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. -- http://fam-tille.de
