[Debichem-devel] Will we manage to upgrade jmol

[Andreas Tille]

Hi Ximin,

thanks a lot for pushing this forward.

On Mon, Dec 05, 2016 at 10:39:00AM +0000, Ximin Luo wrote:
> I don't know, sorry. I haven't gotten that error before, and it worked on the experimental buildds earlier:
> 
> https://buildd.debian.org/status/fetch.php?pkg=jmol&arch=all&ver=14.6.4%2B2016.11.05%2Bdfsg1-1&stamp=1480887799
> 
> It's in experimental now, so you could get it from there:
> 
> https://packages.debian.org/experimental/jmol

I have fetched the libjmol-java_14.6.4+2016.11.05+dfsg1-1_all.deb
package from there and added it to my pbuilder environment.  When
building with this setup I'm running into the following error when
trying to re-build biojava3-live_3.1.0+dfsg-2:


...
cd biojava3-sequencing && ant jar
Buildfile: /build/biojava3-live-3.1.0+dfsg/biojava3-sequencing/build.xml

compile:
    [mkdir] Created dir: /build/biojava3-live-3.1.0+dfsg/build/biojava3-sequencing/classes
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-sequencing/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 19 source files to /build/biojava3-live-3.1.0+dfsg/build/biojava3-sequencing/classes
    [javac] Creating empty /build/biojava3-live-3.1.0+dfsg/build/biojava3-sequencing/classes/org/biojava3/sequencing/io/fastq/package-info.class
     [copy] Warning: /build/biojava3-live-3.1.0+dfsg/biojava3-sequencing/src/main/resources does not exist.

jar:
      [jar] Building jar: /build/biojava3-live-3.1.0+dfsg/dist/biojava3-sequencing.jar

BUILD SUCCESSFUL
Total time: 1 second
cd biojava3-structure && ant jar
Buildfile: /build/biojava3-live-3.1.0+dfsg/biojava3-structure/build.xml

compile:
    [mkdir] Created dir: /build/biojava3-live-3.1.0+dfsg/build/biojava3-structure/classes
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 342 source files to /build/biojava3-live-3.1.0+dfsg/build/biojava3-structure/classes
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:8: error: package javax.vecmath does not exist
    [javac] import javax.vecmath.Point3d;
    [javac]                     ^
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:88: error: cannot find symbol
    [javac] 	private Point3d[] spherePoints;
    [javac] 	        ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:255: error: cannot find symbol
    [javac] 	private Point3d[] generateSpherePoints(int nSpherePoints) {
    [javac] 	        ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:256: error: cannot find symbol
    [javac] 	    Point3d[] points = new Point3d[nSpherePoints];
    [javac] 	    ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:256: error: cannot find symbol
    [javac] 	    Point3d[] points = new Point3d[nSpherePoints];
    [javac] 	                           ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:263: error: cannot find symbol
    [javac] 	        points[k] = new Point3d(Math.cos(phi)*r, y, Math.sin(phi)*r);
    [javac] 	                        ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:307: error: cannot find symbol
    [javac]         for (Point3d point: spherePoints){
    [javac]              ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:309: error: cannot find symbol
    [javac]             Point3d test_point = new Point3d(point.x*radius + atom_i.getX(),
    [javac]             ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:309: error: cannot find symbol
    [javac]             Point3d test_point = new Point3d(point.x*radius + atom_i.getX(),
    [javac]                                      ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:327: error: cannot find symbol
    [javac]                 double diff_sq = test_point.distanceSquared(new Point3d(atom_j.getCoords()));
    [javac]                                                                 ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 10 errors

BUILD FAILED
/build/biojava3-live-3.1.0+dfsg/biojava3-structure/build.xml:72: Compile failed; see the compiler error output for details.

Total time: 3 seconds
debian/rules:28: recipe for target 'override_dh_auto_build' failed


This error does not occure when building against
libjmol-java_12.2.32+dfsg2-1.  I admit my Java knowledge is
way to poor to make some sense out of this and whether there
is a chance to patch biojava3-live to fix this.

Kind regards

     Andreas.


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