[pkg-bioc] svn commit r308 r308 - in /trunk/tools: cannotBuild.list cran2deb.pl
egonw-guest at users.alioth.debian.org
egonw-guest at users.alioth.debian.org
Wed Aug 29 11:04:23 UTC 2007
Author: egonw-guest
Date: Wed Aug 29 11:04:23 2007
New Revision: 308
URL: http://svn.debian.org/wsvn/pkg-bioc/?sc=1&rev=308
Log:
Refactored to have the config data for 'cannot build' outside the Perl script
Added:
trunk/tools/cannotBuild.list (with props)
Modified:
trunk/tools/cran2deb.pl
Added: trunk/tools/cannotBuild.list
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/tools/cannotBuild.list?rev=308&op=file
==============================================================================
--- trunk/tools/cannotBuild.list (added)
+++ trunk/tools/cannotBuild.list Wed Aug 29 11:04:23 2007
@@ -0,0 +1,76 @@
+## NB case matters here, need to lowercase before comparison
+## NB2 we should keep an eye on
+##
+## http://cran.r-project.org/src/contrib/checkSummary.html
+## to see what builds at CRAN (on Debian as far as Linux is concerned)
+
+## PLEASE KEEP LIST IN ALPHABETIC ORDER
+
+## List of packages in CRAN that fail to build on 2006-02-14
+ADaCGH: currently not enough BioC depends on x86
+anm: depends on clim.pact which depends on akima (non-free)
+BRugs: currently only works under Windows...
+coxphf: wants fortan90 compiler
+clim.pact: depends on akima which is non-free
+cyclones: depends on clim.pact which depends on akima (non-free)
+gmodels: depends on gdata, which is not found
+gnomeGUI: obsolete for years, uses Gnome1, use RGtk2 instead'
+gtkDevice: also obsolete for years, cairoDevice with RGtk2'
+gWidgetsrJava: Java again
+hydrosanity: another akima Depends
+iplots: needs rJava which cannot be built
+iid.test: depends on clim.pact which depends on akima (non-free)
+ipred: wants mlbench which is non-free
+JavaGD: needs Java
+JGR: needs rJava which cannot be built
+labdsv: depends on akima which is non-free
+latentnet: depends on locfit which depends on akima (non-free)
+locfit: depends on akima which is non-free
+LogConcDEAD: depends on akima which is non-free
+MBA: boost test in configure broken
+mimR: can only be installed/used under Windows.
+ncvar: RNetCDF not available as udunits not available
+RaschSampler: wants fortan90 compiler
+rcdd: requires cddlib which is not in Debian
+rcom: can only be installed/used under Windows.
+rcdk: needs rJava which cannot be built
+rggobi: missing debs
+RGrace: gdk_draw.c:9: error: syntax error before ')' token
+rJava: Seems to fail with free Java.
+RJDBC: needs rJava that is not yet functional
+RLadyBug: needs rJava that is yet not functional
+Rlsf: Please set the LSF_ENVDIR variable...
+RNetCDF: udunits not available (see below)
+ROracle: set the shell variable ORACLE_HOME...
+RScaLAPACK: Needs libmpich.a (which -dev???).
+RWeka: needs Java
+RWinEdt: can only be installed/used under Windows.
+spectrino: depends on rcom, Windows only
+tcltk2: can only be installed/used under Windows currently!
+tdm: depends on RBrugs which is only Windows
+tm: depends on RWeka, which needs Java
+TWIX: needs iplot, hence rJava
+udunits: libudunits.a not in Debian (Dirk has a local copy)
+wnominate: wants fortan90 compiler
+xlsReadWrite: Windows only
+
+# Bioc
+affyparse: fusion_sdk/calvin_files/data/src/CELData.h:188: error: extra qualification 'affymetrix_calvin_io::CelFileData::' on member 'GetAlgorithmVersion
+beadarraySNP: misses quant smooth package
+rflowcyt: not followed up, package is probably outdated
+RdbiPgSQL: needs environment variable
+widgetInvoke: requests RGtk but only Rgtk2 is available ... may be compatible
+
+# Omegahat
+CORBA: Cannot get dependencies right.
+RDCOMEvents: Not a joke: c:/MinGW/bin/g++: Command not found
+RGtk: Obsolete, use RGtk2 on CRAN instead
+RGtkExtra: RGtkExtra.h:4:18: error: RGtk.h: No such file or directory, RGtkExtra.h:5:31: error: gtkextra/gtkextra.h: No such file or directory
+RGtkIPrimitives: Many build errors
+RJavaDevice: missing build dependency: r-cran-thejavapackageforr. | r-bioc-thejavapackageforr. | r-omegahat-thejavapackageforr
+Rlibstree: Missing library: checking for lst_structs.h... no
+RMatlab: Somewhere hangs
+RSPython: Error while compiling: GeneralConverters.c:298: error: expected declaration specifiers or '...' before 'ToTargetConverter
+SJava: Build issues: /usr/bin/ld: cannot find -lRSNativeJava
+SWinRegistry: getRegistry.c:51: error: expected declaration specifiers before '__declspec'"
+
Propchange: trunk/tools/cannotBuild.list
------------------------------------------------------------------------------
svn:executable = *
Modified: trunk/tools/cran2deb.pl
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/tools/cran2deb.pl?rev=308&op=diff
==============================================================================
--- trunk/tools/cran2deb.pl (original)
+++ trunk/tools/cran2deb.pl Wed Aug 29 11:04:23 2007
@@ -92,6 +92,22 @@ $_system = $_config->system;
## dies with an ugly error
$installRequiredPackages = "echo"; ## provide a default
+sub readList($) {
+ my $list = shift;
+ my %list = ();
+ open(FILE, "<../tools/$list") || die "Cannot open $list!\n";
+ while (<FILE>) {
+ my $line = $_;
+ if ($line =~ m/^#/) {
+ # skip comment line
+ } elsif ($line =~ m/(.*?):(.*)/) {
+ $list{"$1"} = "$2";
+ print "package: $1\nreason: " . $list{"$1"} . "\n";
+ }
+ }
+ return %list;
+}
+
my @debsearchpath = (
".", "builds",
"..", "../builds",
@@ -290,82 +306,7 @@ my %repositoryOf = ();
## NB2 we should keep an eye on
## http://cran.r-project.org/src/contrib/checkSummary.html
## to see what builds at CRAN (on Debian as far as Linux is concerned)
-my %cannotbuild = (
- ## List of packages in CRAN that fail to build on 2006-02-14
- #"baymvb" => "C++ error in la.cc:201 ('accumulate')", ## What is that?
- "ADaCGH" => "currently not enough BioC depends on x86",
- "anm" => "depends on clim.pact which depends on akima (non-free)",
- "BRugs" => "currently only works under Windows...",
- "coxphf" => "wants fortan90 compiler",
- "clim.pact" => "depends on akima which is non-free",
- "cyclones" => "depends on clim.pact which depends on akima (non-free)",
- "gnomeGUI" => "obsolete for years, uses Gnome1, use RGtk2 instead'",
- "gtkDevice" => "also obsolete for years, cairoDevice with RGtk2'",
- "gWidgetsrJava" => "Java again",
- "hydrosanity" => "another akima Depends",
- "iplots" => "needs rJava which cannot be built",
- "iid.test" => "depends on clim.pact which depends on akima (non-free)",
- "ipred" => "wants mlbench which is non-free",
- "JavaGD" => "needs Java ",
- "JGR" => "needs rJava which cannot be built",
- "labdsv" => "depends on akima which is non-free",
- "latentnet" => "depends on locfit which depends on akima (non-free)",
- "locfit" => "depends on akima which is non-free",
- "LogConcDEAD" => "depends on akima which is non-free",
- "MBA" => "boost test in configure broken",
- "mimR" => "can only be installed/used under Windows.",
- "ncvar" => "RNetCDF not available as udunits not available",
- "RaschSampler" => "wants fortan90 compiler",
- "rcdd" => "requires cddlib which is not in Debian",
- "rcom" => "can only be installed/used under Windows.",
- "rcdk" => "needs rJava which cannot be built",
- "RGrace" => "gdk_draw.c:9: error: syntax error before ')' token",
- "rJava" => "Seems to fail with free Java.",
- "RJDBC" => "needs rJava that is not yet functional",
- "RLadyBug" => "needs rJava that is yet not functional",
- "Rlsf" => "Please set the LSF_ENVDIR variable...",
- "RNetCDF" => "udunits not available (see below)",
- "ROracle" => "set the shell variable ORACLE_HOME...",
- "RScaLAPACK" => "Needs libmpich.a (which -dev???).",
- "RWeka" => "needs Java",
- "RWinEdt" => "can only be installed/used under Windows.",
- "spectrino" => "depends on rcom, Windows only",
- "tcltk2" => "can only be installed/used under Windows currently!",
- "tdm" => "depends on RBrugs which is only Windows",
- "TWIX" => "needs iplot, hence rJava",
- "udunits" => "libudunits.a not in Debian (Dirk has a local copy)",
- "wnominate" => "wants fortan90 compiler",
- "xlsReadWrite" => "Windows only",
-
- ## Bioc
- "affyparse" =>
-"fusion_sdk/calvin_files/data/src/CELData.h:188: error: extra qualification 'affymetrix_calvin_io::CelFileData::' on member 'GetAlgorithmVersion",
- "beadarraySNP" => "misses quant smooth package",
- "rflowcyt" => "not followed up, package is probably outdated",
- "RdbiPgSQL" => "needs environment variable",
- "widgetInvoke" =>
- "requests RGtk but only Rgtk2 is available ... may be compatible",
-
- # Omegahat
- CORBA => "Cannot get dependencies right.",
- RDCOMEvents => "Not a joke: c:/MinGW/bin/g++: Command not found",
- RGtk => "Obsolete, use RGtk2 on CRAN instead",
- RGtkExtra =>
-"RGtkExtra.h:4:18: error: RGtk.h: No such file or directory, RGtkExtra.h:5:31: error: gtkextra/gtkextra.h: No such file or directory",
- RGtkIPrimitives => "Many build errors",
- RJavaDevice =>
-"missing build dependency: r-cran-thejavapackageforr. | r-bioc-thejavapackageforr. | r-omegahat-thejavapackageforr",
- Rlibstree => "Missing library: checking for lst_structs.h... no",
- RMatlab => "Somewhere hangs",
- RSPython =>
-"Error while compiling: GeneralConverters.c:298: error: expected declaration specifiers or '...' before 'ToTargetConverter",
- SJava => "Build issues: /usr/bin/ld: cannot find -lRSNativeJava",
- SWinRegistry =>
-"getRegistry.c:51: error: expected declaration specifiers before '__declspec'"
-
- #RDCOMServer => "Depends on SWinRegistry"
-);
-
+my %cannotbuild = readList("cannotBuild.list");
if ( !-f $autogeneratevariable ) {
print STDERR "Could not find the '$autogeneratevariable'. \n";
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