Your message dated Tue, 05 Oct 2021 19:33:45 +0000
with message-id <[email protected]>
and subject line Bug#995406: fixed in bbmap 38.94+dfsg-1
has caused the Debian Bug report #995406,
regarding bbmap: package does not ship resource files
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
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--
995406: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=995406
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: bbmap
Version: 38.93+dfsg-1
Severity: normal
Tags: patch
X-Debbugs-Cc: [email protected]
Dear Maintainer,
The bbmap package does not ship the needed resource files which causes some of
the included tools not to work, e.g. bbduk when trying to process some fastq
data, crashes with output like [1].
I don't have a census which other bbtools require resource files to be usable,
but bbduk is not usable at all in the current state.
My suggested fix (see patch [2]) puts the resource files to the root of
the built jar file. This is were dna.Data.findPath() will indeed find
these files, which can be seen when looking at the verbose output [3]
for findPath() (by setting vb=true in current/dna.Data.java near line
1204). By contrast, the current packaging tries (but also fails) to put
the files under resources/. I don't see a way to trick jh_build with
the JH_JAR_EXTRA mechanism to do what is needed (without changes to
jh_build). The patch applies agaiinst the bbmap source package's
current git master branch and the package builds and run for me on
bullseye.
thanks
(Robert)
[1] error message of bbduk tool:
$ pwd
/tmp/bbduk_test
$ ls
fwd.fastq rev.fastq
$ bbduk.sh in1=fwd.fastq in2=rev.fastq ktrim=r k=21 mink=8 hdist=2 ftm=5 tpe
tbo threads=48 out=out.fastq
java -ea -Xmx76702m -Xms76702m -cp /usr/share/java/bbmap.jar jgi.BBDuk
in1=fwd.fastq in2=rev.fastq ktrim=r k=21 mink=8 hdist=2 ftm=5 tpe tbo
threads=48 out=out.fastq
Executing jgi.BBDuk [in1=fwd.fastq, in2=rev.fastq, ktrim=r, k=21, mink=8,
hdist=2, ftm=5, tpe, tbo, threads=48, out=out.fastq]
Version 38.90
Set threads to 48
maskMiddle was disabled because useShortKmers=true
Warning! Cannot find primes.txt.gz
/tmp/bbduk_test/file:/usr/share/java/bbmap.jar!/primes.txt.gz
java.lang.Exception
at dna.Data.findPath(Data.java:1247)
at dna.Data.findPath(Data.java:1194)
at shared.Primes.fetchPrimes(Primes.java:167)
at shared.Primes.<clinit>(Primes.java:177)
at kmer.ScheduleMaker.<clinit>(ScheduleMaker.java:155)
at jgi.BBDuk.<init>(BBDuk.java:964)
at jgi.BBDuk.main(BBDuk.java:78)
Exception in thread "main" java.lang.ExceptionInInitializerError
at kmer.ScheduleMaker.<clinit>(ScheduleMaker.java:155)
at jgi.BBDuk.<init>(BBDuk.java:964)
at jgi.BBDuk.main(BBDuk.java:78)
Caused by: java.lang.NullPointerException
at fileIO.ByteFile.<init>(ByteFile.java:43)
at fileIO.ByteFile1.<init>(ByteFile1.java:98)
at fileIO.ByteFile1.<init>(ByteFile1.java:94)
at shared.Primes.fetchPrimes(Primes.java:169)
at shared.Primes.<clinit>(Primes.java:177)
... 3 more
[2] proposed patch
diff --git a/debian/rules b/debian/rules
index a44c8e7..479739f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,7 +8,6 @@ PKGSHAREDIR := debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)
export JAVA_HOME := /usr/lib/jvm/default-java
DEBJAR := /usr/share/java
export CLASSPATH := $(DEBJAR)/mpi.jar
-export JH_JAR_EXTRA := resources/*
%:
dh $@ --with javahelper
@@ -23,7 +22,8 @@ override_dh_clean:
override_dh_auto_build:
cd jni && make -f makefile.linux
- JH_JAR_EXTRA=`$(CURDIR)/resources/*` jh_build $(DEB_SOURCE).jar current
+ jh_build $(DEB_SOURCE).jar current
+ cd $(CURDIR)/resources && jar uf $(CURDIR)/$(DEB_SOURCE).jar $(subst
resources/,,$(wildcard resources/*))
override_dh_install:
dh_install
[3] bbduk output like [1] but with proposed patch and verbose output for
findPath() applied:
$ bbduk.sh in1=fwd.fastq in2=rev.fastq ktrim=r k=21 mink=8 hdist=2 ftm=5 tpe
tbo threads=48 out=out.fastq
java -ea -Xmx76702m -Xms76702m -cp /usr/share/java/bbmap.jar jgi.BBDuk
in1=fwd.fastq in2=rev.fastq ktrim=r k=21 mink=8 hdist=2 ftm=5 tpe tbo
threads=48 out=out.fastq
Executing jgi.BBDuk [in1=fwd.fastq, in2=rev.fastq, ktrim=r, k=21, mink=8,
hdist=2, ftm=5, tpe, tbo, threads=48, out=out.fastq]
Version 38.93
Set threads to 48
maskMiddle was disabled because useShortKmers=true
Did not find primes.txt.gz at
/tmp/bbduk_test/file:/usr/share/java/bbmap.jar!/primes.txt.gz
Did not find primes.txt.gz at
/tmp/bbduk_test/file:/usr/share/java/resources/primes.txt.gz
Considering fixing /tmp/bbduk_test/file:/usr/share/java/bbmap.jar!/primes.txt.gz
true
Did not find primes.txt.gz at file:/usr/share/java/bbmap.jar!/primes.txt.gz
Considering getResource
Found URL jar:file:/usr/share/java/bbmap.jar!/primes.txt.gz
Found primes.txt.gz at jar:file:/usr/share/java/bbmap.jar!/primes.txt.gz
0.032 seconds.
Initial:
Memory: max=80429m, total=80429m, free=80346m, used=83m
...
-- System Information:
Debian Release: 11.0
APT prefers stable-security
APT policy: (990, 'stable-security'), (990, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 4.15.0-132-generic (SMP w/96 CPU threads)
Locale: LANG=C, LC_CTYPE=C (charmap=UTF-8) (ignored: LC_ALL set to
en_US.UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /bin/dash
Init: unable to detect
Versions of packages bbmap depends on:
ii libmpj-java 0.44+dfsg-4
Versions of packages bbmap recommends:
ii pigz 2.6-1
bbmap suggests no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: bbmap
Source-Version: 38.94+dfsg-1
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
bbmap, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated bbmap package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 05 Oct 2021 21:06:02 +0200
Source: bbmap
Architecture: source
Version: 38.94+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 995406
Changes:
bbmap (38.94+dfsg-1) unstable; urgency=medium
.
* Team upload.
.
[ Andreas Tille ]
* Include resources files
Closes: #995406
.
[ Étienne Mollier ]
* New upstream version.
* add autopkgtest, following discussion on #995406; thanks Robert Hein for
the help with testing bbduk.sh!
* d/control: add bbmap dependency to a JRE.
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