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Subject: bug#31721: =?UTF-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on many packages
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The =E2=80=9Cgenerate-jar-indices=E2=80=9D phase fails on a couple of packa=
ges, such as

  java-picard (all variants)
  dropseq-tools
  java-cisd-jhdf5

The errors are either about duplicates as in java-picard-2.10.3:

    duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class

or about missing files as in dropseq-tools:

    java.io.FileNotFoundException: /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14=
f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar

I have removed the phase in these packages, but that=E2=80=99s not ideal.

Can we make this phase more robust?

--=20
Ricardo

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Subject: bug#31721: Acknowledgement (=?UTF-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?=
 phase fails on many packages)
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Subject: bug#31721: =?UTF-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on many packages
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Danny Milosavljevic <dannym@HIDDEN> writes:

>> The errors are either about duplicates as in java-picard-2.10.3:
>> 
>>     duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class
>
> That's... bad.  What if those files differed?  Which one would be used at
> runtime?

I wonder where they come from.  Is this from a dependency or are there
actually two such classes?

>> or about missing files as in dropseq-tools:
>> 
>>     java.io.FileNotFoundException: /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar
>
> That's also bad.  How does it run at all if its dependencies are missing?

To satisfy the dropseq-tools build system the dependencies a symlinked
to the build directory.  I suspect that the error is something to do
with that.

> The only thing I can think of that would improve things long term:
>
> The phase can add relative paths to all the dependencies to META-INF/MANIFEST.MF
> before invoking "jar -i".
> Then "jar -i" will index those - and all java packages can use regular inputs
> instead of propagated inputs.  I've tested that locally already - and it
> works fine.

Is it correct that this would ensure that in case of duplicate class
names this would pick the class from the current package?

-- 
Ricardo

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Subject: bug#31721: =?UTF-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on many packages
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From: =?UTF-8?Q?G=C3=A1bor?= Boskovits <boskovits@HIDDEN>
Date: Thu, 7 Jun 2018 10:27:43 +0200
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2018-06-07 9:20 GMT+02:00 Ricardo Wurmus <ricardo.wurmus@HIDDEN>:

>
> Danny Milosavljevic <dannym@HIDDEN> writes:
>
> >> The errors are either about duplicates as in java-picard-2.10.3:
> >>
> >>     duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class
> >
> > That's... bad.  What if those files differed?  Which one would be used at
> > runtime?
>
> I wonder where they come from.  Is this from a dependency or are there
> actually two such classes?
>
>
Is it possible that these come from a package, where a renamed dependency is
used in the original build system, thus avoiding the name duplication? I
will have a
look at this package source... Will report back if I can confirm this
assumption.



> >> or about missing files as in dropseq-tools:
> >>
> >>     java.io.FileNotFoundException: /gnu/store/
> q76y0ximcziplgfpbn26kbw4h3s14f33-dropseq-tools-1.13/share/
> java/lib/biojava-alignment.jar
> >
> > That's also bad.  How does it run at all if its dependencies are missing?
>
> To satisfy the dropseq-tools build system the dependencies a symlinked
> to the build directory.  I suspect that the error is something to do
> with that.
>
> > The only thing I can think of that would improve things long term:
> >
> > The phase can add relative paths to all the dependencies to
> META-INF/MANIFEST.MF
> > before invoking "jar -i".
> > Then "jar -i" will index those - and all java packages can use regular
> inputs
> > instead of propagated inputs.  I've tested that locally already - and it
> > works fine.
>
> Is it correct that this would ensure that in case of duplicate class
> names this would pick the class from the current package?
>
> --
> Ricardo
>
>
>
>

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<div dir=3D"ltr"><div class=3D"gmail_extra"><div class=3D"gmail_quote">2018=
-06-07 9:20 GMT+02:00 Ricardo Wurmus <span dir=3D"ltr">&lt;<a href=3D"mailt=
o:ricardo.wurmus@HIDDEN" target=3D"_blank">ricardo.wurmus@mdc-berlin=
.de</a>&gt;</span>:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 =
0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=3D""><br>
Danny Milosavljevic &lt;<a href=3D"mailto:dannym@HIDDEN">dannym@sc=
ratchpost.org</a>&gt; writes:<br>
<br>
&gt;&gt; The errors are either about duplicates as in java-picard-2.10.3:<b=
r>
&gt;&gt; <br>
&gt;&gt;=C2=A0 =C2=A0 =C2=A0duplicate entry: htsjdk/samtools/<wbr>AbstractB=
AMFileIndex$1.class<br>
&gt;<br>
</span>&gt; That&#39;s... bad.=C2=A0 What if those files differed?=C2=A0 Wh=
ich one would be used at<br>
&gt; runtime?<br>
<br>
I wonder where they come from.=C2=A0 Is this from a dependency or are there=
<br>
actually two such classes?<br>
<span class=3D""><br></span></blockquote><div><br></div><div>Is it possible=
 that these come from a package, where a renamed dependency is</div><div>us=
ed in the original build system, thus avoiding the name duplication? I will=
 have a</div><div>look at this package source... Will report back if I can =
confirm this assumption.</div><div><br></div><div>=C2=A0</div><blockquote c=
lass=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;=
padding-left:1ex"><span class=3D"">
&gt;&gt; or about missing files as in dropseq-tools:<br>
&gt;&gt; <br>
&gt;&gt;=C2=A0 =C2=A0 =C2=A0java.io.FileNotFoundException: /gnu/store/<wbr>=
q76y0ximcziplgfpbn26kbw4h3s14f<wbr>33-dropseq-tools-1.13/share/<wbr>java/li=
b/biojava-alignment.jar<br>
&gt;<br>
</span>&gt; That&#39;s also bad.=C2=A0 How does it run at all if its depend=
encies are missing?<br>
<br>
To satisfy the dropseq-tools build system the dependencies a symlinked<br>
to the build directory.=C2=A0 I suspect that the error is something to do<b=
r>
with that.<br>
<br>
&gt; The only thing I can think of that would improve things long term:<br>
&gt;<br>
&gt; The phase can add relative paths to all the dependencies to META-INF/M=
ANIFEST.MF<br>
&gt; before invoking &quot;jar -i&quot;.<br>
&gt; Then &quot;jar -i&quot; will index those - and all java packages can u=
se regular inputs<br>
&gt; instead of propagated inputs.=C2=A0 I&#39;ve tested that locally alrea=
dy - and it<br>
&gt; works fine.<br>
<br>
Is it correct that this would ensure that in case of duplicate class<br>
names this would pick the class from the current package?<br>
<span class=3D"HOEnZb"><font color=3D"#888888"><br>
-- <br>
Ricardo<br>
<br>
<br>
<br>
</font></span></blockquote></div><br></div></div>

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2018-06-07 10:27 GMT+02:00 G=C3=A1bor Boskovits <boskovits@HIDDEN>:

> 2018-06-07 9:20 GMT+02:00 Ricardo Wurmus <ricardo.wurmus@HIDDEN>:
>
>>
>> Danny Milosavljevic <dannym@HIDDEN> writes:
>>
>> >> The errors are either about duplicates as in java-picard-2.10.3:
>> >>
>> >>     duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class
>> >
>> > That's... bad.  What if those files differed?  Which one would be used
>> at
>> > runtime?
>>
>> I wonder where they come from.  Is this from a dependency or are there
>> actually two such classes?
>>
>>
> Is it possible that these come from a package, where a renamed dependency
> is
> used in the original build system, thus avoiding the name duplication? I
> will have a
> look at this package source... Will report back if I can confirm this
> assumption.
>
> This is what is in build.gradle:
dependencies {
compile('com.intel.gkl:gkl:0.8.5') {
exclude module: 'htsjdk'
}
 So we should exclude htsjdk module from gkl when building java-picard.
Do we have a method to do that easily?


>
>> >> or about missing files as in dropseq-tools:
>> >>
>> >>     java.io.FileNotFoundException: /gnu/store/q76y0ximcziplgfpbn2
>> 6kbw4h3s14f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar
>> >
>> > That's also bad.  How does it run at all if its dependencies are
>> missing?
>>
>> To satisfy the dropseq-tools build system the dependencies a symlinked
>> to the build directory.  I suspect that the error is something to do
>> with that.
>>
>> > The only thing I can think of that would improve things long term:
>> >
>> > The phase can add relative paths to all the dependencies to
>> META-INF/MANIFEST.MF
>> > before invoking "jar -i".
>> > Then "jar -i" will index those - and all java packages can use regular
>> inputs
>> > instead of propagated inputs.  I've tested that locally already - and =
it
>> > works fine.
>>
>> Is it correct that this would ensure that in case of duplicate class
>> names this would pick the class from the current package?
>>
>> --
>> Ricardo
>>
>>
>>
>>
>

--00000000000085e845056e09527d
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<div dir=3D"ltr"><div class=3D"gmail_extra"><div class=3D"gmail_quote">2018=
-06-07 10:27 GMT+02:00 G=C3=A1bor Boskovits <span dir=3D"ltr">&lt;<a href=
=3D"mailto:boskovits@HIDDEN" target=3D"_blank">boskovits@HIDDEN</a>&g=
t;</span>:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;=
border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr"><div class=3D=
"gmail_extra"><div class=3D"gmail_quote"><span class=3D"">2018-06-07 9:20 G=
MT+02:00 Ricardo Wurmus <span dir=3D"ltr">&lt;<a href=3D"mailto:ricardo.wur=
mus@HIDDEN" target=3D"_blank">ricardo.wurmus@HIDDEN</a>&gt;</=
span><wbr>:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex=
;border-left:1px #ccc solid;padding-left:1ex"><span><br>
Danny Milosavljevic &lt;<a href=3D"mailto:dannym@HIDDEN" target=3D=
"_blank">dannym@HIDDEN</a>&gt; writes:<br>
<br>
&gt;&gt; The errors are either about duplicates as in java-picard-2.10.3:<b=
r>
&gt;&gt; <br>
&gt;&gt;=C2=A0 =C2=A0 =C2=A0duplicate entry: htsjdk/samtools/AbstractBAMFil=
<wbr>eIndex$1.class<br>
&gt;<br>
</span>&gt; That&#39;s... bad.=C2=A0 What if those files differed?=C2=A0 Wh=
ich one would be used at<br>
&gt; runtime?<br>
<br>
I wonder where they come from.=C2=A0 Is this from a dependency or are there=
<br>
actually two such classes?<br>
<span><br></span></blockquote><div><br></div></span><div>Is it possible tha=
t these come from a package, where a renamed dependency is</div><div>used i=
n the original build system, thus avoiding the name duplication? I will hav=
e a</div><div>look at this package source... Will report back if I can conf=
irm this assumption.</div><span class=3D""><div><br></div></span></div></di=
v></div></blockquote><div>This is what is in build.gradle:</div><div><table=
 class=3D"gmail-highlight gmail-tab-size gmail-js-file-line-container" styl=
e=3D"box-sizing:border-box;border-collapse:collapse;color:rgb(36,41,46);fon=
t-family:-apple-system,BlinkMacSystemFont,&quot;Segoe UI&quot;,Helvetica,Ar=
ial,sans-serif,&quot;Apple Color Emoji&quot;,&quot;Segoe UI Emoji&quot;,&qu=
ot;Segoe UI Symbol&quot;;font-size:14px;background-color:rgb(255,255,255);t=
ext-decoration-style:initial;text-decoration-color:initial"><tbody style=3D=
"box-sizing:border-box"><tr style=3D"box-sizing:border-box"><td id=3D"gmail=
-LC87" class=3D"gmail-blob-code gmail-blob-code-inner gmail-js-file-line" s=
tyle=3D"box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-al=
ign:top;overflow:visible;font-family:SFMono-Regular,Consolas,&quot;Liberati=
on Mono&quot;,Menlo,Courier,monospace;font-size:12px;color:rgb(36,41,46);wo=
rd-wrap:normal;white-space:pre"><span class=3D"gmail-pl-en" style=3D"box-si=
zing:border-box;color:rgb(111,66,193)">dependencies</span> {</td></tr><tr s=
tyle=3D"box-sizing:border-box"><td id=3D"gmail-L88" class=3D"gmail-blob-num=
 gmail-js-line-number" style=3D"box-sizing:border-box;padding:0px 10px;widt=
h:50px;min-width:50px;font-family:SFMono-Regular,Consolas,&quot;Liberation =
Mono&quot;,Menlo,Courier,monospace;font-size:12px;line-height:20px;color:rg=
ba(27,31,35,0.3);text-align:right;white-space:nowrap;vertical-align:top"></=
td><td id=3D"gmail-LC88" class=3D"gmail-blob-code gmail-blob-code-inner gma=
il-js-file-line" style=3D"box-sizing:border-box;padding:0px 10px;line-heigh=
t:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Conso=
las,&quot;Liberation Mono&quot;,Menlo,Courier,monospace;font-size:12px;colo=
r:rgb(36,41,46);word-wrap:normal;white-space:pre">    compile(<span class=
=3D"gmail-pl-s" style=3D"box-sizing:border-box;color:rgb(3,47,98)"><span cl=
ass=3D"gmail-pl-pds" style=3D"box-sizing:border-box;color:rgb(3,47,98)">&#3=
9;</span>com.intel.gkl:gkl:0.8.5<span class=3D"gmail-pl-pds" style=3D"box-s=
izing:border-box;color:rgb(3,47,98)">&#39;</span></span>) {</td></tr><tr st=
yle=3D"box-sizing:border-box"><td id=3D"gmail-L89" class=3D"gmail-blob-num =
gmail-js-line-number" style=3D"box-sizing:border-box;padding:0px 10px;width=
:50px;min-width:50px;font-family:SFMono-Regular,Consolas,&quot;Liberation M=
ono&quot;,Menlo,Courier,monospace;font-size:12px;line-height:20px;color:rgb=
a(27,31,35,0.3);text-align:right;white-space:nowrap;vertical-align:top"></t=
d><td id=3D"gmail-LC89" class=3D"gmail-blob-code gmail-blob-code-inner gmai=
l-js-file-line" style=3D"box-sizing:border-box;padding:0px 10px;line-height=
:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consol=
as,&quot;Liberation Mono&quot;,Menlo,Courier,monospace;font-size:12px;color=
:rgb(36,41,46);word-wrap:normal;white-space:pre">        exclude <span clas=
s=3D"gmail-pl-c1" style=3D"box-sizing:border-box;color:rgb(0,92,197)">modul=
e</span>: <span class=3D"gmail-pl-s" style=3D"box-sizing:border-box;color:r=
gb(3,47,98)"><span class=3D"gmail-pl-pds" style=3D"box-sizing:border-box;co=
lor:rgb(3,47,98)">&#39;</span>htsjdk<span class=3D"gmail-pl-pds" style=3D"b=
ox-sizing:border-box;color:rgb(3,47,98)">&#39;</span></span></td></tr><tr s=
tyle=3D"box-sizing:border-box"><td id=3D"gmail-L90" class=3D"gmail-blob-num=
 gmail-js-line-number" style=3D"box-sizing:border-box;padding:0px 10px;widt=
h:50px;min-width:50px;font-family:SFMono-Regular,Consolas,&quot;Liberation =
Mono&quot;,Menlo,Courier,monospace;font-size:12px;line-height:20px;color:rg=
ba(27,31,35,0.3);text-align:right;white-space:nowrap;vertical-align:top"></=
td><td id=3D"gmail-LC90" class=3D"gmail-blob-code gmail-blob-code-inner gma=
il-js-file-line" style=3D"box-sizing:border-box;padding:0px 10px;line-heigh=
t:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Conso=
las,&quot;Liberation Mono&quot;,Menlo,Courier,monospace;font-size:12px;colo=
r:rgb(36,41,46);word-wrap:normal;white-space:pre">    }
</td></tr></tbody></table><br></div><div>=C2=A0So we should exclude htsjdk =
module from gkl when building java-picard.</div><div>Do we have a method to=
 do that easily?</div><div><br></div><blockquote class=3D"gmail_quote" styl=
e=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div di=
r=3D"ltr"><div class=3D"gmail_extra"><div class=3D"gmail_quote"><span class=
=3D""><div></div><div>=C2=A0</div><blockquote class=3D"gmail_quote" style=
=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span>
&gt;&gt; or about missing files as in dropseq-tools:<br>
&gt;&gt; <br>
&gt;&gt;=C2=A0 =C2=A0 =C2=A0<a href=3D"http://java.io">java.io</a>.<wbr>Fil=
eNotFoundException: /gnu/store/q76y0ximcziplgfpbn2<wbr>6kbw4h3s14f33-dropse=
q-tools-1.<wbr>13/share/java/lib/biojava-<wbr>alignment.jar<br>
&gt;<br>
</span>&gt; That&#39;s also bad.=C2=A0 How does it run at all if its depend=
encies are missing?<br>
<br>
To satisfy the dropseq-tools build system the dependencies a symlinked<br>
to the build directory.=C2=A0 I suspect that the error is something to do<b=
r>
with that.<br>
<br>
&gt; The only thing I can think of that would improve things long term:<br>
&gt;<br>
&gt; The phase can add relative paths to all the dependencies to META-INF/M=
ANIFEST.MF<br>
&gt; before invoking &quot;jar -i&quot;.<br>
&gt; Then &quot;jar -i&quot; will index those - and all java packages can u=
se regular inputs<br>
&gt; instead of propagated inputs.=C2=A0 I&#39;ve tested that locally alrea=
dy - and it<br>
&gt; works fine.<br>
<br>
Is it correct that this would ensure that in case of duplicate class<br>
names this would pick the class from the current package?<br>
<span class=3D"m_-3161032416014021583HOEnZb"><font color=3D"#888888"><br>
-- <br>
Ricardo<br>
<br>
<br>
<br>
</font></span></blockquote></span></div><br></div></div>
</blockquote></div><br></div></div>

--00000000000085e845056e09527d--

Last modified: Mon, 25 Nov 2019 12:00:02 UTC

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997 nCipher Corporation Ltd, 1994-97 Ian Jackson.