houba

Manipulation of (Large) Memory-Mapped Objects (Vectors, Matrices and Arrays)

v0.1.1 · Feb 20, 2026 · CeCILL-2

Description

Manipulate data through memory-mapped files, as vectors, matrices or arrays. Basic arithmetic functions are implemented, but currently no matrix arithmetic. Can write and read descriptor files for compatibility with the 'bigmemory' package.

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CRAN Check Status

3 ERROR

11 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	148.4s
r-devel-linux-x86_64-debian-gcc	OK	108.1s
r-devel-linux-x86_64-fedora-clang	OK	228.6s
r-devel-linux-x86_64-fedora-gcc	OK	291.8s
r-devel-macos-arm64	OK	47s
r-devel-windows-x86_64	OK	252s
r-oldrel-macos-arm64	ERROR	30s
r-oldrel-macos-x86_64	ERROR	174s
r-oldrel-windows-x86_64	ERROR	250s
r-patched-linux-x86_64	OK	137.5s
r-release-linux-x86_64	OK	134.1s
r-release-macos-arm64	OK	40s
r-release-macos-x86_64	OK	213s
r-release-windows-x86_64	OK	237s

Check details (16 non-OK)

OK r-devel-linux-x86_64-debian-clang

OK r-devel-linux-x86_64-debian-gcc

OK r-devel-linux-x86_64-fedora-clang

OK r-devel-linux-x86_64-fedora-gcc

OK r-devel-macos-arm64

OK r-devel-windows-x86_64

NOTE r-oldrel-macos-arm64

installed package size

  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb

ERROR r-oldrel-macos-arm64

tests

  Running ‘apply.r’ [0s/0s]
  Running ‘arithmetic.r’ [0s/0s]
  Running ‘as-array.r’ [0s/0s]
  Running ‘colSums.r’ [0s/0s]
  Running ‘copy.r’ [0s/0s]
  Running ‘create.r’ [0s/0s]
Running the tests in ‘tests/create.r’ failed.
Complete output:
  > # Various tests about object creation and manipulation
  > require(houba)
  Loading required package: houba
  > 
  > # float mmatrix ------------------------
  > A <- mmatrix("float", 10, 20)
  > a <- as.matrix(A)
  > stopifnot(typeof(a) == "double")
  > 
  > # set max size
  > houba(max.size = 10)
  $max.size
  [1] 10
  
  > stopifnot( typeof(A[1:10]) == "double" )
  > stopifnot( typeof(A[1:11]) == "S4" )
  > 
  > # assignement and subsetting
  > A[1,1] <- 12
  > A[3,] <- 1.34
  > stopifnot( all(abs(as.matrix(A[1:3, 1:2] - c(12, 0, 1.34, 0, 0, 1.34))) < 1e-6)  )
  > 
  > A[5] <- pi
  > stopifnot( all(abs(as.vector(A[,1] - c(12, 0, 1.34, 0, pi, 0, 0, 0, 0, 0))) < 1e-6) )
  > 
  > # int mmatrix ---------------------------
  > B <- mmatrix("int", 10, 20)
  > b <- as.matrix(B)
  > stopifnot(typeof(b) == "integer")
  > 
  > # assignement and subsetting
  > B[1,1] <- 12
  > B[3,] <- 1.34
  > stopifnot( all(as.matrix(B[1:3, 1:2]) == c(12L, 0L, 1L, 0L, 0L, 1L)) )
  > 
  > B[5] <- 2
  > stopifnot( all(as.vector(B[5, 1:3]) == c(2L, 0L, 0L)) )
  > 
  > # assignement with other mmatrix values
  > houba(max.size = 0) # force non conversion to R 
  $max.size
  [1] 0
  
  > B[2,] <- A[3,]
  > stopifnot( all(as.vector(B[2, 1:4]) == c(1L, 1L, 1L, 1L)) )
  > 
  > B[5] <- A[3]
  > stopifnot( all(as.vector(B[5, 1:3]) == c(1L, 0L, 0L)) )
  > 
  > # double mvector -------------------------
  > V <- mvector("double", 10)
  > v <- as.vector(V)
  > V[1:4] <- pi
  > stopifnot( all(as.vector(V[3:6]) == c(pi, pi, 0, 0)) ) 
  > 
  > # int array --------------------------
  > C <- marray("int", 2:4)
  > C[,,1] <- 7
  > C[,2,] <- B[5]
  Error in `[<-`(`*tmp*`, , 2, , value = new("mvector", ptr = <pointer: 0x15aa14f40>,  : 
    argument is missing, with no default
  Calls: [<- -> [<- -> myMissing
  Execution halted

NOTE r-oldrel-macos-x86_64

installed package size

  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb

ERROR r-oldrel-macos-x86_64

tests

  Running ‘apply.r’ [0s/1s]
  Running ‘arithmetic.r’ [1s/1s]
  Running ‘as-array.r’ [0s/1s]
  Running ‘colSums.r’ [0s/1s]
  Running ‘copy.r’ [0s/1s]
  Running ‘create.r’ [0s/1s]
Running the tests in ‘tests/create.r’ failed.
Complete output:
  > # Various tests about object creation and manipulation
  > require(houba)
  Loading required package: houba
  > 
  > # float mmatrix ------------------------
  > A <- mmatrix("float", 10, 20)
  > a <- as.matrix(A)
  > stopifnot(typeof(a) == "double")
  > 
  > # set max size
  > houba(max.size = 10)
  $max.size
  [1] 10
  
  > stopifnot( typeof(A[1:10]) == "double" )
  > stopifnot( typeof(A[1:11]) == "S4" )
  > 
  > # assignement and subsetting
  > A[1,1] <- 12
  > A[3,] <- 1.34
  > stopifnot( all(abs(as.matrix(A[1:3, 1:2] - c(12, 0, 1.34, 0, 0, 1.34))) < 1e-6)  )
  > 
  > A[5] <- pi
  > stopifnot( all(abs(as.vector(A[,1] - c(12, 0, 1.34, 0, pi, 0, 0, 0, 0, 0))) < 1e-6) )
  > 
  > # int mmatrix ---------------------------
  > B <- mmatrix("int", 10, 20)
  > b <- as.matrix(B)
  > stopifnot(typeof(b) == "integer")
  > 
  > # assignement and subsetting
  > B[1,1] <- 12
  > B[3,] <- 1.34
  > stopifnot( all(as.matrix(B[1:3, 1:2]) == c(12L, 0L, 1L, 0L, 0L, 1L)) )
  > 
  > B[5] <- 2
  > stopifnot( all(as.vector(B[5, 1:3]) == c(2L, 0L, 0L)) )
  > 
  > # assignement with other mmatrix values
  > houba(max.size = 0) # force non conversion to R 
  $max.size
  [1] 0
  
  > B[2,] <- A[3,]
  > stopifnot( all(as.vector(B[2, 1:4]) == c(1L, 1L, 1L, 1L)) )
  > 
  > B[5] <- A[3]
  > stopifnot( all(as.vector(B[5, 1:3]) == c(1L, 0L, 0L)) )
  > 
  > # double mvector -------------------------
  > V <- mvector("double", 10)
  > v <- as.vector(V)
  > V[1:4] <- pi
  > stopifnot( all(as.vector(V[3:6]) == c(pi, pi, 0, 0)) ) 
  > 
  > # int array --------------------------
  > C <- marray("int", 2:4)
  > C[,,1] <- 7
  > C[,2,] <- B[5]
  Error in `[<-`(`*tmp*`, , 2, , value = new("mvector", ptr = <pointer: 0x7f7de2f21f70>,  : 
    argument is missing, with no default
  Calls: [<- -> [<- -> myMissing
  Execution halted

ERROR r-oldrel-windows-x86_64

tests

  Running 'apply.r' [1s]
  Running 'arithmetic.r' [1s]
  Running 'as-array.r' [1s]
  Running 'colSums.r' [1s]
  Running 'copy.r' [1s]
  Running 'create.r' [1s]
  Running 'dim.r' [1s]
  Running 'extract-replace.r' [1s]
  Running 'inplace.r' [1s]
  Running 'marray.r' [1s]
  Running 'restore.r' [1s]
Running the tests in 'tests/create.r' failed.
Complete output:
  > # Various tests about object creation and manipulation
  > require(houba)
  Loading required package: houba
  > 
  > # float mmatrix ------------------------
  > A <- mmatrix("float", 10, 20)
  > a <- as.matrix(A)
  > stopifnot(typeof(a) == "double")
  > 
  > # set max size
  > houba(max.size = 10)
  $max.size
  [1] 10
  
  > stopifnot( typeof(A[1:10]) == "double" )
  > stopifnot( typeof(A[1:11]) == "S4" )
  > 
  > # assignement and subsetting
  > A[1,1] <- 12
  > A[3,] <- 1.34
  > stopifnot( all(abs(as.matrix(A[1:3, 1:2] - c(12, 0, 1.34, 0, 0, 1.34))) < 1e-6)  )
  > 
  > A[5] <- pi
  > stopifnot( all(abs(as.vector(A[,1] - c(12, 0, 1.34, 0, pi, 0, 0, 0, 0, 0))) < 1e-6) )
  > 
  > # int mmatrix ---------------------------
  > B <- mmatrix("int", 10, 20)
  > b <- as.matrix(B)
  > stopifnot(typeof(b) == "integer")
  > 
  > # assignement and subsetting
  > B[1,1] <- 12
  > B[3,] <- 1.34
  > stopifnot( all(as.matrix(B[1:3, 1:2]) == c(12L, 0L, 1L, 0L, 0L, 1L)) )
  > 
  > B[5] <- 2
  > stopifnot( all(as.vector(B[5, 1:3]) == c(2L, 0L, 0L)) )
  > 
  > # assignement with other mmatrix values
  > houba(max.size = 0) # force non conversion to R 
  $max.size
  [1] 0
  
  > B[2,] <- A[3,]
  > stopifnot( all(as.vector(B[2, 1:4]) == c(1L, 1L, 1L, 1L)) )
  > 
  > B[5] <- A[3]
  > stopifnot( all(as.vector(B[5, 1:3]) == c(1L, 0L, 0L)) )
  > 
  > # double mvector -------------------------
  > V <- mvector("double", 10)
  > v <- as.vector(V)
  > V[1:4] <- pi
  > stopifnot( all(as.vector(V[3:6]) == c(pi, pi, 0, 0)) ) 
  > 
  > # int array --------------------------
  > C <- marray("int", 2:4)
  > C[,,1] <- 7
  > C[,2,] <- B[5]
  Error in `[<-`(`*tmp*`, , 2, , value = new("mvector", ptr = <pointer: 0x0000024ee08e7670>,  : 
    argument is missing, with no default
  Calls: [<- -> [<- -> myMissing
  Execution halted
Running the tests in 'tests/marray.r' failed.
Complete output:
  > require(houba)
  Loading required package: houba
  > 
  > a <- mvector("int", 2)
  > a[2] <- 1
  > stopifnot( a[2] == 1 )
  > 
  > a <- mmatrix("float", 6, 3)
  > a[] <- 1:18
  > stopifnot( all(a[1,] == c(1, 7, 13)) )
  > 
  > a <- marray("double", 2:4)
  > a[] <- 1:24
  > stopifnot( all(a[2,1,] == c(2, 8, 14, 20)) )
  Error in a[2, 1, ] : argument is missing, with no default
  Calls: stopifnot -> [ -> [ -> myMissing
  Execution halted

OK r-patched-linux-x86_64

OK r-release-linux-x86_64

OK r-release-macos-arm64

OK r-release-macos-x86_64

OK r-release-windows-x86_64

Check History

ERROR 11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Mar 9, 2026

ERROR r-oldrel-macos-arm64

installed package size

  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb

ERROR r-oldrel-macos-x86_64

installed package size

  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb

ERROR r-oldrel-windows-x86_64

tests

  Running 'apply.r' [1s]
  Running 'arithmetic.r' [1s]
  Running 'as-array.r' [1s]
  Running 'colSums.r' [1s]
  Running 'copy.r' [1s]
  Running 'create.r' [1s]
  Running 'dim.r' [1s]
  Running 'extract-replace.r' [1s]
  Running 'inplace.r' [1s]
  Running 'marray.r' [1s]
  Running 'restore.r' [1s]
Running the tests in 'tests/create.r' failed.
Complete output:
  > # Various tests about object creation and manipulation
  > require(houba)
  Loading required package: houba
  > 
  > # float mmatrix --

Dependency Network

Version History

new 0.1.1 Mar 9, 2026