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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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PreCompiled binaries? #22

Closed apelin20 closed 9 years ago

apelin20 commented 9 years ago

Any chance you can precompile this for a few OS systems? Getting ant to work is a pain. I know I spend a day getting it right on one machine but forgot what was the fix and now have to do it again.

lindenb commented 9 years ago

I switched from Ant to Make yesterday... https://github.com/lindenb/jvarkit/commit/c9671c904fe8e56e36e71ef81b6dfcb423523dc1

apelin20 commented 9 years ago

I really want to believe you:) Really really want to....

http://pastebin.com/ri3mfzxG

EDIT: CentOS @BioPower3-IBM ~/programs/jvarkit $ uname -a Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

EDIT2: ok I know remember, we had an issue for this opened https://github.com/lindenb/jvarkit/issues/8 and to solution was: yum install ant-nodeps Suggestion, maybe a ./configure implementation to check for dependencies?

However, now I get a new error: http://pastebin.com/yjLG7F80

@BioPower3-IBM ~/programs/jvarkit $ java -version java version "1.7.0_45" OpenJDK Runtime Environment (rhel-2.4.3.3.el6-x86_64 u45-b15) OpenJDK 64-Bit Server VM (build 24.45-b08, mixed mode)

EDIT3: Ok, found a fix. Turns out I had jdk 1.7 and 1.6 installed on my machine, and ant was dependant on 1.6 while the jre used was 1.7. This was helpful http://stackoverflow.com/questions/22389322/java-illegal-start-of-type-in-correct-project. I removed ant & and-nodep + removed jdk 1.6 and got jdk 1.7 + openjdk-devel 1.7 then reinstalled ant and ant-nodeps.

New issue, banrenamechr fails make: *\ No rule to make target /home/adrian/programs/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/mem/BWAMemScan.java', needed bybamsnvwig'. Stop. http://pastebin.com/sCw4ZVvZ

lindenb commented 9 years ago

Suggestion, maybe a ./configure implementation to check for dependencies?

this is a problem with the htsjdk library, not from my program.

Your last error is in:

/home/adrian/programs/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/backlocate
        private Map<String,Set<String>> geneSymbol2kg=new HashMap<>();

instead of java -v , show me javac -version . (java != javac) I'm pretty sure that your javac is outdated.

apelin20 commented 9 years ago

Yeah you are right I fixed that, see EDIT3. Now I have this problem: @BioPower3-IBM ~/programs/jvarkit $ make bamsnvwig make: *\ No rule to make target /home/adrian/programs/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/mem/BWAMemScan.java', needed bybamsnvwig'. Stop.

make seems to run into that after compiling banrenamechr: http://pastebin.com/sCw4ZVvZ

lindenb commented 9 years ago

As I said in https://github.com/lindenb/jvarkit/wiki/Compilation

the target 'all' exists in the Makefile but it will generate a large number of tools I don't use/maintain anymore.

don't try to build all tools, just build what you need.

lindenb commented 9 years ago

I've pushed a message about this: https://github.com/lindenb/jvarkit/commit/95427139ae896b3d582ba046943aff22425f4c8d

apelin20 commented 9 years ago

Good one :) Thanks for the help!