Re: New version of pilon has build issues
Hi Bruce,
cool that you are reading the Debian Med list and want to help. :-)
Kind regards
Andreas.
On Thu, Feb 04, 2021 at 11:12:17PM -0500, Bruce Walker wrote:
> 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 <andreas@an3as.eu> 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
> >
>
>
--
http://fam-tille.de
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