exec/rf_build_packages.R

In rfTools: R-Forge Build and Check Tools

## rf Windows Toolchain: rf_build_pkgs.R
## R-Forge Windows build/check system script
## This script loads the R-Forge infrastructure package which includes
## all binary-building code
## In previous versions this file was called 'rforge_build_packages.R'
## Licence GPL-2
## Author: Stefan Theussl
## Last Change: 2012-05-30

require( "rfTools", lib = "R:/lib/local" )

## R-devel path
R_DEVEL <- "R:/lib/R/R-devel"

## release, patched | devel
is_devel <- R.version[["status"]] == "Under development (unstable)"

## local library path (this is where the packages (and dependencies get installed to)
if( is_devel ){
    maj.version <- paste( R.Version()$maj, unlist(strsplit(R.Version()$min, "[.]"))[1], sep = "." )
    local_lib <- file.path("R:/lib/local", sprintf("%s-dev", maj.version) )
} else {
  maj.version <- paste( R.Version()$maj, unlist(strsplit(R.Version()$min, "[.]"))[1], sep = "." )
  local_lib <- file.path("R:/lib/local", maj.version)
}


## environment variables from Kurt's check script
Sys.setenv(R_BROWSER="false")
Sys.setenv(R_PDFVIEWER="false")



# TODO
# comment out to pull devel/release folders from xmgallagher rather than hardcoded urls from bioc website
# i.e.
# system("mount \\\\xmgallagher.wu.ac.at\\srv\\nfs\\R S:")
# file:
#patched
#bioc_url        = "file://S:/Bioconductor/release/bioc/",
#bioc_data       = "file://S:/Bioconductor/release/data/annotation",
#bioc_experiment = "file://S:/Bioconductor/release/data/experiment",
#devel
#bioc_url        = "file://S:/Bioconductor/devel/bioc/",
#bioc_data       = "file://S:/Bioconductor/devel/data/annotation",
#bioc_experiment = "file://S:/Bioconductor/devel/data/experiment",

## make bioc URLs
R_flavor <- switch( R.version$status,
                    "Patched" = "R-patched",
                    "Under development (unstable)" = "R-devel",
                    "R-patched" )
bioc_url <- ifelse( R_flavor == "R-devel",
                    "http://bioconductor.statistik.tu-dortmund.de/packages/3.4/bioc",
                    "http://bioconductor.statistik.tu-dortmund.de/packages/3.3/bioc")
bioc_data <- ifelse( R_flavor == "R-devel",
                    "http://bioconductor.statistik.tu-dortmund.de/packages/3.4/data/annotation",
                    "http://bioconductor.statistik.tu-dortmund.de/packages/3.3/data/annotation")
bioc_exp <- ifelse( R_flavor == "R-devel",
                    "http://bioconductor.statistik.tu-dortmund.de/packages/3.4/data/experiment",
                    "http://bioconductor.statistik.tu-dortmund.de/packages/3.3/data/experiment")

## we have to set 'R_LIBS' again otherwise package dependencies are not found
Sys.setenv("R_LIBS" = local_lib)

## STAGING AREA
stmp <- "T:"

## build root, where the builds/checks are done
build_root <- "R:/run/building"
if(!file.exists(build_root))
  dir.create(build_root)


system("mount \\\\xsshelob-dmz.wu.ac.at\\srv\\nfs\\rforge\\staging T:")
## take a source build and uncompress
if( !is_devel ){
    src_dir <- rf_takeover_prepared_build(stmp, build_root, type = "win")
} else {
  src_dir <- Sys.getenv( "RF_SRC_DIR" )
  src_dir <- ifelse( src_dir == "", NULL, src_dir ) 
}

if( is.null(src_dir) ){
    writeLines("No submission found. Exiting.")
    q( save = "no" ) }

## load pkg meta info
load( file.path(build_root, src_dir, "PKG_STAT.rda") )


if( !is_devel ){
## build and check packages patched
Sys.setenv("R_LIBS" = local_lib)
## setup control file
control <- rf_build_control(path_to_pkg_src  = file.path(build_root, src_dir),            ## R-Forge uncompressed pkg source
                            path_to_pkg_log  = file.path(build_root, src_dir, "RF_LOGS"), ## Log directory
                            path_to_pkg_root = file.path(build_root, src_dir, "RF_PKG_ROOT"), ## R-Forge root (contains /src ,/bin)
                            path_to_local_texmf = "",                      ## path to local texmf
                            path_to_local_library = local_lib,             ## path to local pkg library
                            path_to_local_pkg_libs = file.path(build_root, "PKG_LIBS"),       ## path to local per pkg libraries in case of R-Forge deps
                            path_to_check_dir = file.path(build_root, src_dir, "RF_PKG_CHECK"), ## path to check dir
                            stoplist = file.path(system.file("stoplists", package = "rfTools"), "windows.csv"),      ## path to stoplist
                            cpu_time_limit = 600,                          ## CPU time limit
                            mail_domain_name_of_sender = "stefan7th@r-forge.wu.ac.at", ## "xmorthanc.wu.ac.at"
                            mail_relay_server = "r-forge.wu.ac.at",                    ## only necessary with sendEmail
                            mail_programme = "sendEmail")                       ## on Windows: sendEmail

## start building ...
rf_build_packages( rf_pkg_status,
                   platform        = "Windows",
                   architecture    = "x86_64",
                   bioc_url        = bioc_url,
                   bioc_data       = bioc_data,
                   bioc_experiment = bioc_exp,
                   control         = control )

rf_check_packages( rf_pkg_status,
                   platform        = "Windows",
                   architecture    = "x86_64",
                   bioc_url        = bioc_url,
                   bioc_data       = bioc_data,
                   bioc_experiment = bioc_exp,
                   control         = control )

## now devel
#Sys.setenv( "RF_SRC_DIR" = src_dir )

## call R-devel here, will go then to else path
#system( sprintf( "%s --vanilla < %s", R_DEVEL, system.file(file.path("exec", "rf_build_packages"), package = "rfTools") ))

} else {

## check packages devel
control_devel <- rf_build_control(path_to_pkg_src  = file.path(build_root, src_dir),          ## R-Forge uncompressed pkg source
                            path_to_pkg_log  = file.path(build_root, src_dir, "RF_LOGS_DEVEL"),## Log directory
                            path_to_pkg_root = file.path(build_root, src_dir, "RF_PKG_ROOT"), ## R-Forge root (contains /src ,/bin)
                            path_to_local_texmf = "",                   ## path to local texmf
                            path_to_local_library = local_lib,                                ## path to local pkg library
			    path_to_local_pkg_libs = file.path(build_root, "PKG_LIBS_DEVEL"),       ## path to local per pkg libraries in case of R-Forge deps
                            path_to_check_dir = file.path(build_root, src_dir, "RF_PKG_CHECK_DEVEL"), ## path to check dir
                            stoplist = file.path(system.file("stoplists", package = "rfTools"), "windows.csv"), ## path to stoplist
                            cpu_time_limit = 600,                                             ## CPU time limit
                            mail_domain_name_of_sender = "stefan7th@r-forge.wu.ac.at",## "xmorthanc.wu.ac.at" 
                            mail_relay_server = "r-forge.wu.ac.at",                                           ## only necessary with sendEmail
                            mail_programme = "sendEmail")                                          ## on Windows: sendEmail


rf_check_packages( rf_pkg_status,
                   platform        = "Windows",
                   architecture    = "x86_64",
                   bioc_url        = bioc_url,
                   bioc_data       = bioc_data,
                   bioc_experiment = bioc_exp,
                   control         = control_devel)

}



if( !is_devel ){
TAR <- Sys.getenv("TAR")
WINDOWS <- .Platform$OS.type == "windows"
if (!nzchar(TAR)) {
  TAR <- if (WINDOWS)
    "tar --force-local"
  else "internal"
}

files <- file.path(src_dir, c("RF_LOGS", "RF_PKG_CHECK", "RF_PKG_ROOT"))
#res <- utils::tar( file.path(stmp, paste("WIN", src_dir, "tar.gz", sep = ".")),
#                  files = files, compression = "gzip", compression_level = 9, tar = TAR,
#                  extra_flags = sprintf("-C %s", build_root) )
#temporary tar fix
shell_cmd=file.path("R:","lib","local", "rfTools", "exec", "rf_open_cmdshell.bat")
sys_cmd=paste("tar -C", build_root, "-zcf",
        file.path(stmp, paste("WIN", src_dir, "tar.gz", sep = ".")),
        paste(files, sep = "" , collapse=" "))
system(shell_cmd, input = sys_cmd)
## cleanup build dir
unlink(file.path(build_root, src_dir), recursive = TRUE)

## and remove uncompressed src submission
file.remove( file.path(stmp, paste("SRC.", src_dir, ".tar.gz.processing.WIN", sep = "")) )
#print(file.path(stmp, paste("SRC.", src_dir, ".tar.gz.processing.WIN", sep = "")))
system("umount -f T:")
}

TRUE