Debian Bug report logs - #679180
arm* builds fail: SHLIB_LIBADD: No such file or directory

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Luca Falavigna <dktrkranz@debian.org>

To: submit@bugs.debian.org

Subject: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Tue, 26 Jun 2012 23:27:09 +0200 (CEST)

Source: raschsampler
Version: 0.8-5-1
Severity: serious
Justification: fails to build from source


raschsampler fails to build from source on arm*, but built in the past:

fi
* installing *source* package 'RaschSampler' ...
** package 'RaschSampler' successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory `/build/buildd-raschsampler_0.8-5-1-armhf-YQ24R3/raschsampler-0.8-5/src'
gfortran  -fpic -O3 -pipe  -g  -c  RaschSampler.f90 -o RaschSampler.o
gfortran -shared -o RaschSamplerSHLIB_EXT RaschSampler.o SHLIB_LIBADD -L/usr/lib/R/lib -lR
gfortran: error: SHLIB_LIBADD: No such file or directory
make[1]: *** [RaschSamplerSHLIB_EXT] Error 1
make[1]: Leaving directory `/build/buildd-raschsampler_0.8-5-1-armhf-YQ24R3/raschsampler-0.8-5/src'
make[1]: Entering directory `/build/buildd-raschsampler_0.8-5-1-armhf-YQ24R3/raschsampler-0.8-5/src'
make[1]: Leaving directory `/build/buildd-raschsampler_0.8-5-1-armhf-YQ24R3/raschsampler-0.8-5/src'
ERROR: compilation failed for package 'RaschSampler'
* removing '/build/buildd-raschsampler_0.8-5-1-armhf-YQ24R3/raschsampler-0.8-5/debian/r-cran-raschsampler/usr/lib/R/site-library/RaschSampler'
make: *** [R_any_arch] Error 1

https://buildd.debian.org/status/fetch.php?pkg=raschsampler&arch=armel&ver=0.8-5-1&stamp=1338782046
https://buildd.debian.org/status/fetch.php?pkg=raschsampler&arch=armhf&ver=0.8-5-1&stamp=1332118956

Message #10 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Julian Gilbey <julian@d-and-j.net>

To: Luca Falavigna <dktrkranz@debian.org>, 679180@bugs.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Wed, 27 Jun 2012 10:19:26 +0100

On Tue, Jun 26, 2012 at 11:27:09PM +0200, Luca Falavigna wrote:
> Source: raschsampler
> Version: 0.8-5-1
> Severity: serious
> Justification: fails to build from source
> 
> 
> raschsampler fails to build from source on arm*, but built in the past:
> 
> fi
> * installing *source* package 'RaschSampler' ...
> ** package 'RaschSampler' successfully unpacked and MD5 sums checked
> ** libs
> make[1]: Entering directory `/build/buildd-raschsampler_0.8-5-1-armhf-YQ24R3/raschsampler-0.8-5/src'
> gfortran  -fpic -O3 -pipe  -g  -c  RaschSampler.f90 -o RaschSampler.o
> gfortran -shared -o RaschSamplerSHLIB_EXT RaschSampler.o SHLIB_LIBADD -L/usr/lib/R/lib -lR
> gfortran: error: SHLIB_LIBADD: No such file or directory

That is just plain bizarre.  The entire build is performed by running
the command "R CMD INSTALL ...", which just calls R with various
arguments.  If this is happening to this package, it should be
happening to lots of other R packages as well which build libraries.
Are you seeing this problems with other R packages or is it unique to
this one?

   Julian

Message #15 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Luca Falavigna <dktrkranz@debian.org>

To: Julian Gilbey <julian@d-and-j.net>

Cc: 679180@bugs.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Wed, 27 Jun 2012 12:10:29 +0200

2012/6/27 Julian Gilbey <julian@d-and-j.net>:
> Are you seeing this problems with other R packages or is it unique to
> this one?

I noticed there are a lot of this failures, but I have realized that
after I sent this bug.

Message #20 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Julian Gilbey <julian@d-and-j.net>

To: Luca Falavigna <dktrkranz@debian.org>

Cc: 679180@bugs.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Wed, 27 Jun 2012 11:52:40 +0100

On Wed, Jun 27, 2012 at 12:10:29PM +0200, Luca Falavigna wrote:
> 2012/6/27 Julian Gilbey <julian@d-and-j.net>:
> > Are you seeing this problems with other R packages or is it unique to
> > this one?
> 
> I noticed there are a lot of this failures, but I have realized that
> after I sent this bug.

No worries!  It should probably be reassigned to r-base-dev, then.

   Julian

Message #25 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Luca Falavigna <dktrkranz@debian.org>

To: 679180@bugs.debian.org, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sat, 14 Jul 2012 11:28:25 +0200

reassign 679180 r-base-core
retitle 679180 arm* builds fail: SHLIB_LIBADD: No such file or directory
found 679180 2.15.1-1
thanks


I've narrowed the problem to the following snippet in
src/library/tools/R/install.R:
mconf <- readLines(file.path(R.home(),
                             paste0("etc", Sys.getenv("R_ARCH")),
                                     "Makeconf"))
SHLIB_EXT <- sub(".*= ", "", grep("^SHLIB_EXT", mconf, value = TRUE))
SHLIB_LIBADD <- sub(".*= ", "", grep("^SHLIB_LIBADD", mconf, value = TRUE))


This should normally happen:
> mconf <- readLines(file.path(R.home(),
+                              paste0("etc", Sys.getenv("R_ARCH")),
+                                      "Makeconf"))
> SHLIB_EXT <- sub(".*= ", "", grep("^SHLIB_EXT", mconf, value = TRUE))
> SHLIB_LIBADD <- sub(".*= ", "", grep("^SHLIB_LIBADD", mconf, value = TRUE))
> SHLIB_EXT
[1] ".so"
> SHLIB_LIBADD
[1] ""

but on harris.debian.org porterbox I get the following:
> mconf <- readLines(file.path(R.home(),
+                              paste0("etc", Sys.getenv("R_ARCH")),
+                                      "Makeconf"))
> SHLIB_EXT <- sub(".*= ", "", grep("^SHLIB_EXT", mconf, value = TRUE))
> SHLIB_LIBADD <- sub(".*= ", "", grep("^SHLIB_LIBADD", mconf, value = TRUE))
> SHLIB_EXT
[1] "SHLIB_EXT .so"
> SHLIB_LIBADD
[1] "SHLIB_LIBADD "


It seems sub is not behaving good:
> test <- "Hello world = hi"
> sub(".*=", "", test)
[1] "Hello world  hi"
> sub(".* =", "", test)
[1] "Hello hi"

Message #38 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Luca Falavigna <dktrkranz@debian.org>

To: 679180@bugs.debian.org, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sat, 14 Jul 2012 11:48:47 +0200

[Message part 1 (text/plain, inline)]

tags 679180 + patch
thanks


Passing "perl = TRUE" parameter to sub function seems enough to fix the problem:

> mconf <- readLines(file.path(R.home(),
+                              paste0("etc", Sys.getenv("R_ARCH")),
+                                      "Makeconf"))
> SHLIB_EXT <- sub(".*= ", "", grep("^SHLIB_EXT", mconf, value = TRUE), perl = TRUE)
> SHLIB_LIBADD <- sub(".*= ", "", grep("^SHLIB_LIBADD", mconf, value = TRUE), perl = TRUE)
> SHLIB_EXT
[1] ".so"
> SHLIB_LIBADD
[1] ""

I'm attaching a patch, which hopefully should be OK as workaround for this bug.

[679180.patch (application/octet-stream, attachment)]

Message #45 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Dirk Eddelbuettel <edd@debian.org>

To: Luca Falavigna <dktrkranz@debian.org>

Cc: 679180@bugs.debian.org, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sat, 14 Jul 2012 06:58:56 -0500

Luca,

On 14 July 2012 at 11:48, Luca Falavigna wrote:
| tags 679180 + patch
| thanks
| 
| 
| Passing "perl = TRUE" parameter to sub function seems enough to fix the problem:

Thank you __so much__ for digging through this!

R comes with three regexp engines (three, as the count goes: old pre-POSIX,
POSIX [ and both those from libc as I recall] plus pcre).  Obviously the
default is broken and switching to pcre helps.

I am just a little worried that maybe we get a side effect on other
systems. Shall we maybe protect this by an architecture test? What does this
say on these arm* machines?

R> Sys.info()
                                     sysname                                      release                                      version 
                                     "Linux"                           "3.0.0-17-generic" "#30-Ubuntu SMP Thu Mar 8 20:45:39 UTC 2012" 
                                    nodename                                      machine                                        login 
                                       "max"                                     "x86_64"                                    "unknown" 
                                        user                               effective_user 
                                       "edd"                                        "edd" 
R> Sys.info()["machine"]
 machine 
"x86_64" 
 
On the other hand, the use inside the install should be fine ...

Dirk

| > mconf <- readLines(file.path(R.home(),
| +                              paste0("etc", Sys.getenv("R_ARCH")),
| +                                      "Makeconf"))
| > SHLIB_EXT <- sub(".*= ", "", grep("^SHLIB_EXT", mconf, value = TRUE), perl = TRUE)
| > SHLIB_LIBADD <- sub(".*= ", "", grep("^SHLIB_LIBADD", mconf, value = TRUE), perl = TRUE)
| > SHLIB_EXT
| [1] ".so"
| > SHLIB_LIBADD
| [1] ""
| 
| I'm attaching a patch, which hopefully should be OK as workaround for this bug.
| xuntyped binary data, 679180.patch   [Click mouse-2 t3483.633873483.633873483.63387o save to a file]

-- 
Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com  

Message #50 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Luca Falavigna <dktrkranz@debian.org>

To: Dirk Eddelbuettel <edd@debian.org>

Cc: 679180@bugs.debian.org, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sat, 14 Jul 2012 14:14:10 +0200

2012/7/14 Dirk Eddelbuettel <edd@debian.org>:
> I am just a little worried that maybe we get a side effect on other
> systems. Shall we maybe protect this by an architecture test? What does this
> say on these arm* machines?

I think the real cause behind this is a bug in POSIX regexes in
eglibc, I'll try to debug this further. But I agree it could be safer
to limit it to arm* only, as the breakages is limited to those ports
only: http://tinyurl.com/7fac63c

Here is the output for armel (taken from abel.d.o):
> Sys.info()
                          sysname                           release
                          "Linux"                          "2.6.32"
                          version                          nodename
"#1 Fri Jan 20 18:19:54 UTC 2012"                            "abel"
                          machine                             login
                       "armv5tel"                         "unknown"
                             user                    effective_user
                      "dktrkranz"                       "dktrkranz"
> Sys.info()["machine"]
   machine
"armv5tel"

And this is the one for armhf (taken from harris.d.o):
> Sys.info()
                          sysname                           release
                          "Linux"                     "3.2.0-3-mx5"
                          version                          nodename
"#1 Thu Jun 28 11:42:19 UTC 2012"                          "harris"
                          machine                             login
                         "armv7l"                         "unknown"
                             user                    effective_user
                      "dktrkranz"                       "dktrkranz"
> Sys.info()["machine"]
 machine
"armv7l"

I'm not sure if buildds can have different strings for "machine",
though. Perhaps checking for "arm" at the beginning of the string
could be better, pretending the regex works... ;)

Message #55 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Dirk Eddelbuettel <edd@debian.org>

To: Luca Falavigna <dktrkranz@debian.org>

Cc: Dirk Eddelbuettel <edd@debian.org>, 679180@bugs.debian.org, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sat, 14 Jul 2012 08:11:20 -0500

On 14 July 2012 at 14:14, Luca Falavigna wrote:
| 2012/7/14 Dirk Eddelbuettel <edd@debian.org>:
| > I am just a little worried that maybe we get a side effect on other
| > systems. Shall we maybe protect this by an architecture test? What does this
| > say on these arm* machines?
| 
| I think the real cause behind this is a bug in POSIX regexes in
| eglibc, I'll try to debug this further.

Could not agree more. I can help you trace down which library functions are
being called if you need help. 

| But I agree it could be safer
| to limit it to arm* only, as the breakages is limited to those ports
| only: http://tinyurl.com/7fac63c
| 
| Here is the output for armel (taken from abel.d.o):
| > Sys.info()
|                           sysname                           release
|                           "Linux"                          "2.6.32"
|                           version                          nodename
| "#1 Fri Jan 20 18:19:54 UTC 2012"                            "abel"
|                           machine                             login
|                        "armv5tel"                         "unknown"
|                              user                    effective_user
|                       "dktrkranz"                       "dktrkranz"
| > Sys.info()["machine"]
|    machine
| "armv5tel"
| 
| And this is the one for armhf (taken from harris.d.o):
| > Sys.info()
|                           sysname                           release
|                           "Linux"                     "3.2.0-3-mx5"
|                           version                          nodename
| "#1 Thu Jun 28 11:42:19 UTC 2012"                          "harris"
|                           machine                             login
|                          "armv7l"                         "unknown"
|                              user                    effective_user
|                       "dktrkranz"                       "dktrkranz"
| > Sys.info()["machine"]
|  machine
| "armv7l"
| 
| I'm not sure if buildds can have different strings for "machine",
| though. Perhaps checking for "arm" at the beginning of the string
| could be better, pretending the regex works... ;)

Good catch on the regexp :)  

We could try

    R> Sys.info()["machine"] %in% c("armv7l", "armv5tel")
    [1] FALSE

with a test on my side as 
    R> Sys.info()["machine"] %in% c("armv7l", "armv5tel", "x86_64")
    [1] TRUE
    R> 

We could also use substr(..., 1, 3) as in

R> substr( Sys.info()["machine"], 1, 3)
machine 
  "x86" 
R> substr( Sys.info()["machine"], 1, 3) == "arm"
machine 
  FALSE 
R> 

Maybe that last one is best?

Dirk

-- 
Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com  

Message #60 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Luca Falavigna <dktrkranz@debian.org>

To: Dirk Eddelbuettel <edd@debian.org>

Cc: 679180@bugs.debian.org, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sat, 14 Jul 2012 15:30:00 +0200

2012/7/14 Dirk Eddelbuettel <edd@debian.org>:
> We could also use substr(..., 1, 3) as in
> R> substr( Sys.info()["machine"], 1, 3)
> machine
>   "x86"
> R> substr( Sys.info()["machine"], 1, 3) == "arm"
> machine
>   FALSE
> R>

I got this on the failing machine, so at least this simple match is performed:
> substr( Sys.info()["machine"], 1, 3) == "arm"
machine
   TRUE

> Maybe that last one is best?

I think this is preferable, as I'm not sure "armv7l" and "armv5tel"
are the only machine strings we can expect from buildds.

Message #65 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Julien Cristau <jcristau@debian.org>

To: Dirk Eddelbuettel <edd@debian.org>, 679180@bugs.debian.org

Cc: Luca Falavigna <dktrkranz@debian.org>, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sat, 14 Jul 2012 15:48:16 +0200

[Message part 1 (text/plain, inline)]

On Sat, Jul 14, 2012 at 08:11:20 -0500, Dirk Eddelbuettel wrote:

> We could try
> 
>     R> Sys.info()["machine"] %in% c("armv7l", "armv5tel")
>     [1] FALSE
> 
There's more possible values for uname -m, please don't make it too
specific.

Cheers,
Julien

[signature.asc (application/pgp-signature, inline)]

Message #70 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Dirk Eddelbuettel <edd@debian.org>

To: Julien Cristau <jcristau@debian.org>

Cc: Dirk Eddelbuettel <edd@debian.org>, 679180@bugs.debian.org, Luca Falavigna <dktrkranz@debian.org>, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sat, 14 Jul 2012 09:21:35 -0500

On 14 July 2012 at 15:48, Julien Cristau wrote:
| On Sat, Jul 14, 2012 at 08:11:20 -0500, Dirk Eddelbuettel wrote:
| 
| > We could try
| > 
| >     R> Sys.info()["machine"] %in% c("armv7l", "armv5tel")
| >     [1] FALSE
| > 
| There's more possible values for uname -m, please don't make it too
| specific.

All in agreement then -- and I shall prepare a 2.15.1-2 upload with Luca's
__much appreciated__ patch to sub(), conditional on machine being "arm...."
(using the substr test).

Dirk

-- 
Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com  

Message #75 received at 679180-close@bugs.debian.org (full text, mbox, reply):

From: Dirk Eddelbuettel <edd@debian.org>

To: 679180-close@bugs.debian.org

Subject: Bug#679180: fixed in r-base 2.15.1-2

Date: Sat, 14 Jul 2012 15:47:27 +0000

Source: r-base
Source-Version: 2.15.1-2

We believe that the bug you reported is fixed in the latest version of
r-base, 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 679180@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Dirk Eddelbuettel <edd@debian.org> (supplier of updated r-base 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 ftpmaster@debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Sat, 14 Jul 2012 09:44:24 -0500
Source: r-base
Binary: r-base r-base-core r-base-dev r-mathlib r-base-html r-doc-pdf r-doc-html r-doc-info r-recommended r-base-core-dbg
Architecture: source i386 all
Version: 2.15.1-2
Distribution: unstable
Urgency: low
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Changed-By: Dirk Eddelbuettel <edd@debian.org>
Description: 
 r-base     - GNU R statistical computation and graphics system
 r-base-core - GNU R core of statistical computation and graphics system
 r-base-core-dbg - GNU R debug symbols for statistical comp. language and environmen
 r-base-dev - GNU R installation of auxiliary GNU R packages
 r-base-html - GNU R html docs for statistical computing system functions
 r-doc-html - GNU R html manuals for statistical computing system
 r-doc-info - GNU R info manuals statistical computing system
 r-doc-pdf  - GNU R pdf manuals for statistical computing system
 r-mathlib  - GNU R standalone mathematics library
 r-recommended - GNU R collection of recommended packages [metapackage]
Closes: 679180
Changes: 
 r-base (2.15.1-2) unstable; urgency=low
 .
   * src/library/tools/R/install.R: Pass "perl = TRUE" parameter to sub()
     function when defining SHLIB_* macros to work-around an erroneus
     string replacement which causes build failures on arm* architectures
     but make the change conditonal on actually being on arm*.
     With big thanks to Luca Falavigna for finding this fix. (Closes: #679180)
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Message #80 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Dirk Eddelbuettel <edd@debian.org>

To: Dirk Eddelbuettel <edd@debian.org>

Cc: Julien Cristau <jcristau@debian.org>, 679180@bugs.debian.org, Luca Falavigna <dktrkranz@debian.org>, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sun, 15 Jul 2012 07:08:17 -0500

Now that we have a new r-base package (with the arm* fix thanks to Luca),
what is the best way to rebuild the various r-cran-* packages on armel that
need a rebuild?

And does one of you know / have a sql query against a Debian db to find
these?  I can poke around my rendered page at 

   http://qa.debian.org/developer.php?login=edd@debian.org

but that is probably not the most efficient way.

Dirk

-- 
Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com  

Message #85 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Luca Falavigna <dktrkranz@debian.org>

To: Dirk Eddelbuettel <edd@debian.org>

Cc: 679180@bugs.debian.org, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sun, 15 Jul 2012 23:07:31 +0200

[Message part 1 (text/plain, inline)]

reopen 679180
notfixed 679180 2.15.1-2
thanks

Unfortunately, the patch didn't work as expected for two reasons:
* PCRE engine is used when arm* architecture is not found, we wanted
the other way round.
* perl = TRUE option has to be passed to sub() function, not grep() one.

I'm attaching a patch which should work now.
Dirk, could you please check it and upload a new revision?

[679180-2nd.patch (application/octet-stream, attachment)]

Message #94 received at 679180-close@bugs.debian.org (full text, mbox, reply):

From: Dirk Eddelbuettel <edd@debian.org>

To: 679180-close@bugs.debian.org

Subject: Bug#679180: fixed in r-base 2.15.1-3

Date: Sun, 15 Jul 2012 22:17:36 +0000

Source: r-base
Source-Version: 2.15.1-3

We believe that the bug you reported is fixed in the latest version of
r-base, 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 679180@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Dirk Eddelbuettel <edd@debian.org> (supplier of updated r-base 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 ftpmaster@debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Sun, 15 Jul 2012 16:17:25 -0500
Source: r-base
Binary: r-base r-base-core r-base-dev r-mathlib r-base-html r-doc-pdf r-doc-html r-doc-info r-recommended r-base-core-dbg
Architecture: source i386 all
Version: 2.15.1-3
Distribution: unstable
Urgency: low
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Changed-By: Dirk Eddelbuettel <edd@debian.org>
Description: 
 r-base     - GNU R statistical computation and graphics system
 r-base-core - GNU R core of statistical computation and graphics system
 r-base-core-dbg - GNU R debug symbols for statistical comp. language and environmen
 r-base-dev - GNU R installation of auxiliary GNU R packages
 r-base-html - GNU R html docs for statistical computing system functions
 r-doc-html - GNU R html manuals for statistical computing system
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 r-doc-pdf  - GNU R pdf manuals for statistical computing system
 r-mathlib  - GNU R standalone mathematics library
 r-recommended - GNU R collection of recommended packages [metapackage]
Closes: 679180
Changes: 
 r-base (2.15.1-3) unstable; urgency=low
 .
   * src/library/tools/R/install.R: Pass "perl = TRUE" parameter to sub()
     and correcting error in logic of patch used in -2.	(Closes: #679180)
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Message #99 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Luca Falavigna <dktrkranz@debian.org>

To: Dirk Eddelbuettel <edd@debian.org>

Cc: 679180@bugs.debian.org, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Mon, 16 Jul 2012 00:46:22 +0200

[Message part 1 (text/plain, inline)]

reopen 679180
notfixed 679180 2.15.1-3
thanks


Fix provided in 2.15.1-3 is still half-way, as "perl = TRUE" parameter
is passed to grep() function in the second hunk :(

Answering your previous question, I isolated a list of packages to be
given-back, and submitted it to w-b team for processing:
https://lists.debian.org/debian-wb-team/2012/07/msg00061.html

[679180-3.patch (application/octet-stream, attachment)]

Message #108 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Dirk Eddelbuettel <edd@debian.org>

To: Luca Falavigna <dktrkranz@debian.org>

Cc: Dirk Eddelbuettel <edd@debian.org>, 679180@bugs.debian.org, r-base@packages.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Sun, 15 Jul 2012 17:54:40 -0500

On 16 July 2012 at 00:46, Luca Falavigna wrote:
| reopen 679180
| notfixed 679180 2.15.1-3
| thanks
| 
| 
| Fix provided in 2.15.1-3 is still half-way, as "perl = TRUE" parameter
| is passed to grep() function in the second hunk :(

Yeebus. My bad.

-4 will be comming shortly.

Dirk
 
| Answering your previous question, I isolated a list of packages to be
| given-back, and submitted it to w-b team for processing:
| https://lists.debian.org/debian-wb-team/2012/07/msg00061.html
| untyped binary data, 679180-3.patch [Press RETURN to save to a file]

-- 
Dirk Eddelbuettel | edd@debian.org | http://dirk.eddelbuettel.com  

Message #115 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Adam Conrad <adconrad@debian.org>

To: 679180@bugs.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Mon, 16 Jul 2012 20:44:16 +0000

On Mon, Jul 16, 2012 at 08:27:50PM +0000, Adam Conrad wrote:
> PS: (FWIW, the original patch was mine, not Luca's, it seems to have
>     gotten mis/re-attributed along the way...)

Disregard this bit, BTW.  Luca told me on IRC that we arrived at our
shockingly similar workarounds independently.

Anyhow.  More from said IRC discussion, while I was brain-dumping
at Luca:

< infinity> DktrKranz: If you feel like debugging further, I *suspect* 
            the error either lies in the bundled tre (in src/extra/tre), 
            or in the code in R itself that's calling it.
< infinity> DktrKranz: 20 to 1 odds say it's an alignment issue or 
            something.
< infinity> DktrKranz: And, for added fun, the bundled tre is a forked 
            version from upstream tre.  So, it could just be that it was 
            subtly broken in the fork.
< infinity> DktrKranz: It still *could* be eglibc's fault, as we're also 
            calling into eglibc to mangle wchars and such, but if wchar 
            was fundamentally broken in eglibc on ARM, I think I'd have 
            seen a lot more fallout.
< infinity> DktrKranz: So, it's probably either R mis-mangling types or 
            doing dodgy pointer math, or tre doing similar.

Message #120 received at 679180@bugs.debian.org (full text, mbox, reply):

From: Adam Conrad <adconrad@debian.org>

To: 679180@bugs.debian.org

Subject: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory

Date: Mon, 16 Jul 2012 20:27:50 +0000

So, a few things about this bug.  It's almost certainly not a glibc
bug, but rather a bug in the bundled library that gets (ab)used to
handle POSIX extended regexes in non-UTF-8 locales.  The substing
failure doesn't show when either using PCRE and a C locale, or using
any combination of flags in a UTF-8 locale.

Another point worth noting is that it seems completely daft to use
a substring match to detect that you're on an architecture where
substring matching is broken.  My original patch that just forced
PCRE on all arches is sane enough, in that PCRE works well
everywhere and has a sane test suite to make sure that it the case.

That said, the reason I hadn't forwarded my patch to Debian yet was
because it's a hideous workaround and, obviously, the root cause
needs to be hunted down, as this only helps r-base's install routine,
but does nothing for applications that actually call into regex
routines in a C locale.

Anyhow, I think that having arch-specific testing and twiddling there
probably just makes things even less obvious and harder to track and
debug later, but that's just my opinion.  Your call, I suppose.

... Adam

PS: (FWIW, the original patch was mine, not Luca's, it seems to have
    gotten mis/re-attributed along the way...)

Message #125 received at 679180-close@bugs.debian.org (full text, mbox, reply):

From: Dirk Eddelbuettel <edd@debian.org>

To: 679180-close@bugs.debian.org

Subject: Bug#679180: fixed in r-base 2.15.1-4

Date: Thu, 19 Jul 2012 21:48:02 +0000

Source: r-base
Source-Version: 2.15.1-4

We believe that the bug you reported is fixed in the latest version of
r-base, 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 679180@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Dirk Eddelbuettel <edd@debian.org> (supplier of updated r-base 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 ftpmaster@debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Sun, 15 Jul 2012 17:56:35 -0500
Source: r-base
Binary: r-base r-base-core r-base-dev r-mathlib r-base-html r-doc-pdf r-doc-html r-doc-info r-recommended r-base-core-dbg
Architecture: source i386 all
Version: 2.15.1-4
Distribution: unstable
Urgency: low
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Changed-By: Dirk Eddelbuettel <edd@debian.org>
Description: 
 r-base     - GNU R statistical computation and graphics system
 r-base-core - GNU R core of statistical computation and graphics system
 r-base-core-dbg - GNU R debug symbols for statistical comp. language and environmen
 r-base-dev - GNU R installation of auxiliary GNU R packages
 r-base-html - GNU R html docs for statistical computing system functions
 r-doc-html - GNU R html manuals for statistical computing system
 r-doc-info - GNU R info manuals statistical computing system
 r-doc-pdf  - GNU R pdf manuals for statistical computing system
 r-mathlib  - GNU R standalone mathematics library
 r-recommended - GNU R collection of recommended packages [metapackage]
Closes: 679180
Changes: 
 r-base (2.15.1-4) unstable; urgency=low
 .
   * src/library/tools/R/install.R: Pass "perl = TRUE" parameter to sub()
     really passing it to sub and not to grep		(Closes: #679180)
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