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To: Ricardo Wurmus <ricardo.wurmus@HIDDEN>
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--00000000000085e845056e09527d
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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
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable
<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"><<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"><<a href=3D"mailto:ricardo.wur=
mus@HIDDEN" target=3D"_blank">ricardo.wurmus@HIDDEN</a>></=
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 <<a href=3D"mailto:dannym@HIDDEN" target=3D=
"_blank">dannym@HIDDEN</a>> writes:<br>
<br>
>> The errors are either about duplicates as in java-picard-2.10.3:<b=
r>
>> <br>
>>=C2=A0 =C2=A0 =C2=A0duplicate entry: htsjdk/samtools/AbstractBAMFil=
<wbr>eIndex$1.class<br>
><br>
</span>> That's... bad.=C2=A0 What if those files differed?=C2=A0 Wh=
ich one would be used at<br>
> 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,"Segoe UI",Helvetica,Ar=
ial,sans-serif,"Apple Color Emoji","Segoe UI Emoji",&qu=
ot;Segoe UI Symbol";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,"Liberati=
on Mono",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,"Liberation =
Mono",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,"Liberation Mono",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)">=
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)">'</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,"Liberation M=
ono",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,"Liberation Mono",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)">'</span>htsjdk<span class=3D"gmail-pl-pds" style=3D"b=
ox-sizing:border-box;color:rgb(3,47,98)">'</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,"Liberation =
Mono",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,"Liberation Mono",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>
>> or about missing files as in dropseq-tools:<br>
>> <br>
>>=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>
><br>
</span>> That'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>
> The only thing I can think of that would improve things long term:<br>
><br>
> The phase can add relative paths to all the dependencies to META-INF/M=
ANIFEST.MF<br>
> before invoking "jar -i".<br>
> Then "jar -i" will index those - and all java packages can u=
se regular inputs<br>
> instead of propagated inputs.=C2=A0 I've tested that locally alrea=
dy - and it<br>
> 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--
bug-guix@HIDDEN:bug#31721; Package guix.
Full text available.Received: (at 31721) by debbugs.gnu.org; 7 Jun 2018 08:27:51 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Jun 07 04:27:51 2018 Received: from localhost ([127.0.0.1]:37399 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1fQqGt-0004T8-Fi for submit <at> debbugs.gnu.org; Thu, 07 Jun 2018 04:27:51 -0400 Received: from mail-io0-f178.google.com ([209.85.223.178]:44064) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <boskovits@HIDDEN>) id 1fQqGs-0004Sv-DD for 31721 <at> debbugs.gnu.org; Thu, 07 Jun 2018 04:27:50 -0400 Received: by mail-io0-f178.google.com with SMTP id g7-v6so10836097ioh.11 for <31721 <at> debbugs.gnu.org>; Thu, 07 Jun 2018 01:27:50 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:in-reply-to:references:from:date:message-id:subject:to :cc; bh=UtNN+xt1WrKUr4b2NMmBK3mMdUfKCWIiUSFOv4SGCOg=; b=XWp4vqnQk2tLjjz8qILNmP6SYIX+4imDNjQpbXF5VBxOTMnAOrBosdkE7/WjMeR8dd TJjLo3j5IoQtmIWWV/xEIZGlYOL1QXQ8LOhZj3uLkKJEnymHSu2ChBCckRgvo4zZJDrA p7FHksxgDQd2+FGjIJFxq9SdNUY7iVAwXIX8JHwDmnva1jBUjVb80PXfA75NFJAX81s/ KMvEOxIfqcS8tx1YKq/TxsWLtlW0HWcDD/mIFPDthsVu0gtr/JMKqtwYCuGnHH7VLUgM yaNeAxn7rDSfE3Y6G8jWcu+fUw/QxUkEg+5dIUsoEop5dfGLie8TxJcKud1qFgFWTLEa YpCQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:in-reply-to:references:from:date :message-id:subject:to:cc; bh=UtNN+xt1WrKUr4b2NMmBK3mMdUfKCWIiUSFOv4SGCOg=; b=qkTYqPRCSlyUVx0lE/V9HLl3P1apJr6TP3OlqoBGX7k7nNapaolFtz09/0CxXQDWhE kYB9wVgwK3a2twZ34ZgzY2CmCJyyF5fCy9hop1Uc/56pyEQnqGpRMZlS/DlFDF9YiiK0 z9afkPlt4imMs0/RLID7S6kFjlcfwyV9ClkdKjlzgs1/opV75It2HGzZVLT9cOr6gA+j KgQT8Xu+HWRG7mmEmL+g0xslY221TOvYo9QEs1lsr+5IqBJaQA6ossy0RLgql97b2zbo N1RGvR1m5q9UiL6U1uaoDGDcuUdszyWS3zeLojzqG3/czYx9Q/hUEwwZL7wr+cHA187p 7NmQ== X-Gm-Message-State: APt69E1vX1TFOzDSIFpgWrIxvWOlZwOgHlAanopC9Q7R/uE6ajjnzkoq WagWraHQEXLZWiJuPzFprSzgBOEvatpAQvusHw== X-Google-Smtp-Source: ADUXVKLYVc4eVq83MKNrUJ7KUGBof+WXzbb/jKDT5/EEu8nVU3usGOS79dB0XA6tGlDSX/5IaE+oKL3LHxyRYy18ke4= X-Received: by 2002:a6b:94c9:: with SMTP id w192-v6mr637544iod.89.1528360064218; Thu, 07 Jun 2018 01:27:44 -0700 (PDT) MIME-Version: 1.0 Received: by 2002:a4f:a84d:0:0:0:0:0 with HTTP; Thu, 7 Jun 2018 01:27:43 -0700 (PDT) In-Reply-To: <877enbyse2.fsf@HIDDEN> References: <8736y11o2q.fsf@HIDDEN> <20180607010620.31fbf16c@HIDDEN> <877enbyse2.fsf@HIDDEN> From: =?UTF-8?Q?G=C3=A1bor_Boskovits?= <boskovits@HIDDEN> Date: Thu, 7 Jun 2018 10:27:43 +0200 Message-ID: <CAE4v=pitxJ_W3M1uacrGqAEg-NG7V1XaD+iSFJ-o7Kg4rXtq8A@HIDDEN> Subject: =?UTF-8?Q?Re=3A_bug=2331721=3A_=E2=80=9Cgenerate=2Djar=2Dindices=E2=80=9D_phase_fail?= =?UTF-8?Q?s_on_many_packages?= To: Ricardo Wurmus <ricardo.wurmus@HIDDEN> Content-Type: multipart/alternative; boundary="000000000000b77d38056e090ec9" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 31721 Cc: Danny Milosavljevic <dannym@HIDDEN>, 31721 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --000000000000b77d38056e090ec9 Content-Type: text/plain; charset="UTF-8" 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 > > > > --000000000000b77d38056e090ec9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <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"><<a href=3D"mailt= o:ricardo.wurmus@HIDDEN" target=3D"_blank">ricardo.wurmus@mdc-berlin= .de</a>></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 <<a href=3D"mailto:dannym@HIDDEN">dannym@sc= ratchpost.org</a>> writes:<br> <br> >> The errors are either about duplicates as in java-picard-2.10.3:<b= r> >> <br> >>=C2=A0 =C2=A0 =C2=A0duplicate entry: htsjdk/samtools/<wbr>AbstractB= AMFileIndex$1.class<br> ><br> </span>> That's... bad.=C2=A0 What if those files differed?=C2=A0 Wh= ich one would be used at<br> > 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""> >> or about missing files as in dropseq-tools:<br> >> <br> >>=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> ><br> </span>> That'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> > The only thing I can think of that would improve things long term:<br> ><br> > The phase can add relative paths to all the dependencies to META-INF/M= ANIFEST.MF<br> > before invoking "jar -i".<br> > Then "jar -i" will index those - and all java packages can u= se regular inputs<br> > instead of propagated inputs.=C2=A0 I've tested that locally alrea= dy - and it<br> > 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> --000000000000b77d38056e090ec9--
bug-guix@HIDDEN:bug#31721; Package guix.
Full text available.Received: (at 31721) by debbugs.gnu.org; 7 Jun 2018 07:20:58 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Jun 07 03:20:58 2018 Received: from localhost ([127.0.0.1]:37376 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1fQpE9-0002vL-UM for submit <at> debbugs.gnu.org; Thu, 07 Jun 2018 03:20:58 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:37230) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <Ricardo.Wurmus@HIDDEN>) id 1fQpE8-0002vC-5Z for 31721 <at> debbugs.gnu.org; Thu, 07 Jun 2018 03:20:56 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 1632C1179B9B; Thu, 7 Jun 2018 09:20:55 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:user-agent:references :received:received:received:received; s=mdc; t=1528356049; x= 1530170450; bh=OaPac1sGa7qkYxWefMZ5gBL2ZYfmhT5LnwsPfCUNlEo=; b=H +dAR86FhotiN9bHetPL6GQ2k6DLmI2jpD0ME3JoVGgp9KHebbs7xpyagmC2s5hMc RgS8WVZT0RCycsQCSpg3iHe6iGojQK89FubBwZg/LTbR0sNCSyCHQs/lPQYi91ca rYSobzcfvp4wi+bxPvfOYVyLEePnYTbpYliP0B2Idw= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id OOxCMSIBe5Hs; Thu, 7 Jun 2018 09:20:49 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Thu, 7 Jun 2018 09:20:49 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) by HTCAONE.mdc-berlin.net (141.80.180.120) with Microsoft SMTP Server (TLS) id 14.3.399.0; Thu, 7 Jun 2018 09:20:48 +0200 Received: from localhost (141.80.113.51) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server id 14.3.399.0; Thu, 7 Jun 2018 09:20:47 +0200 References: <8736y11o2q.fsf@HIDDEN> <20180607010620.31fbf16c@HIDDEN> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus <ricardo.wurmus@HIDDEN> To: Danny Milosavljevic <dannym@HIDDEN> Subject: Re: =?utf-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on many packages In-Reply-To: <20180607010620.31fbf16c@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 7 Jun 2018 09:20:37 +0200 Message-ID: <877enbyse2.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.2.1013-23892.005 X-TM-AS-Result: No-5.814000-8.000000-10 X-TMASE-MatchedRID: O/y65JfDwwt73HU3OUveQfHkpkyUphL9M9g+YfdqJKHfUZT83lbkEDCs Ame4bhohs6xTkEgjiiSC2+nAZJSfpgH/zrweiLuzcxGQfOZHrIfvSp2iuuHtorUV4VfJ6SB0vsU 5jRUBF/oUSFM3d6sZGaaurWop/1N8AW5RnLqQx4cYteHAndhXo30tCKdnhB581kTfEkyaZdz6C0 ePs7A07SAJgyd9wrc8J4LDjIHJEcpK0o9X7v8PUdlPzWENHBupIT3gBanW/MHufPjdhb/qGw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.814000-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.2.1013-23892.005 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 31721 Cc: 31721 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) 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
bug-guix@HIDDEN:bug#31721; Package guix.
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From: Ricardo Wurmus <ricardo.wurmus@HIDDEN>
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Subject: =?utf-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on
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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
Ricardo Wurmus <ricardo.wurmus@HIDDEN>:bug-guix@HIDDEN.
Full text available.bug-guix@HIDDEN:bug#31721; Package guix.
Full text available.
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