al->length;
+    long int i, j, l, n, p;
+    igraph_vector_int_t* v;
+
+    n = al->length;
     for (i = 0; i < n; i++) {
-        igraph_vector_int_t *v = &al->incs[i];
-        long int j, p = 1, l = igraph_vector_int_size(v);
-        for (j = 1; j < l; j++) {
-            long int e = (long int) VECTOR(*v)[j];
-            /* Non-loop edges and one end of loop edges are fine. */
-            /* We use here, that the vector is sorted and we also keep it sorted */
-            if (IGRAPH_FROM(graph, e) != IGRAPH_TO(graph, e) ||
-                VECTOR(*v)[j - 1] != e) {
-                VECTOR(*v)[p++] = e;
+        v = &al->incs[i];
+        l = igraph_vector_int_size(v);
+        if (l > 0) {
+            p = 1;
+            for (j = 1; j < l; j++) {
+                long int e = (long int) VECTOR(*v)[j];
+                /* Non-loop edges and one end of loop edges are fine. */
+                /* We assume that the vector is sorted and we also keep it sorted */
+                if (VECTOR(*v)[j - 1] != e) {
+                    VECTOR(*v)[p++] = e;
+                }
             }
+            igraph_vector_int_resize(v, p);
         }
-        igraph_vector_int_resize(v, p);
     }
 
     return 0;