new version spam[64].2.1.2 material

DESCRIPTION

 Package: spam
-Version: 2.0-05
-Date: 2016-11-19
+Type: Package
+Title: SPArse Matrix
+Version: 2.1-2
+Date: 2017-12-21
 Authors@R: c(person("Reinhard", "Furrer", role = c("aut", "cre"),
-                    email = "reihard.furrer@math.uzh.ch"),
-             person("Florian", "Gerber", role = "ctb",
+                    email = "reinhard.furrer@math.uzh.ch"),
+             person("Florian", "Gerber", role = c("ctb"),
 	                email = "florian.gerber@math.uzh.ch"),
+	     person("Daniel", "Gerber", role = "ctb",
+			email = "daniel_gerber_2222@hotmail.com"),
              person("Kaspar", "Moesinger", role = "ctb",
-	                email = "kaspar.moesinger@gmail.com"))
-Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb], Kaspar Moesinger [ctb] 
-Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
+	                email = "kaspar.moesinger@gmail.com"),
+             person("Youcef", "Saad", role = "ctb",
+                        comment = "SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/"),
+             person(c("Esmond", "G."), "Ng", role = "ctb",
+                        comment = "Fortran Cholesky routines"),
+             person(c("Barry", "W."), "Peyton", role = "ctb",
+                        comment = "Fortran Cholesky routines"),
+             person(c("Joseph", "W.H."), "Liu", role = "ctb",
+                        comment = "Fortran Cholesky routines"),
+             person(c("Alan", "D."), "George", role = "ctb",
+                        comment = "Fortran Cholesky routines")
+		 	)
 Depends:
     R (>= 3.1),
     dotCall64,
@@ -24,13 +37,12 @@ Suggests:
     truncdist
 VignetteBuilder: R.rsp
 Description: Set of functions for sparse matrix algebra.
-    Differences with SparseM/Matrix are:
+    Differences with other sparse matrix packages are:
     (1) we only support (essentially) one sparse matrix format,
     (2) based on transparent and simple structure(s),
-    (3) tailored for MCMC calculations within GMRF.
-    (4) S3 and S4 like-"compatible"  ...     and it is fast.
+    (3) tailored for MCMC calculations within G(M)RF.
+    (4) and it is fast and scalable (with the extension package spam64).
 LazyLoad: Yes
 LazyData: Yes
 License: LGPL-2
-Title: SPArse Matrix
-URL: http://www.math.uzh.ch/furrer/software/spam/
\ No newline at end of file
+URL: https://git.math.uzh.ch/reinhard.furrer/spam

NAMESPACE

-useDynLib(spam)
+useDynLib(spam, .registration = TRUE)
 
 import(grid)
 import("dotCall64")
@@ -39,10 +39,14 @@ S3method("solve","spam")
 S3method("subset","spam")
 S3method("summary","spam")
 S3method("summary","spam.chol.NgPeyton")
+S3method("print","summary.spam")
+S3method("print","summary.spam.chol.NgPeyton")
 S3method("t","spam")
 S3method("tail","spam")
 S3method("update","spam.chol.NgPeyton")
-  
+
+S3method("cbind","spam")
+S3method("rbind","spam")
 
 # Generic functions
 export(
@@ -54,6 +58,10 @@ export(
        "spam.Version",
 	
        "validate_spam",
+       "validspamobject",   # __DEPRECATED__
+
+       "spam.options",      # __DEPRECATED__
+       "spam.getOption",   # __DEPRECATED__
 
        "nearest.dist",
        "spam_rdist",
@@ -255,7 +263,6 @@ exportMethods(
               "t",
               "diag",
               "diag<-",
-              "diag<-",
               "upper.tri",
               "lower.tri",
               

R/apply.R

-# This is file ../spam/R/apply.R
-# This file is part of the spam package, 
-#      http://www.math.uzh.ch/furrer/software/spam/
-# by Reinhard Furrer [aut, cre], Florian Gerber [ctb]
-     
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+# HEADER ####################################################
+# This is file spam/R/apply.R.                              #
+# It is part of the R package spam,                         #
+#  --> https://CRAN.R-project.org/package=spam              #
+#  --> https://CRAN.R-project.org/package=spam64            #
+#  --> https://git.math.uzh.ch/reinhard.furrer/spam         #
+# by Reinhard Furrer [aut, cre], Florian Gerber [ctb],      #
+#    Daniel Gerber [ctb], Kaspar Moesinger [ctb],           #
+#    Youcef Saad [ctb] (SPARSEKIT),                         #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines),      #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines)       #
+# HEADER END ################################################
 
 
 # primitive apply function.

R/constructors.R

-# This is file ../spam/R/constructors.R
-# This file is part of the spam package, 
-#      http://www.math.uzh.ch/furrer/software/spam/
-# by Reinhard Furrer [aut, cre], Florian Gerber [ctb]
+# HEADER ####################################################
+# This is file spam/R/constructors.R.                       #
+# It is part of the R package spam,                         #
+#  --> https://CRAN.R-project.org/package=spam              #
+#  --> https://CRAN.R-project.org/package=spam64            #
+#  --> https://git.math.uzh.ch/reinhard.furrer/spam         #
+# by Reinhard Furrer [aut, cre], Florian Gerber [ctb],      #
+#    Daniel Gerber [ctb], Kaspar Moesinger [ctb],           #
+#    Youcef Saad [ctb] (SPARSEKIT),                         #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines),      #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines)       #
+# HEADER END ################################################
+
      
 
 "rowpointers<-" <- function(x, value) {

R/covmat.R

-# This is file ../spam/R/covmat.R
-# This file is part of the spam package, 
-#      http://www.math.uzh.ch/furrer/software/spam/
-# by Reinhard Furrer [aut, cre], Florian Gerber [ctb]
-     
+# HEADER ####################################################
+# This is file spam/R/covmat.R.                             #
+# It is part of the R package spam,                         #
+#  --> https://CRAN.R-project.org/package=spam              #
+#  --> https://CRAN.R-project.org/package=spam64            #
+#  --> https://git.math.uzh.ch/reinhard.furrer/spam         #
+# by Reinhard Furrer [aut, cre], Florian Gerber [ctb],      #
+#    Daniel Gerber [ctb], Kaspar Moesinger [ctb],           #
+#    Youcef Saad [ctb] (SPARSEKIT),                         #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines),      #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines)       #
+# HEADER END ################################################
 
 
 # construct various precision matrices

R/deprecated.R

+# HEADER ####################################################
+# This is file spam/R/deprecated.R.                         #
+# It is part of the R package spam,                         #
+#  --> https://CRAN.R-project.org/package=spam              #
+#  --> https://CRAN.R-project.org/package=spam64            #
+#  --> https://git.math.uzh.ch/reinhard.furrer/spam         #
+# by Reinhard Furrer [aut, cre], Florian Gerber [ctb],      #
+#    Daniel Gerber [ctb], Kaspar Moesinger [ctb],           #
+#    Youcef Saad [ctb] (SPARSEKIT),                         #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines),      #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines)       #
+# HEADER END ################################################
+
+
+validspamobject <- function( ...) {
+#    .Deprecated('validate_spam()')
+    message("`validspamobject()` is deprecated. Use `validate_spam()` directly")
+    validate_spam( ...)
+    }
+
+spam.getOption <- function(...) {
+#    .Deprecated(msg="`spam.getOption( arg)` is deprecated.\n Use `getOption( spam.arg)` directly")
+    message("`spam.getOption( arg)` is deprecated. Use `getOption( spam.arg)` directly")
+    getOption(...)
+    
+}
+spam.options <- function(...) {
+#    .Deprecated(msg="`spam.options( arg)` is deprecated.\n Use `options( spam.arg)` directly")
+    message("`spam.options( arg)` is deprecated. Use `options( spam.arg)` directly")
+
+    if (nargs() == 0) {
+        tmp <- names(options())
+        return(options()[ grep( "spam.", tmp)])
+    }
+
+    args <- list(...)
+    names(args) <- paste0("spam.", names(args))
+    do.call("options", args)
+}    
+

R/diff.R

-# This is file ../spam/R/diff.R
-# This file is part of the spam package, 
-#      http://www.math.uzh.ch/furrer/software/spam/
-# by Reinhard Furrer [aut, cre], Florian Gerber [ctb]
+# HEADER ####################################################
+# This is file spam/R/diff.R.                               #
+# It is part of the R package spam,                         #
+#  --> https://CRAN.R-project.org/package=spam              #
+#  --> https://CRAN.R-project.org/package=spam64            #
+#  --> https://git.math.uzh.ch/reinhard.furrer/spam         #
+# by Reinhard Furrer [aut, cre], Florian Gerber [ctb],      #
+#    Daniel Gerber [ctb], Kaspar Moesinger [ctb],           #
+#    Youcef Saad [ctb] (SPARSEKIT),                         #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines),      #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines)       #
+# HEADER END ################################################
+
      
 
 

R/dim.R

-# This is file ../spam/R/dim.R
-# This file is part of the spam package, 
-#      http://www.math.uzh.ch/furrer/software/spam/
-# by Reinhard Furrer [aut, cre], Florian Gerber [ctb]
-     
+# HEADER ####################################################
+# This is file spam/R/dim.R.                                #
+# It is part of the R package spam,                         #
+#  --> https://CRAN.R-project.org/package=spam              #
+#  --> https://CRAN.R-project.org/package=spam64            #
+#  --> https://git.math.uzh.ch/reinhard.furrer/spam         #
+# by Reinhard Furrer [aut, cre], Florian Gerber [ctb],      #
+#    Daniel Gerber [ctb], Kaspar Moesinger [ctb],           #
+#    Youcef Saad [ctb] (SPARSEKIT),                         #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines),      #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines)       #
+# HEADER END ################################################
+
 
 # This is the actual dim...
 
@@ -46,56 +60,107 @@
 # dim and derivatives
 
 "pad<-.spam" <- function(x,value) {
-  if ( (min(value)<1 ) || any(!is.finite(value)))
-    stop("dims should be postive integers.")
-  if (!identical( length(value), 2L)) stop("dims should be of length 2.")
-  dimx <- x@dimension
-  last <- value[1]+1
 
+    force64 <- getOption("spam.force64")
+
+    # check if value is valid
+    if ( (min(value)<1 ) || any(!is.finite(value)))
+        stop("dims should be postive integers.")
+    if (!identical( length(value), 2L))
+        stop("dims should be of length 2.")
+    
+    dimx <- x@dimension
+    last <- value[1]+1
+    
   # In three steps:
   #  1) Address col truncation
             # to safe time, we also take into account if we have fewer or equal rows
   #  2) Augment rows
   #  3) if fewer rows and more columns, truncate
   # In any case, dimensions are fixed at the end.
+
   
   # If fewer cols required, we run reducedim
   if (dimx[2]>value[2]){
+
 #     subroutine reducedim(a,ja,ia,eps,bnrow,bncol,k,b,jb,ib)
-    z <- .Fortran("reducedim",
-                  oldra=as.double(x@entries),
-                  oldja=as.integer(x@colindices),
-                  oldia=as.integer(x@rowpointers),
-                  eps=as.double(getOption("spam.eps")),
-                  as.integer(min(value[1],dimx[1])),as.integer(value[2]),
-                  nz=1L,
-                  entries=vector("double",length(x@entries)),
-                  colindices=vector("integer",length(x@entries)),
-                  rowpointers=vector("integer",last),
-                  NAOK = getOption("spam.NAOK"), PACKAGE = "spam")
-    if (identical(z$nz,1L) )
-      return(new("spam",rowpointers=c(1L,rep.int(2L,as.integer(value[1]))),
-                 dimension=as.integer(value)))
-
-    nz <- z$nz-1
-    slot(x,"entries",check=FALSE) <- z$entries[1:nz]
-    slot(x,"colindices",check=FALSE) <- z$colindices[1:nz]
-    slot(x,"rowpointers",check=FALSE) <- z$rowpointers[1:min(last,dimx[1]+1)]
+
+      if( force64 || .format.spam(x)$package == "spam64")
+          SS <- .format64()
+      else
+          SS <- .format32
+      
+      z <- .C64("reducedim",
+                SIGNATURE=c("double", SS$signature, SS$signature,
+                    "double", SS$signature, SS$signature, SS$signature,
+                    "double", SS$signature, SS$signature),
+                oldra = x@entries,
+                oldja = x@colindices,
+                oldia = x@rowpointers,
+                
+                eps = getOption("spam.eps"),
+                min(value[1],dimx[1]),
+                value[2],
+                nz = 1,
+                
+                entries=vector_dc("double",length(x@entries)),
+                colindices=vector_dc(SS$type,length(x@entries)),
+                rowpointers=vector_dc(SS$type,last),
+
+                INTENT=c("r", "r", "r", 
+                         "r", "r", "r", "w", 
+                         "w", "w", "w"),
+                NAOK = getOption("spam.NAOK"),
+                PACKAGE = SS$package)
+                
+    if (z$nz==1 ){ #was identical( z$nz,1L)
+        ## print("2")
+            return(
+                .newSpam(
+                    entries=x@entries,
+                    colindices=x@colindices,
+                    rowpointers=c(1,rep_len64(2,value[1])), 
+                    dimension=value,
+                    force64=force64
+                    )
+                )
+    }
+      nz <- z$nz-1
+      x <- .newSpam(
+          entries=z$entries[1:nz],
+          colindices=z$colindices[1:nz],
+          rowpointers=z$rowpointers[1:min(last,dimx[1]+1)], 
+          dimension=value, #actually here dim 2 = value 2 but dim1 maybe not yet
+          force64=force64
+          )
   }
-  # augment rows
+    # augment rows
   if  (dimx[1]<value[1]){
-    slot(x,"rowpointers",check=FALSE) <- c(x@rowpointers,rep.int(
-                           x@rowpointers[length(x@rowpointers)],value[1]-dimx[1]))
+      ## print("3")
+      x <- .newSpam(
+              entries=x@entries,
+              colindices=x@colindices,
+              rowpointers= c( x@rowpointers,
+                  rep_len64( x@rowpointers[length(x@rowpointers)],value[1]-dimx[1])),
+              dimension=value,
+              force64=force64
+              )
   }
-  # special case: fewer rows and more columns, truncate
-  if ((dimx[1]>value[1])&(dimx[2]<value[2])) {
-    lastelement <- (x@rowpointers[last]-1)
-    slot(x,"entries",check=FALSE) <- x@entries[1:lastelement]
-    slot(x,"colindices",check=FALSE) <- x@colindices[1:lastelement]
-    slot(x,"rowpointers",check=FALSE) <- x@rowpointers[1:last]
+
+    # special case: fewer rows and more columns, truncate
+  if((dimx[1]>=value[1])&(dimx[2]<=value[2])) { ## added =, think about it again 
+      ## print("4")
+      lastelement <- (x@rowpointers[last]-1)
+
+      x <- .newSpam(
+          entries= x@entries[1:lastelement],
+          colindices= x@colindices[1:lastelement],
+          rowpointers= x@rowpointers[1:last],
+          dimension=value,
+          force64=force64
+          )
   }
-        
-  slot(x,"dimension",check=FALSE) <- as.integer(value)                  
+    #before dim x = value x was here with slot option
   return(x)
 
 }

R/dist.R

+# HEADER ####################################################
+# This is file spam/R/dist.R.                               #
+# It is part of the R package spam,                         #
+#  --> https://CRAN.R-project.org/package=spam              #
+#  --> https://CRAN.R-project.org/package=spam64            #
+#  --> https://git.math.uzh.ch/reinhard.furrer/spam         #
+# by Reinhard Furrer [aut, cre], Florian Gerber [ctb],      #
+#    Daniel Gerber [ctb], Kaspar Moesinger [ctb],           #
+#    Youcef Saad [ctb] (SPARSEKIT),                         #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines),      #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines)       #
+# HEADER END ################################################
+
+
 ### in base:
 # dist(x, method = "euclidean", diag = FALSE, upper = FALSE, p=2)
 #
@@ -96,15 +116,18 @@ nearest.dist <- function( x, y=NULL, method = "euclidean",
   
   # EXPLICIT-STORAGE-FORMAT     
   if(max(n1,n2,nnz) > 2147483647 - 1 | getOption("spam.force64"))
-      SS <- .format64
+      SS <- .format64()
   else
       SS <- .format32
   
   if(2147483647 < nnz) stop("Distance matrix is too dense (1)")
-  
+
   repeat {
     d <- NULL # Free the memory allocated by a previous attemp
     d <- .C64("closestdist",
+    ##              subroutine closestdist( ncol, x,nrowx, y, nrowy,
+    ##  &    part, p, method, 
+    ##  &    eta, colindices, rowpointers, entries, nnz, iflag)
               SIGNATURE=c(SS$signature, "double", SS$signature, "double", SS$signature,
                           SS$signature, "double", SS$signature, "double", SS$signature,
                           SS$signature, "double", SS$signature, SS$signature),
@@ -127,11 +150,10 @@ nearest.dist <- function( x, y=NULL, method = "euclidean",
               nnz=nnz,
               iflag=0,
               
-                                        #TODO: Check the intents!
-              INTENT=c("rw", "rw", "rw", "rw",
-                       "rw", "rw", "rw", "rw", 
-                       "rw", "rw", "rw", "rw", 
-                       "rw", "rw"),
+              INTENT = c("r", "r", "r", "r",
+                     "r", "r", "rw", "r", 
+                     "r", "w", "w", "w", 
+                     "rw", "w"),
               NAOK = getOption("spam.NAOK"),
               PACKAGE=SS$package)
     
@@ -140,7 +162,7 @@ nearest.dist <- function( x, y=NULL, method = "euclidean",
         
       # EXPLICIT-STORAGE-FORMAT     
       if(max(n1,n2,nnz) > 2147483647 - 1 | getOption("spam.force64"))
-        SS <- .format64
+        SS <- .format64()
       else
         SS <- .format32
         

R/foreign.R

-# This is file ../spam/R/foreign.R
-# This file is part of the spam package, 
-#      http://www.math.uzh.ch/furrer/software/spam/
-# by Reinhard Furrer [aut, cre], Florian Gerber [ctb]
-     
+# HEADER ####################################################
+# This is file spam/R/foreign.R.                            #
+# It is part of the R package spam,                         #
+#  --> https://CRAN.R-project.org/package=spam              #
+#  --> https://CRAN.R-project.org/package=spam64            #
+#  --> https://git.math.uzh.ch/reinhard.furrer/spam         #
+# by Reinhard Furrer [aut, cre], Florian Gerber [ctb],      #
+#    Daniel Gerber [ctb], Kaspar Moesinger [ctb],           #
+#    Youcef Saad [ctb] (SPARSEKIT),                         #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines),      #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George [ctb] (Fortran Cholesky routines)       #
+# HEADER END ################################################
 
 
 
@@ -47,6 +60,9 @@ as.spam.matrix.csr <- function(x)
 # 1b) spam <-> Matrix
 
 as.dgRMatrix.spam <- function(x) {
+    if(.format.spam(x)$package != "spam"){
+        stop("dgRMatrix structure is not compatible with numeric/large integer type.")
+    }
     if (requireNamespace("Matrix")) {
       newx <- new(p=0:0,"dgRMatrix")
       slot(newx,"x",check=FALSE) <- x@entries
@@ -58,6 +74,9 @@ as.dgRMatrix.spam <- function(x) {
   }
 
 as.dgCMatrix.spam <- function(x)  {
+    if(.format.spam(x)$package != "spam"){
+        stop("dgCMatrix structure is not compatible with numeric/large integer type.")
+    } 
     if (requireNamespace("Matrix")) {
       dimx <- x@dimension
       nz <- x@rowpointers[dimx[1] + 1] - 1
@@ -67,6 +86,28 @@ as.dgCMatrix.spam <- function(x)  {
                     rowpointers = vector("integer", dimx[2] + 1),
                     NAOK = getOption("spam.NAOK"),
                     PACKAGE = "spam")
+      ## SS <- .format.spam(x)
+      ## z <- .C64("transpose",
+      ##           SIGNATURE = c( SS$signature, SS$signature,
+      ##                         "double", SS$signature, SS$signature,
+      ##                         "double", SS$signature, SS$signature),
+                
+      ##           n = dimx[1],
+      ##           m = dimx[2],
+                
+      ##           a = x@entries,
+      ##           ja = x@colindices,
+      ##           ia = x@rowpointers,
+                
+      ##           entries = vector_dc("double",nz),
+      ##           colindices = vector_dc(SS$type, nz),
+      ##           rowpointers = vector_dc(SS$type, dimx[2] + 1),
+
+      ##           INTENT = c("r", "r",
+      ##                      "r", "r", "r",
+      ##                      "w", "w", "w"),
+      ##           NAOK = getOption("spam.NAOK"),
+      ##           PACKAGE = SS$package)
       newx <- new(p=0:0,"dgCMatrix")
       slot(newx,"x",check=FALSE) <- z$entries
       slot(newx,"i",check=FALSE) <- z$colindices-1L

R/helper.R

-# This is file ../spam/R/helper.R
-# This file is part of the spam package, 
-#      http://www.math.uzh.ch/furrer/software/spam/
-# by Reinhard Furrer [aut, cre], Florian Gerber [ctb]
-     
+# HEADER ####################################################
+# This is file spam/R/helper.R.                             #
+# It is part of the R package spam,                         #
+#  --> https://CRAN.R-project.org/package=spam              #
+#  --> https://CRAN.R-project.org/package=spam64            #
+#  --> https://git.math.uzh.ch/reinhard.furrer/spam         #
+# by Reinhard Furrer [aut, cre], Florian Gerber [ctb],      #
+#    Daniel Gerber [ctb], Kaspar Moesinger [ctb],           #
+#    Youcef Saad [ctb] (SPARSEKIT),                         #
+#    Esmond G. Ng [ctb] (Fortran Cholesky routines),        #
+#    Barry W. Peyton [ctb] (Fortran Cholesky routines),     #
+#    Joseph W.H. Liu [ctb] (Fortran Cholesky routines),     #
+#    Alan D. George