installed docbook ports are not always correctly reflected in xml catalog

[jabronson@…]

attaching log

[sewebster@…]

The log shows a problem retrieving http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd I can load this file fine (in my web browser for instance). Can you? Perhaps it was as temporary network problem?

[sewebster@…]

Cc Me!

[jmroot (Joshua Root)]

The port shouldn't be trying to download anything in the build phase. Looks similar to #2695 or #14967.

[jabronson@…]

Replying to sewebster@…:

The log shows a problem retrieving http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd I can load this file fine (in my web browser for instance). Can you? Perhaps it was as temporary network problem?

I can load it fine in my web browser too, so it's not a network problem...

[ryandesign (Ryan Carsten Schmidt)]

Do you use a proxy server? If so, have you told MacPorts about it (see macports.conf)?

[jabronson@…]

Replying to ryandesign@…:

Do you use a proxy server? If so, have you told MacPorts about it (see macports.conf)?

I use ​GlimmerBlocker for filtering ads. But if I could access that url in a browser (and via curl at the command line), could that really be the culprit? If so let me know what to put in my macports.conf and I'll report back. Worth mentioning I'm in Brazil, in case it's relevant.

[sewebster@…]

I don't know how to set up macports.conf, and I couldn't find anything about proxies in the guide or the man page, but one thing you could try, would be to turn your ad blocker off and then see if things work.

[jabronson@…]

Replying to sewebster@…:

I don't know how to set up macports.conf, and I couldn't find anything about proxies in the guide or the man page, but one thing you could try, would be to turn your ad blocker off and then see if things work.

Should have said I tried that already, no dice.

[jabronson@…]

I just took a look at this again and noticed the problem is an earlier syntax error that propagates up and makes it look like an I/O error:

:info:build /usr/bin/make  all-am
:info:build for xml in xmlif.xml xmlto.xml; do \
:info:build       FORMAT_DIR=./format \
:info:build        /bin/sh ./xmlto -o man/man1 man ./doc/$xml ; \
:info:build     done || ( RC=$?; exit $RC )
:info:build for xml in xmlif.xml xmlto.xml; do \
:info:build       FORMAT_DIR=./format \
:info:build        /bin/sh ./xmlto -o man/man1 man ./doc/$xml ; \
:info:build     done || ( RC=$?; exit $RC )
:info:build xmlto: /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_textproc_xmlto/work/xmlto-0.0.23/./doc/xmlif.xml does not validate (status 3)
:info:build xmlto: Fix document syntax or use --skip-validation option
:info:build I/O error : Attempt to load network entity http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_textproc_xmlto/work/xmlto-0.0.23/./doc/xmlif.xml:4: warning: failed to load external entity "http://ww
:info:build    "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd">

Can the port maintainers please take a look at this again?

[jabronson@…]

I'm unable to upgrade all of these ports because they depend on xmlto:

rabbitmq-server                @1.7.2_0 
texlive                        @2009_3+doc+medium 
texlive-basic                  @15576_1+doc 
texlive-bin                    @2009_6+no_x11 
texlive-bin-extra              @15618_3+doc 
texlive-context                @14390_1+doc 
texlive-documentation-base     @13822_1+doc 
texlive-documentation-english  @15727_1+doc 
texlive-fonts-recommended      @13822_1+doc 
texlive-fontutils              @15606_3+doc 
texlive-generic-recommended    @13822_1+doc 
texlive-htmlxml                @13822_2+doc 
texlive-lang-czechslovak       @14727_1+doc 
texlive-lang-dutch             @14727_1+doc 
texlive-lang-french            @14727_1+doc 
texlive-lang-german            @14751_1+doc 
texlive-lang-italian           @13822_1+doc 
texlive-lang-polish            @14727_1+doc 
texlive-lang-portuguese        @13822_1+doc 
texlive-lang-spanish           @13822_1+doc 
texlive-lang-ukenglish         @14727_1+doc 
texlive-latex                  @15495_1+doc 
texlive-latex-extra            @15852_1+doc 
texlive-latex-recommended      @15271_1+doc 
texlive-luatex                 @13992_1+doc 
texlive-math-extra             @15560_1+doc 
texlive-metapost               @15388_1+doc 
texlive-pictures               @15543_1+doc 
texlive-xetex                  @14329_1+doc 

Is anyone else having this problem?

[mf2k (Frank Schima)]

Replying to jabronson@…:

Is anyone else having this problem?

No. Because you should be using the following command to upgrade:

sudo port -p upgrade outdated

The -p flag says to proceed after an error.

[jabronson@…]

How about actually fixing the error?

[mf2k (Frank Schima)]

Replying to jabronson@…:

How about actually fixing the error?

I can't reproduce the error. There is no maintainer for this port. If you can fix it and submit a patch, that would be helpful.

[jabronson@…]

Replying to macsforever2000@…:

I can't reproduce the error. There is no maintainer for this port. If you can fix it and submit a patch, that would be helpful.

The attached patch works around the issue by passing "--skip-validation" to xmlto during the build phase. To address the actual reported problem, though:

Replying to jabronson@…:

I just took a look at this again and noticed the problem is an earlier syntax error that propagates up and makes it look like an I/O error

I inspected the files in question, xmlif.xml and xmlto.xml, and they're both valid xml. (The only thing I found which could be problematic was a right single quote character (’) on line 272 of xmlto.xml. Why they didn't just use the ascii apostrophe I have no idea.)

Replying to macsforever2000@…:

Is anyone else having this problem?

No. Because you should be using the following command to upgrade: sudo port -p upgrade outdated

#27387 is evidence to the contrary. And passing the -p flag did not solve the problem.

[mf2k (Frank Schima)]

r73800. It still builds fine for me. Thanks for the patch!

[jabronson@…]

my pleasure. if the actual cause of the problem ends up getting discovered and a better fix turns up, we should use that instead of the workaround.

[jmroot (Joshua Root)]

Reopening since #27439 shows that r73800 didn't actually fix the real problem.

[jmroot (Joshua Root)]

Could people perhaps be mistakenly running the command shown in the notes (now only when using portdbformat flat) after installing, rather than after uninstalling?

[vinc17@…]

Cc Me!

[jabronson@…]

Replying to jmr@…:

Could people perhaps be mistakenly running the command shown in the notes (now only when using portdbformat flat) after installing, rather than after uninstalling?

Sorry, what command? What notes? Was I supposed to uninstall something?

I have portdbformat set to sqlite. The commands I'm running corresponding to the tickets I've opened that were marked as duplicates of this one are port install libzzip (#27439) and port install gtk-doc (#27780).

Thanks for your help.

[ballapete (Peter "Pete" Dyballa)]

I had a similar defect with gtk-doc-1.15 (​https://trac.macports.org/ticket/27771), which was found to be a duplicate of this defect. I finally managed to build a work-around from Fink's /sw/etc/xml/catalog file. It does not have entries like

<nextCatalog catalog="/opt/local/share/xml/docbook/4.1.2/catalog.xml" />
<nextCatalog catalog="/opt/local/share/xml/docbook/4.2/catalog.xml" />

but more "explicite" ones:

  <public publicId="-//OASIS//DTD DocBook XML CALS Table Model V4.1.2//EN" uri="file:///sw/share/xml/dtd/docbookx/4.1.2/calstblx.dtd"/>
  <public publicId="-//OASIS//DTD DocBook XML CALS Table Model V4.1//EN" uri="file:///sw/share/xml/dtd/docbookx/4.1/calstblx.dtd"/>
  <public publicId="-//OASIS//DTD DocBook XML CALS Table Model V4.2//EN" uri="file:///sw/share/xml/dtd/docbookx/4.2.0/calstblx.dtd"/>

With some sed edit commands and egrep I created a new /opt/local/etc/xml/catalog file, saving the original one to avoid Timemachine. Configure finds:

checking for XML catalog (/opt/local/etc/xml/catalog)... found
checking for xmlcatalog... /opt/local/bin/xmlcatalog
checking for DocBook XML DTD V4.3 in XML catalog... found
checking for DocBook XSL Stylesheets in XML catalog... found
checking for source-highlight... /opt/local/bin/source-highlight
checking for TEST_DEPS... yes
checking whether to enable runtime debugging code... no
configure: creating ./config.status

and gtk-doc-1.15 is upgraded.

[ballapete (Peter "Pete" Dyballa)]

Cc Me!

[deesto (John S. De Stefano Jr.)]

Cc Me!

[jabronson@…]

Replying to jabronson@…:

Could people perhaps be mistakenly running the command shown in the notes (now only when using portdbformat flat) after installing, rather than after uninstalling?

Sorry, what command? What notes? Was I supposed to uninstall something?

Oh, you're talking about comment:4:ticket:27771. That wasn't the case in my case, anyway.

Can a fix be created based on Peter_Dyballa's workaround?

[mauricio_ville@…]

Cc Me!

[sinuhet.merlin@…]

Cc Me!

[a.vincelli@…]

Cc Me!

[jmroot (Joshua Root)]

/opt/local/etc/xml/catalog from a system that does not exhibit the problem

[a.vincelli@…]

Cc Me!

[ryandesign (Ryan Carsten Schmidt)]

Has duplicates #28305 and #28313.

[fiee (Henning Hraban Ramm)]

fixed catalog:

<?xml version="1.0"?>
<!DOCTYPE catalog PUBLIC "-//OASIS//DTD Entity Resolution XML Catalog V1.0//EN" "http://www.oasis-open.org/committees/entity/release/1.0/catalog.dtd">
<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
  <nextCatalog catalog="/opt/local/share/xsl/docbook-xsl/catalog.xml"/>
  <nextCatalog catalog="/opt/local/share/xml/docbook/5.0/catalog.xml"/>
  <nextCatalog catalog="/opt/local/share/xml/docbook/4.5/catalog.xml"/>
  <nextCatalog catalog="/opt/local/share/xml/docbook/4.4/catalog.xml"/>
  <nextCatalog catalog="/opt/local/share/xml/docbook/4.3/catalog.xml"/>
  <nextCatalog catalog="/opt/local/share/xml/docbook/4.2/catalog.xml"/>
  <nextCatalog catalog="/opt/local/share/xml/docbook/4.1.2/catalog.xml"/>
  <system systemId="http://glade.gnome.org/glade-2.0.dtd" uri="/opt/local/share/xml/libglade/glade-2.0.dtd"/>
</catalog>

(upgrade of gtk-doc failed due to missing DocBook 4.3 entry, and that blocked all dependent ports)

[mauricio_ville@…]

I solved this problem by reinstalling the docbooks, i.e.:

sudo port upgrade --force $(port list installed | grep docbook | awk '{print $1}')

[jabronson@…]

Replying to mauricio_ville@…:

I solved this problem by reinstalling the docbooks, i.e.:

sudo port upgrade --force $(port list installed | grep docbook | awk '{print $1}')

Worked for me too, thank you thank you! First time I've been able to upgrade a bunch of ports in 8 months.

[jmroot (Joshua Root)]

I'll just note that nobody has yet attached the catalog file from a system that exhibits the problem.

[jabronson@…]

Replying to jmr@…:

I'll just note that nobody has yet attached the catalog file from a system that exhibits the problem.

Just noticed your attachment three months ago with comment "/opt/local/etc/xml/catalog from a system that does not exhibit the problem". I would have attached mine but without more context or an explicit request I unfortunately didn't read between the lines. Hopefully someone who hasn't yet --forced their way out of this can provide their catalog file.

[ballapete (Peter "Pete" Dyballa)]

Replying to jmr@…:

I'll just note that nobody has yet attached the catalog file from a system that exhibits the problem.

Here is mine – in a minute or so, since I have to press two different buttons at opposite regions of this page.

[ballapete (Peter "Pete" Dyballa)]

Original defective /opt/local/etc/xml/catalog file

[cooljeanius (Eric Gallager)]

Cc Me!

[pancake@…]

I have found several dupped issues related to the same problem, and its something that it's been buggy since the begining and the bugs get opened again and again. This is the solution I did to solve the same problem I was able to reproduce right now.

$ cat xml-catalog.sh
#!/bin/sh
echo '<?xml version="1.0"?>'
echo '<!DOCTYPE catalog PUBLIC "-//OASIS//DTD Entity Resolution XML Catalog V1.0//EN" "http://www.oasis-open.org/committees/entity/release/1.0/catalog.dtd">'
echo '<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">'
CATS=`find  /opt/local/share/| grep catalog.xml$`
for a in ${CATS} ; do
	echo '<nextCatalog catalog="'$a'"/>'
done
echo '</catalog>'

This script will generate the /opt/local/etc/xml/catalog. the gtk-doc program fails if this file contain entries that point to outdated or non-existent versions of those catalogs.

This script or a similar one should be used after installing/upgrading/removing any package that contains a file named catalog.xml. This way it will keep consistency.

Related issues are:

• #17662
• #26151
• #34077
• #28092
• #28313
• #27771
• #42470

...