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Re: New version of pilon has build issues

Hi Bruce and Andreas,

Le 05/02/2021 à 05:12, Bruce Walker a écrit :

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).
This is likely an issue linked to Scala, as Scala is unfortunately stuck to version 2.11 in Debian. Updating Scala in Debian would imply updating Scala Build Tool, which in turn should be compiled with Scala... Well, quite a lot of work (which will need to be done one day, still).
Bruce, besides, could you please tell us what version of htsjdk you are relying on? I am noticing the error 

error: value asScala is not a member of htsjdk.samtools.SAMRecordIterator



—bruce


Best regards,
Pierre





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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