Re: New version of pilon has build issues
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
>
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