add option to not cleanup (debug) packages to build. update aliases/hashes from db.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/cran2deb@301 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

diff --git a/trunk/R/build.R b/trunk/R/build.R
index 3855a27d8251a88bc580a50213ea7adaea61ef3b..540610f2fda99fb14ffb37f82c954f350bd91641 100644 (file)
--- a/trunk/R/build.R
+++ b/trunk/R/build.R
@@ -1,5 +1,5 @@
 
-build <- function(name,extra_deps,force=F) {
+build <- function(name,extra_deps,force=F,do_cleanup=T) {
     # can't, and hence don't need to, build base packages
     if (name %in% base_pkgs) {
         return(T)
@@ -58,7 +58,11 @@ build <- function(name,extra_deps,force=F) {
         }
         return(pkg$debversion)
     })())
-    cleanup(dir)
+    if (do_cleanup) {
+        cleanup(dir)
+    } else {
+        notice('output is in',dir,'. you must clean this up yourself.')
+    }
     if (is.null(result)) {
         # nothing was done so escape asap.
         return(result)

diff --git a/trunk/R/log.R b/trunk/R/log.R
index 2a9be4edbd51b78d8e586ecc612dd08ba8a84a5a..3d74bae7221123116434b59d94747fdb38bdd532 100644 (file)
--- a/trunk/R/log.R
+++ b/trunk/R/log.R
@@ -54,6 +54,7 @@ log_system <- function(...) {
     if (inherits(r,'try-error')) {
         fail('system failed on:',paste(...))
     }
+    log_add(paste('C:',...))
     for (line in r[[2]]) {
         if (!length(grep('^[WENI]:',line))) {
             line = paste('I:',line)

diff --git a/trunk/data/populate_depend_aliases b/trunk/data/populate_depend_aliases
index de68484ec9c8f751f7cd76c4bcc061dbf47c6223..efdd16fc45ad1353149d02150b80a768efc8a1f8 100644 (file)
--- a/trunk/data/populate_depend_aliases
+++ b/trunk/data/populate_depend_aliases
@@ -56,7 +56,7 @@ alias_run pari-gp pari-gp
 alias_build proj proj 
 alias_run proj proj 
 alias_build quantlib libquantlib0-dev 
-alias_run quantlib libquantlib-0.9.7 
+alias_run quantlib libquantlib-0.9.9 
 alias_run sqlite libsqlite3-0 
 alias_build sqlite libsqlite3-dev 
 alias_build zlib zlib1g-dev 
@@ -67,7 +67,7 @@ alias_build autotools autotools-dev
 alias_build tcl tcl8.5-dev 
 alias_build tk tk8.5-dev 
 alias_build odbc unixodbc-dev 
-alias_build mysql libmysqlclient15-dev 
+alias_build mysql libmysqlclient-dev 
 alias_build mpi libopenmpi-dev 
 alias_build pvm pvm-dev 
 alias_build hdf5 libhdf5-serial-dev 
@@ -123,3 +123,11 @@ alias_build pkg-config pkg-config
 alias_run pkg-config pkg-config 
 alias_build rgtk2 r-cran-rgtk2 
 alias_run rgtk2 r-cran-rgtk2 
+alias_build libitpp libitpp-dev 
+alias_build libxerces-c libxerces-c-dev 
+alias_build protobuf-compiler protobuf-compiler 
+alias_build libprotobuf-dev libprotobuf-dev 
+alias_build libprotoc-dev libprotoc-dev 
+alias_build postgresql_java libpg-java 
+alias_run postgresql_java libpg-java 
+alias_build armadillo libarmadillo-dev 

diff --git a/trunk/data/populate_forcedep b/trunk/data/populate_forcedep
index 294048052d50d6aee7e127fabd30217cf0b7b22e..94467e90286cecfc15aaa17c3cd54bb0208f34ed 100644 (file)
--- a/trunk/data/populate_forcedep
+++ b/trunk/data/populate_forcedep
@@ -20,7 +20,6 @@ force boost RBGL
 force netcdf RNetCDF 
 force libtiff biOps 
 force fftw-dev rimage 
-force r-recommended spBayes 
 force libxt Cairo 
 force autotools qp 
 force boost MBA 
@@ -50,3 +49,18 @@ force colorspace DoE.base
 force pkg-config mvgraph 
 force glade RGtk2 
 force rgtk2 rattle 
+force libitpp psgp 
+force java farmR 
+force gsl mvabund 
+force colorspace nnDiag 
+force autotools fftw 
+force protobuf-compiler RProtoBuf 
+force libprotobuf-dev RProtoBuf 
+force libprotoc-dev RProtoBuf 
+force pkg-config RProtoBuf 
+force colorspace simPopulation 
+force java RpgSQL 
+force netcdf ncdf4 
+force colorspace vcdExtra 
+force boost RcppArmadillo 
+force pkg-config fftw 

diff --git a/trunk/data/populate_license_hashes b/trunk/data/populate_license_hashes
index d13d08d3b808dfaf9058a2a386a7f43aaa57a4b6..005e2b9102c3c52c836b9b34bf321cfa8586cfc6 100644 (file)
--- a/trunk/data/populate_license_hashes
+++ b/trunk/data/populate_license_hashes
@@ -13,14 +13,11 @@ accept x11
 accept distrib-noncomm 
 accept gpl+acm 
 accept unclear 
-accept acepack 
-accept ff 
 accept nistnls 
 accept rtiff 
 accept mvpart 
 accept mmcm 
 accept grade 
-accept eupl 
 accept agpl 
 accept scagnostics 
 accept akima 
@@ -33,6 +30,20 @@ accept acm
 accept camassclass 
 accept rwt 
 accept tcltk2 
+accept agpl-3 
+accept gpl-2-qa 
+accept ff_license 
+accept rindex_license 
+accept eupl 
+accept statnet 
+accept degreenet 
+accept geometry 
+accept ergm 
+accept acepack 
+accept ff 
+accept mspath 
+accept ever 
+accept latentnet 
 hash_sha1 apache 2b8b815229aa8a61e483fb4ba0588b8b6c491890 
 hash_sha1 artistic be0627fff2e8aef3d2a14d5d7486babc8a4873ba 
 hash_sha1 bsd 095d1f504f6fd8add73a4e4964e37f260f332b6a 
@@ -85,7 +96,6 @@ hash_sha1 agpl 86d2ea18c092d87328f06d22d997af59cee10fc4
 hash_sha1 gpl d093976b85026cb225a12908088bb19dd9d480b7 
 hash_sha1 gpl 0e9f026efef26009619f9048637eb2a498379c88 
 hash_sha1 acepack 6bdcfb412d82fe3ad5b64650d900c2845d08fbc6 
-hash_sha1 ff 0ce6a854127045f0b2efc9be8bacebb3da42a855 
 hash_sha1 agpl d3c31418974fd4d69032bc1f5c58e13c1634ca40 
 hash_sha1 agpl 6bdfdd431d081dd0bacf493ba3563f3480ab8936 
 hash_sha1 nistnls 735b08919865788221c3139506b4f508e6636dfa 
@@ -118,3 +128,26 @@ hash_sha1 unclear befc3a63448173d57ad7304319ceaf01302ba035
 hash_sha1 tcltk2 e7d59565ab5ec7245fbfea74384798e5f6a9f483 
 hash_sha1 tcltk2 7ddf1b18f9624b0a6ded40c70be329cadd074af8 
 hash_sha1 gpl 6866382245b1802189e6e8b956196ce4715fc67f 
+hash_sha1 agpl-3 70ae9c1442b696a7b3ded90579785030ff7bdbb4 
+hash_sha1 agpl-3 a596e7f3a3125045173253bddfc8e4b3cba09004 
+hash_sha1 rindex_license fa72fc5a881001769d691af7ab529699c08edda0 
+hash_sha1 eupl 4418cb312744f1b1a76420cf3ed43dded454e1a2 
+hash_sha1 eupl 4b4f67314d4b0cbdcf18e8c765374bfc49c699d1 
+hash_sha1 statnet 73d704179dcbe75498f174941036db921e4aab98 
+hash_sha1 statnet d6cfab1f34efdeb09ff17948ef37eb82bb151d71 
+hash_sha1 degreenet bcfb8b637a823520e18cd00570ab67ac34355e9b 
+hash_sha1 degreenet c1a8f1e9fda548a222131a42db976a9b841a8b84 
+hash_sha1 geometry 4265480ee7ad0ef41f684d20c8204356e12c525c 
+hash_sha1 geometry c52bef65629df25bcd18e97236f5405e7c408097 
+hash_sha1 ergm 2f7fb32f8c752f73fd9f32e92af697c8395ad3ae 
+hash_sha1 ergm e36db453758cb8173f7cd80561feaea796f767ce 
+hash_sha1 acepack 698e04a130a50d9e0b990f4bd2569fa54366102a 
+hash_sha1 acepack 44801e90a3c00a7fe4f5a6bff8c9eaf743d717f4 
+hash_sha1 ff 220e79fccd4f8e4874b8c8c481fe7ff9b8e3c850 
+hash_sha1 ff 1e0f7f00f430604860afdb5fe911be5db07d5913 
+hash_sha1 mspath 58c267c9ae997b5814c5fcaaf6233783f937a2c3 
+hash_sha1 mspath 0a4121a7735852e842112b0dd667160f99df39d4 
+hash_sha1 ever a3ab3a534d3514d56ae1ea76414e51543af5bef8 
+hash_sha1 ever 8b25578cf5d509b042115c54824e8423d95f4061 
+hash_sha1 latentnet a67ae6964aa0ede190721cfd17c2509b7799e881 
+hash_sha1 latentnet d72813ddddb94f752d9929bdbe622179a623986b 

diff --git a/trunk/data/populate_sysreq b/trunk/data/populate_sysreq
index 8a7f257ac7b7ae9844f15407a58315082599771d..852a6179c422accc0b2a62094bd8c88a6476100a 100644 (file)
--- a/trunk/data/populate_sysreq
+++ b/trunk/data/populate_sysreq
@@ -85,3 +85,18 @@ sysreq ignore http://mpfr.org/%
 sysreq gmp gmp (gnu multiple precision library 
 sysreq ignore see readme 
 sysreq tk-img img 
+sysreq ignore activetcl 
+sysreq libitpp libitpp 
+sysreq libxerces-c libxerces-c 
+sysreq ignore java runtime 
+sysreq protobuf protocol buffer compiler (to create c++ header 
+sysreq ignore Protocol Buffer compiler (% 
+sysreq ignore source files .proto % 
+sysreq ignore library (version 2.2.0 or later) 
+sysreq ignore library 
+sysreq libpng libpng% 
+sysreq postgresql postgresql 
+sysreq postgresql_java postgresql jdbc driver 
+sysreq ignore gmt 
+sysreq armadillo armadillo 
+sysreq java jri 

diff --git a/trunk/exec/build b/trunk/exec/build
index 4744987e065a8e747fd0380c757c44e6ab8511b2..6feaf5d7d49cd9a4a1a8b03407b288a113228409 100755 (executable)
--- a/trunk/exec/build
+++ b/trunk/exec/build
@@ -1,6 +1,7 @@
 #!/usr/bin/env r
-## DOC: cran2deb build [-D extra_dep1,extra_dep2,...] package1 package2 ...
+## DOC: cran2deb build [-d] [-D extra_dep1,extra_dep2,...] package1 package2 ...
 ## DOC:     builds a particular package.
+## DOC:                -d   leave the staging directory around for debugging.
 ## DOC:
 suppressPackageStartupMessages(library(cran2deb))
 
@@ -9,7 +10,8 @@ if (exists('argv')) { # check for littler
     extra_deps = list()
     extra_deps$deb = c()
     extra_deps$r = c()
-    opts = c('-D','-R')
+    do_cleanup = T
+    opts = c('-D','-R','-d')
     # first argument is the root --- this is dealt with elsewhere.
     for (i in 2:argc) {
         if (!(argv[i] %in% opts)) {
@@ -31,13 +33,16 @@ if (exists('argv')) { # check for littler
             extra_deps$r = c(extra_deps$r,strsplit(chomp(argv[i+1]),',')[[1]])
             extra_deps$deb = c(extra_deps$deb,lapply(extra_deps$r,pkgname_as_debian))
         }
+        if (argv[i] == '-d') { #debug
+            do_cleanup = F
+        }
     }
     if (argc == 0) {
-        err('usage: cran2deb build [-D extra_dep1,extra_dep2,...] package package ...')
+        err('usage: cran2deb build [-d] [-D extra_dep1,extra_dep2,...] package package ...')
     }
     build_order <- r_dependency_closure(c(extra_deps$r,argv))
     notice('build order',paste(build_order,collapse=', '))
     for (pkg in build_order) {
-        build(pkg,extra_deps,force=pkg %in% argv)
+        build(pkg,extra_deps,force=pkg %in% argv, do_cleanup)
     }
 }

diff --git a/trunk/exec/update b/trunk/exec/update
index 53bc9279f21800d92d613c6ed8f4f6336a0400f6..b457c912bb08f71ef134abbf06df13b028073f1d 100755 (executable)
--- a/trunk/exec/update
+++ b/trunk/exec/update
@@ -23,6 +23,7 @@ if (![ -e /var/cache/cran2deb/cache.rda ] || [ $delta -gt $update_period ]) {
     if ([ -e /var/cache/pbuilder/base-cran2deb-$sys.tgz ]) {
         mode=update
     }
+    echo C: sudo pbuilder $mode --override-config --configfile /etc/cran2deb/sys/$sys/pbuilderrc
     sudo pbuilder $mode --override-config --configfile /etc/cran2deb/sys/$sys/pbuilderrc
     $root/exec/update_cache $root
 }