Contents

Here we describe the steps taken to process the original HDF5 source code to produce the modified version distributed with this package. This is for record keeping only, users of the Rhdf5lib package are not expected to follow any of the steps detailed here.

library(stringr)

Download the HDF5 source tarball and unpack into a temporary directory. We rename the output folder to hdf5.

hdf5_source <- tempfile()
download.file(url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.bz2", dest = hdf5_source)
untar(tarfile = hdf5_source, exdir = tempdir())
system2("mv", args = c(file.path(tempdir(), "hdf5-1.10.5"), file.path(tempdir(), "hdf5")))
hdf5_dir <- file.path(tempdir(), "hdf5")

Delete folders we are not distributing.

unlink(x = file.path(hdf5_dir, c("examples", "fortran", "java", 
             "release_docs", "test", "testpar", "tools", 
             "c++/examples", "c++/test", 
             "hl/fortran", "hl/examples", "hl/tools", "hl/test",
             "hl/c++/examples", "hl/c++/test")),
       recursive = TRUE)

Next we make some modifications to configure scripts and make files, removing references to the folders we have deleted.

configure_ac <- xfun::read_utf8(file.path(hdf5_dir, "configure.ac"))

## modify list of build files
start <- which(str_detect(configure_ac, pattern = "AC_CONFIG_FILES"))
end <- which(str_detect(configure_ac[start:(length(configure_ac))], pattern = "\\)$"))[1] + start - 1
config_files <- configure_ac[start:end]
rm_idx <- which(str_detect(config_files, pattern = "test/|testpar/|tools/|examples/|fortran/|java/|h5c++/"))
config_files <- config_files[-rm_idx]
config_files[length(config_files)] <- paste0(tail(config_files, 1), "])")
configure_ac[start] <- paste(config_files, collapse = "\n")
configure_ac <- configure_ac[-((start+1):(end))]

## remove reference to h5cc
h5cc <- str_which(configure_ac, pattern = "chmod 755 tools/src/misc/h5cc")
configure_ac <- configure_ac[-((h5cc):(h5cc+4))]

## fortran headers
fortran_inc <- str_which(configure_ac, pattern = "AC_CONFIG_HEADERS\\(\\[fortran/src/H5config_f\\.inc")
configure_ac[fortran_inc:(fortran_inc+1)] <- paste("##", configure_ac[fortran_inc:(fortran_inc+1)])

## write 
xfun::write_utf8(configure_ac, con = file.path(hdf5_dir, "configure.ac"))

## C++ makefile
make_cplusplus <- xfun::read_utf8(file.path(hdf5_dir, 'c++/Makefile.am'))
idx <- str_which(make_cplusplus, "BUILD_CXX_CONDITIONAL")
make_cplusplus[idx] <- "if BUILD_CXX_CONDITIONAL\n   SUBDIRS=src\nendif\nDIST_SUBDIRS = src"
make_cplusplus <- make_cplusplus[-((idx+1):(length(make_cplusplus)-2))] 
xfun::write_utf8(make_cplusplus, con = file.path(hdf5_dir, "c++/Makefile.am"))

## HL makefile
make_hl <- xfun::read_utf8(file.path(hdf5_dir, 'hl/Makefile.am'))
idx <- str_which(make_hl, "BUILD_HDF5_HL_CONDITIONAL")
make_hl[idx] <- "if BUILD_HDF5_HL_CONDITIONAL\n   SUBDIRS=src $(CXX_DIR)\nendif\nDIST_SUBDIRS = src c++"
make_hl <- make_hl[-((idx+1):(length(make_hl)-2))] 
xfun::write_utf8(make_hl, con = file.path(hdf5_dir, "hl/Makefile.am"))

## HL C++ makefile
make_hl_cpp <- xfun::read_utf8(file.path(hdf5_dir, 'hl/c++/Makefile.am'))
idx <- str_which(make_hl_cpp, "^SUBDIRS=src")
make_hl_cpp[idx] <- "SUBDIRS=src\nDIST_SUBDIRS=src"
make_hl_cpp <- make_hl_cpp[-((idx+1):(length(make_hl_cpp)-2))] 
xfun::write_utf8(make_hl_cpp, con = file.path(hdf5_dir, "hl/c++/Makefile.am"))

## Primary makefile
make <- xfun::read_utf8(file.path(hdf5_dir, 'Makefile.am'))
idx <- str_which(make, "SUBDIRS = src test")[1]
make[idx] <- "SUBDIRS = src . $(CXX_DIR) $(HDF5_HL_DIR)"
make[idx+1] <- "DIST_SUBDIRS = src . c++ hl"
make[idx+2]  <- ""
idx <- str_which(make, "# Make all, tests, and \\(un\\)install")
make[(idx+1):(idx+6)] <- paste0("##", make[(idx+1):(idx+6)])
xfun::write_utf8(make, con = file.path(hdf5_dir, "Makefile.am"))

Address problem in source code reported on CRAN Solaris builder.

code <- xfun::read_utf8(file.path(hdf5_dir, 'c++', 'src', 'H5Library.cpp'))
code <- str_replace(code, '([ ]{1,})(exit\\()', replacement = '\\1std::\\2' )
xfun::write_utf8(code, con = file.path(hdf5_dir, 'c++', 'src', 'H5Library.cpp'))

Process the modified scripts.

system(command = paste0("cd ", hdf5_dir, " && autoconf"))
system(command = paste0("cd ", hdf5_dir, " && aclocal"))
system(command = paste0("cd ", hdf5_dir, " && automake"))
unlink(file.path(hdf5_dir, "autom4te.cache"), recursive = TRUE)

0.1 SZIP

Now we carry out a similar process for the SZIP library.

szip_source <- tempfile()
download.file(url = "https://support.hdfgroup.org/ftp/lib-external/szip/2.1.1/src/szip-2.1.1.tar.gz",
              dest = szip_source)
untar(tarfile = szip_source, exdir = tempdir())
system2("mv", args = c(file.path(tempdir(), "szip-2.1.1"), file.path(tempdir(), "szip")))
szip_dir <- file.path(tempdir(), "szip")
unlink(x = file.path(szip_dir, "test"),
       recursive = TRUE)
xfun::read_utf8(file.path(szip_dir, "configure.ac")) %>%
  str_remove("test/Makefile") %>%
  xfun::write_utf8(file.path(szip_dir, "configure.ac"))

xfun::read_utf8(file.path(szip_dir, "Makefile.am")) %>%
  str_replace(pattern = "SUBDIRS=src test", replacement = "SUBDIRS=src") %>%
  xfun::write_utf8(file.path(szip_dir, "Makefile.am"))
system(command = paste0("cd ", szip_dir, " && autoconf"))
system(command = paste0("cd ", szip_dir, " && aclocal"))
system(command = paste0("cd ", szip_dir, " && automake"))
unlink(file.path(szip_dir, "autom4te.cache"), recursive = TRUE)

0.2 Create tarball

Move the SZIP source into the HDF5 distribution and create the tarball that will be distributed with the R package. We use the system tar command here as I can’t figure out how to include only the base directory in the tarball when using R’s inbuilt function.

system2("mv", args = c(szip_dir, file.path(hdf5_dir, "szip")))
system2("tar", args = c("-C", tempdir(), "-czf", file.path(tempdir(), "hdf5small_cxx_hl_1.10.5.tar.gz"), "hdf5"))

Finally copy this to the /tmp/ so it is easy to find, inspect, and move to the package directory if correct.

if(file.exists("/tmp/hdf5small_cxx_hl_1.10.5.tar.gz")) { file.remove("/tmp/hdf5small_cxx_hl_1.10.5.tar.gz") }
file.copy(file.path(tempdir(), "hdf5small_cxx_hl_1.10.5.tar.gz"), to = "/tmp/")