Hi Andreas, I am the upstream author of Pilon, and I built the new 1.24 release using a modern 2.13.x Scala compiler and library (along with a java 11 JRE, previously was java 8). I’m sure the issue is in those changes. I will take a look when I get a chance (probably over the weekend).
—bruce > On Feb 4, 2021, at 5:03 PM, Andreas Tille <[email protected]> wrote: > > Hi, > > I've commited the latest upstream version of pilon to Git[1] but > there are build issues: > > ... > debian/rules override_dh_auto_build > make[1]: Entering directory '/build/pilon-1.24' > scalac -classpath /usr/share/java/htsjdk.jar -d pilon.jar > src/main/scala/org/broadinstitute/pilon/* > src/main/scala/org/broadinstitute/pilon/BamFile.scala:24: error: object jdk > is not a member of package scala > import scala.jdk.CollectionConverters._ > ^ > src/main/scala/org/broadinstitute/pilon/BamFile.scala:65: error: value > asScala is not a member of java.util.List[htsjdk.samtools.SAMSequenceRecord] > val seqs = r.getFileHeader.getSequenceDictionary.getSequences.asScala > ^ > src/main/scala/org/broadinstitute/pilon/BamFile.scala:96: error: value > asScala is not a member of htsjdk.samtools.SAMRecordIterator > val reads = r.queryUnmapped.asScala.filter(validateRead(_)).toList > ^ > src/main/scala/org/broadinstitute/pilon/BamFile.scala:119: error: value > asScala is not a member of htsjdk.samtools.SAMRecordIterator > possible cause: maybe a semicolon is missing before `value asScala'? > (region.start-10000) max 0, (region.stop+10000) min > region.contig.length).asScala > > ^ > src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala:22: error: object > jdk is not a member of package scala > import scala.jdk.CollectionConverters._ > ^ > src/main/scala/org/broadinstitute/pilon/BamFile.scala:297: error: value > asScala is not a member of htsjdk.samtools.SAMRecordIterator > for (read <- r.iterator.asScala) { > ^ > src/main/scala/org/broadinstitute/pilon/BamFile.scala:341: error: value > asScala is not a member of htsjdk.samtools.SAMRecordIterator > val reads = r.queryOverlapping(region.name, region.start, > region.stop).asScala.filter(validateRead(_)).toList > ^ > src/main/scala/org/broadinstitute/pilon/Scaffold.scala:31: error: object jdk > is not a member of package scala > import scala.jdk.CollectionConverters._ > ^ > src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala:136: error: value > asScala is not a member of java.util.List[htsjdk.samtools.CigarElement] > val cigarElements = cigar.getCigarElements.asScala > ^ > src/main/scala/org/broadinstitute/pilon/Scaffold.scala:351: error: value > asScala is not a member of htsjdk.samtools.SAMRecordIterator > for (read <- reader.iterator.asScala if (!read.getReadUnmappedFlag)) { > ^ > 10 errors found > make[1]: *** [debian/rules:10: override_dh_auto_build] Error 1 > > > Any idea how this can be fixed? > > Kind regards > > Andreas. > > > [1] https://salsa.debian.org/med-team/pilon > > -- > http://fam-tille.de >
