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---
title: "Creating this HDF5 distribution"
author:
- name: Mike L. Smith
affiliation: de.NBI & EMBL Heidelberg
package: Rhdf5lib
output:
BiocStyle::html_document
vignette: |
%\VignetteIndexEntry{Creating this HDF5 distribution}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
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.
```{r setup, include=FALSE}
knitr::opts_chunk$set(eval = FALSE)
```
```{r, loadLibraries}
library(stringr)
```
Download the HDF5 source tarball and unpack into a temporary directory. We rename the output folder to *hdf5*.
```{r}
hdf5_source <- tempfile()
download.file(url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7.tar.bz2", dest = hdf5_source)
untar(tarfile = hdf5_source, exdir = tempdir())
system2("mv", args = c(file.path(tempdir(), "hdf5-1.10.7"), file.path(tempdir(), "hdf5")))
```
```{r}
hdf5_dir <- file.path(tempdir(), "hdf5")
```
Delete folders we are not distributing.
```{r}
unlink(x = file.path(hdf5_dir, c("examples", "fortran", "java",
"release_docs", "test", "testpar", "tools",
"c++/examples", "c++/test",
"hl/fortran", "hl/examples", "hl/tools", "hl/test",
"hl/c++/examples", "hl/c++/test")),
recursive = TRUE)
```
Next we make some modifications to configure scripts and make files, removing references to the folders we have deleted.
```{r}
configure_ac <- xfun::read_utf8(file.path(hdf5_dir, "configure.ac"))
## modify list of build files
start <- which(str_detect(configure_ac, pattern = "AC_CONFIG_FILES"))
end <- which(str_detect(configure_ac[start:(length(configure_ac))], pattern = "\\)$"))[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 [a-z/]*/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")[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.
```{r}
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.
```{r}
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)
```
## SZIP
Now we carry out a similar process for the SZIP library.
```{r}
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")))
```
```{r}
szip_dir <- file.path(tempdir(), "szip")
```
```{r}
unlink(x = file.path(szip_dir, "test"),
recursive = TRUE)
```
```{r}
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"))
```
```{r}
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)
```
## 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.*
```{r, createTarball}
system2("mv", args = c(szip_dir, file.path(hdf5_dir, "szip")))
system2("tar", args = c("-C", tempdir(), "-czf", file.path(tempdir(), "hdf5small_cxx_hl_1.10.7.tar.gz"), "hdf5"))
```
Finally copy this to the `/tmp/` so it is easy to find, inspect, and move to the package directory if correct.
```{r}
if(file.exists("/tmp/hdf5small_cxx_hl_1.10.7.tar.gz")) { file.remove("/tmp/hdf5small_cxx_hl_1.10.7.tar.gz") }
file.copy(file.path(tempdir(), "hdf5small_cxx_hl_1.10.7.tar.gz"), to = "/tmp/")
```
|
