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#1 2015-12-12 05:26:00

Salkay
Member
Registered: 2014-05-22
Posts: 419

[SOLVED] Errors updating haskell-related packages

I upgraded today with sudo pacman -Syu. This upgrade included a whole lot of haskell-related packages, including the following.

haskell-text-1.2.1.3-4-x86_64
haskell-hashable-1.2.3.3-2-x86_64
haskell-primitive-0.6-4-x86_64
haskell-vector-0.11.0.0-4-x86_64
haskell-scientific-0.3.4.4-2-x86_64
haskell-attoparsec-0.13.0.1-6-x86_64
haskell-unordered-containers-0.2.5.1-3-x86_64
haskell-mtl-2.2.1-5-x86_64
haskell-syb-0.6-3-x86_64
haskell-dlist-0.7.1.2-2-x86_64
haskell-aeson-0.10.0.0-4-x86_64
haskell-hourglass-0.2.9-2-x86_64
haskell-memory-0.10-2-x86_64
haskell-asn1-types-0.3.1-2-x86_64
haskell-asn1-encoding-0.9.3-2-x86_64
haskell-asn1-parse-0.9.4-2-x86_64
haskell-stm-2.4.4-5-x86_64
haskell-async-2.0.2-2-x86_64
haskell-base64-bytestring-1.0.0.1-5-x86_64
haskell-blaze-builder-0.4.0.1-2-x86_64
haskell-blaze-markup-0.7.0.3-2-x86_64
haskell-blaze-html-0.8.1.1-3-x86_64
haskell-byteable-0.1.1-2-x86_64
haskell-case-insensitive-1.2.0.5-3-x86_64
haskell-cereal-0.5.1.0-2-x86_64
haskell-cmark-0.4.1-2-x86_64
haskell-transformers-compat-0.4.0.4-3-x86_64
haskell-exceptions-0.8.0.2-2-x86_64
haskell-transformers-base-0.4.4-2-x86_64
haskell-monad-control-1.0.0.4-2-x86_64
haskell-lifted-base-0.2.3.6-2-x86_64
haskell-mmorph-1.0.4-2-x86_64
haskell-resourcet-1.1.7-2-x86_64
haskell-conduit-1.2.6-2-x86_64
haskell-data-default-class-0.0.1-10-x86_64
haskell-parsec-3.1.9-6-x86_64
haskell-network-2.6.2.1-4-x86_64
haskell-socks-0.5.4-4-x86_64
haskell-cryptonite-0.9-2-x86_64
haskell-pem-0.2.2-2-x86_64
haskell-x509-1.6.3-3-x86_64
haskell-x509-store-1.6.1-3-x86_64
haskell-x509-validation-1.6.3-3-x86_64
haskell-tls-1.3.3-5-x86_64
haskell-x509-system-1.6.1-4-x86_64
haskell-connection-0.2.5-5-x86_64
haskell-data-default-instances-base-0.0.1-12-x86_64
haskell-data-default-instances-containers-0.0.1-10-x86_64
haskell-data-default-instances-dlist-0.0.1-11-x86_64
haskell-old-locale-1.0.0.7-7-x86_64
haskell-data-default-instances-old-locale-0.0.1-10-x86_64
haskell-data-default-0.5.3-11-x86_64
haskell-cookie-0.4.1.6-2-x86_64
haskell-deepseq-generics-0.1.1.2-2-x86_64
haskell-digest-0.0.1.2-2-x86_64
haskell-enclosed-exceptions-1.0.1.1-2-x86_64
haskell-extensible-exceptions-0.1.1.4-13-x86_64
haskell-old-time-1.1.0.3-7-x86_64
haskell-unix-compat-0.4.1.4-3-x86_64
haskell-filemanip-0.3.6.3-4-x86_64
haskell-haddock-library-1.2.1-2-x86_64
haskell-regex-base-0.93.2-24-x86_64
haskell-regex-pcre-builtin-0.94.4.8.8.35-2-x86_64
haskell-utf8-string-1.0.1.1-1-x86_64
haskell-highlighting-kate-0.6-4-x86_64
haskell-hslua-0.4.1-2-x86_64
haskell-network-uri-2.6.0.3-2-x86_64
haskell-http-4000.2.20-5-x86_64
haskell-http-types-0.9-3-x86_64
haskell-mime-types-0.1.0.6-3-x86_64
haskell-random-1.1-5-x86_64
haskell-zlib-0.6.1.1-2-x86_64
haskell-streaming-commons-0.1.15-2-x86_64
haskell-http-client-0.4.24-4-x86_64
haskell-http-client-tls-0.2.2-7-x86_64
haskell-juicypixels-3.2.6.4-2-x86_64
haskell-pandoc-types-1.12.4.7-5-x86_64
haskell-sha-1.6.4.2-4-x86_64
haskell-tagsoup-0.13.5-2-x86_64
haskell-temporary-1.2.0.3-2-x86_64
haskell-xml-1.3.14-2-x86_64
haskell-texmath-0.8.4-3-x86_64
haskell-yaml-0.8.15.2-3-x86_64
haskell-zip-archive-0.2.3.7-2-x86_64

At first, upgrading failed with the following error.

error: failed to commit transaction (conflicting files)
ghc: /usr/share/doc/ghc/html/libraries/doc-index-126.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-35.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-37.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-38.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-42.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-46.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-61.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-94.html exists in filesystem
Errors occurred, no packages were upgraded.

None of these files were owned by an existing package (I'm not sure how), so I deleted them, then upgraded again. This time it upgraded, but with a whole lot of errors.

(  7/100) upgrading device-mapper                                                                                              [############################################################################] 100%
==> Unregistering cabalized packages...
unregistering would break the following packages: pandoc-1.15.2.1 yaml-0.8.15.2 conduit-1.2.6 (ignoring)
unregistering would break the following packages: enclosed-exceptions-1.0.1.1 lifted-base-0.2.3.6 monad-control-1.0.0.4 (ignoring)
unregistering would break the following packages: http-client-tls-0.2.2 (ignoring)
unregistering would break the following packages: texmath-0.8.4 (ignoring)
unregistering would break the following packages: x509-system-1.6.1 tls-1.3.3 x509-validation-1.6.3 x509-store-1.6.1 x509-1.6.3 (ignoring)
unregistering would break the following packages: JuicyPixels-3.2.6.4 aeson-0.10.0.0 attoparsec-0.13.0.1 scientific-0.3.4.4 (ignoring)
unregistering would break the following packages: highlighting-kate-0.6 (ignoring)
unregistering would break the following packages: temporary-1.2.0.3 pem-0.2.2 exceptions-0.8.0.2 regex-pcre-builtin-0.94.4.8.8.35 regex-base-0.93.2 filemanip-0.3.6.3 HTTP-4000.2.20 network-uri-2.6.0.3 parsec-3.1.9 (ignoring)
unregistering would break the following packages: asn1-parse-0.9.4 asn1-encoding-0.9.3 asn1-types-0.3.1 (ignoring)
unregistering would break the following packages: streaming-commons-0.1.15 (ignoring)
unregistering would break the following packages: socks-0.5.4 (ignoring)
unregistering would break the following packages: tagsoup-0.13.5 xml-1.3.14 mime-types-0.1.0.6 http-types-0.9 cookie-0.4.1.6 case-insensitive-1.2.0.5 cmark-0.4.1 blaze-builder-0.4.0.1 unordered-containers-0.2.5.1 hashable-1.2.3.3 (ignoring)
unregistering would break the following packages: data-default-0.5.3 (ignoring)
unregistering would break the following packages: data-default-instances-dlist-0.0.1 data-default-instances-containers-0.0.1 (ignoring)
unregistering would break the following packages: old-time-1.1.0.3 (ignoring)
==> Done.
(  8/100) upgrading ghc                                                                                                        [############################################################################] 100%
==> All cabalized packages need to be reinstalled now.
==> See /usr/share/haskell/ for a tentative list of affected packages.
(  9/100) upgrading gtk2                                                                                                       [############################################################################] 100%
ghc-pkg: cannot find package text-1.2.1.3
error: command failed to execute correctly
( 10/100) upgrading haskell-text                                                                                               [############################################################################] 100%
Reading package info from stdin ... done.
ghc-pkg: cannot find package hashable-1.2.3.3
error: command failed to execute correctly

Almost all of the last 90 packages had the same error, e.g.

ghc-pkg: cannot find package yaml-0.8.15.2
error: command failed to execute correctly

Is this something I should be concerned about?

Last edited by Salkay (2015-12-16 09:46:15)

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#2 2015-12-12 05:30:20

jasonwryan
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From: .nz
Registered: 2009-05-09
Posts: 28,151
Website

Re: [SOLVED] Errors updating haskell-related packages

Are you installing packages with both cabal and pacman? Using two package managers is generally a recipe for unhappiness...


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#3 2015-12-12 05:48:22

Salkay
Member
Registered: 2014-05-22
Posts: 419

Re: [SOLVED] Errors updating haskell-related packages

I don't think so. I don't even know what cabal is. I just searched my command history and have never typed "cabal" into it.

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#4 2015-12-12 08:46:56

AKL
Member
Registered: 2008-07-29
Posts: 54

Re: [SOLVED] Errors updating haskell-related packages

Same problem here, but I didn't delete anything so far.


Endut! Hoch Hech!

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#5 2015-12-12 08:58:13

Tétrapyle
Member
Registered: 2014-01-03
Posts: 32

Re: [SOLVED] Errors updating haskell-related packages

Same problem here... following pacman -Syyu

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#6 2015-12-12 09:32:21

Maeda
Member
Registered: 2015-02-17
Posts: 32

Re: [SOLVED] Errors updating haskell-related packages

Same problem here. Someone is working on this problem ?
Thanks.


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#7 2015-12-12 10:04:38

Raynman
Member
Registered: 2011-10-22
Posts: 1,250

Re: [SOLVED] Errors updating haskell-related packages

Salkay wrote:

Almost all of the last 90 packages had the same error, e.g.

ghc-pkg: cannot find package yaml-0.8.15.2
error: command failed to execute correctly

Is this something I should be concerned about?

Usually not. The haskell packages (the ones providing libraries anyway) are tied to a specific ghc version. That's why the post-upgrade message for ghc says "All cabalized packages need to be reinstalled now." The packages in the repos have been rebuilt against the new version, but their .install scripts don't distinguish between such a rebuild and a standard upgrade (where the ghc version stays the same, but the dependent package is bumped to a newer version). For upgrades, packages are unregistered, then upgraded and then the upgraded version is registered with ghc. When ghc has just been upgraded, the unregistering fails because the previous version was registered with the old ghc version.

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#8 2015-12-12 15:19:11

vl.still
Member
Registered: 2013-01-08
Posts: 7

Re: [SOLVED] Errors updating haskell-related packages

I have the same problem, I have not installed any packages using cabal. This seems to me as bug in older versions of GHC:

- file /usr/share/doc/ghc/html/libraries/doc-index-126.htm exists in the filesystem
- it seems to not belong to any package, however, file /usr/share/doc/ghc/html/libraries/ghc-7.10.2/doc-index-126.html should belong to ghc-7.10.2 but does not exists in the filesystem.

Update: I succeeded with the update using --force (this overrides all conflicting files, which seems to be safe for ghc docs).

Last edited by vl.still (2015-12-13 22:21:57)

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#9 2015-12-13 02:27:18

flounders
Member
From: North Carolina
Registered: 2015-03-01
Posts: 16

Re: [SOLVED] Errors updating haskell-related packages

I'm having the same issue. A bug report should probably be filed if no one else has found a way to get around this. I know the last ghc upgrade also involved my having to reinstall all the upgraded packages to get things working smoothly.

As far as I know the way most Haskellers use cabal, it should not affect packages at the system wide level. I'm affected by this and I have never run cabal as root or with sudo. When cabal is used this way it has it's own local package store in ~/.cabal and ~/.ghc. It shouldn't be affecting the rest of the system.

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#10 2015-12-13 12:12:25

gauthma
Member
Registered: 2010-02-16
Posts: 205
Website

Re: [SOLVED] Errors updating haskell-related packages

I also stumbed on this. My solution was to uninstall ghc and the haskell packages I use (they are few), together with dependencies (i.e. with pacman's cascade functionality), update the system, and re-install the needed packages (with -f so as to overwrite the already existing files of ghc, which were owned by no package).

After having done this, everything seems to be running smoothly...

PS: Maybe I'm missing something but, if its packages are not installed *system-wide*, why would cabal have anything to do with this problem?

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#11 2015-12-13 14:55:32

flounders
Member
From: North Carolina
Registered: 2015-03-01
Posts: 16

Re: [SOLVED] Errors updating haskell-related packages

gauthma wrote:

PS: Maybe I'm missing something but, if its packages are not installed *system-wide*, why would cabal have anything to do with this problem?

The only reason I brought up that point is because of what jasonwryan posted earlier:

jasonwryan wrote:

Are you installing packages with both cabal and pacman? Using two package managers is generally a recipe for unhappiness...

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#12 2015-12-13 17:11:24

Maeda
Member
Registered: 2015-02-17
Posts: 32

Re: [SOLVED] Errors updating haskell-related packages

Someone opened a bug report ?


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#13 2015-12-13 17:27:38

vwyodajl
Member
Registered: 2012-01-21
Posts: 183

Re: [SOLVED] Errors updating haskell-related packages

even with the most recent updates today with haskell still have the same issue

error: failed to commit transaction (conflicting files)
ghc: /usr/share/doc/ghc/html/libraries/doc-index-126.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-35.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-37.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-38.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-42.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-46.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-61.html exists in filesystem
ghc: /usr/share/doc/ghc/html/libraries/doc-index-94.html exists in filesystem
Errors occurred, no packages were upgraded.

I have one box that I just manually removed the conflicting files then updated. When updating again today for the haskell changes just synced out it was still having issues

(9/9) checking available disk space                [######################] 100%
unregistering would break the following packages: pandoc-1.15.2.1 http-client-tls-0.2.2 connection-0.2.5 (ignoring)
(1/9) upgrading haskell-tls                        [######################] 100%
Reading package info from stdin ... done.
(2/9) upgrading haskell-connection                 [######################] 100%
Reading package info from stdin ... done.
(3/9) upgrading haskell-highlighting-kate          [######################] 100%
Reading package info from stdin ... done.
(4/9) upgrading haskell-http-client-tls            [######################] 100%
Reading package info from stdin ... done.
(5/9) upgrading lib32-libdbus                      [######################] 100%
(6/9) upgrading lib32-sqlite                       [######################] 100%
(7/9) upgrading lib32-systemd                      [######################] 100%
(8/9) upgrading openresolv                         [######################] 100%
(9/9) upgrading pandoc                             [######################] 100%
Reading package info from stdin ... done.

Like others I never use cabal.

Last edited by vwyodajl (2015-12-13 17:28:18)

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#14 2015-12-13 19:40:03

xanb
Member
Registered: 2012-07-24
Posts: 414

Re: [SOLVED] Errors updating haskell-related packages

Same happens to me.
Any solution?


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#15 2015-12-13 19:48:01

Raynman
Member
Registered: 2011-10-22
Posts: 1,250

Re: [SOLVED] Errors updating haskell-related packages

Please stop kicking with empty posts, talking about opening bug reports and asking for solutions without describing an actual problem.

The question was "should I be worried about these messages". I said no. Before that question a minor issue was mentioned regarding the html files in /usr/share/doc. This kind of thing is in the wiki and a sticky with frequently asked questions/problems and the OP already included a simple solution.

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#16 2015-12-14 10:10:59

Maeda
Member
Registered: 2015-02-17
Posts: 32

Re: [SOLVED] Errors updating haskell-related packages

OK.

First, I deleted those $%*! .html files.

Then I did the same solution as my previous problem, removing ghc related packages, installing ghc again, and then installing ghc related packages previously removed. Got some warning messages with xmonad package, but `xmonad --recompile` is OK.

\o/

Once again, it's not the way we should do it I think. Why is this happening ? I always use pacman to install/update...


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#17 2015-12-16 08:07:44

xanb
Member
Registered: 2012-07-24
Posts: 414

Re: [SOLVED] Errors updating haskell-related packages

Maeda wrote:

OK.

First, I deleted those $%*! .html files.

Then I did the same solution as my previous problem, removing ghc related packages, installing ghc again, and then installing ghc related packages previously removed. Got some warning messages with xmonad package, but `xmonad --recompile` is OK.

\o/

Once again, it's not the way we should do it I think. Why is this happening ? I always use pacman to install/update...

Is there any way to do it automatically? Something like pacman [list packages depending on ghc and uninstall them]


Owning one OpenRC (artoo way) and other three systemd machines

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#18 2015-12-16 09:45:59

Salkay
Member
Registered: 2014-05-22
Posts: 419

Re: [SOLVED] Errors updating haskell-related packages

Raynman wrote:

Please stop kicking with empty posts, talking about opening bug reports and asking for solutions without describing an actual problem.

The question was "should I be worried about these messages". I said no.

To be honest, I was a little unsure as to how certain you were..

Raynman wrote:

Usually not.

I was waiting for a more definitive answer, although perhaps you were just being wary. In any case, I appreciate the comment.

FWIW, I uninstalled pandoc and dependencies (which was why ghc and the haskell packages were installed), checked /usr/share/doc/ghc (which had now disappeared), reinstalled the packages, and it's all fine now. Thanks for the comments.

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#19 2015-12-16 13:10:10

Raynman
Member
Registered: 2011-10-22
Posts: 1,250

Re: [SOLVED] Errors updating haskell-related packages

Salkay wrote:
Raynman wrote:

Usually not.

I was waiting for a more definitive answer, although perhaps you were just being wary. In any case, I appreciate the comment

Well, I've seen some more complicated situations with previous updates where some worrying (and fixing) was needed, so I didn't want to make it seem like you can ignore all messages related to Haskell packages and I tried to provide some insight into what's going on. That can then also be applied to future messages. So you could read the "usually not" as "in this and similar cases not (but keep using your brain)".

Another example:

vwyodajl wrote:

When updating again today for the haskell changes just synced out it was still having issues

(9/9) checking available disk space                [######################] 100%
unregistering would break the following packages: pandoc-1.15.2.1 http-client-tls-0.2.2 connection-0.2.5 (ignoring)
(1/9) upgrading haskell-tls                        [######################] 100%
Reading package info from stdin ... done.
(2/9) upgrading haskell-connection                 [######################] 100%
Reading package info from stdin ... done.
(3/9) upgrading haskell-highlighting-kate          [######################] 100%
Reading package info from stdin ... done.
(4/9) upgrading haskell-http-client-tls            [######################] 100%
Reading package info from stdin ... done.
(5/9) upgrading lib32-libdbus                      [######################] 100%
(6/9) upgrading lib32-sqlite                       [######################] 100%
(7/9) upgrading lib32-systemd                      [######################] 100%
(8/9) upgrading openresolv                         [######################] 100%
(9/9) upgrading pandoc                             [######################] 100%
Reading package info from stdin ... done.

Like others I never use cabal.

Some packages are upgraded together, one (haskell-tls) is a dependency of a few others, so it's upgraded first. As I said before, the package is unregistered before the upgrade. This breaks the dependent packages, so --force is used by the .install script and ghc-pkg prints a warning (with "(ignoring)" because of the --force flag). But the new version is then installed and by the end of the pacman transaction, everything should be good. So this ouput doesn't support "still having issues".

Perhaps with a bunch of extra effort the expected (and known to be harmless) messages could be filtered out, but we probably don't want to simply redirect stderr to /dev/null because other issues might go unnoticed.

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#20 2015-12-18 19:04:41

cdown
Member
From: London, England
Registered: 2013-02-09
Posts: 55
Website

Re: [SOLVED] Errors updating haskell-related packages

I had the same problem and just found all of the affected files and removed them, then upgraded. You can do this easily by checking the exit code of `pacman -Qo`:

for file in /usr/share/doc/ghc/html/libraries/doc-index*; do
    pacman -Qo "$file" >/dev/null 2>&1 || sudo rm "$file"
done

After this you should be able to upgrade ghc without filesystem conflicts.

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#21 2015-12-24 15:23:25

xanb
Member
Registered: 2012-07-24
Posts: 414

Re: [SOLVED] Errors updating haskell-related packages

xanb wrote:
Maeda wrote:

OK.

First, I deleted those $%*! .html files.

Then I did the same solution as my previous problem, removing ghc related packages, installing ghc again, and then installing ghc related packages previously removed. Got some warning messages with xmonad package, but `xmonad --recompile` is OK.

\o/

Once again, it's not the way we should do it I think. Why is this happening ? I always use pacman to install/update...

Is there any way to do it automatically? Something like pacman [list packages depending on ghc and uninstall them]

# pacman -Rs pandoc ghc $(pacman -Qq | grep haskell)


Owning one OpenRC (artoo way) and other three systemd machines

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