Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
On Mon, Jul 16, 2012 at 08:27:50PM +, 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. -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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...) -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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=e...@debian.org but that is probably not the most efficient way. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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 Description: Binary data
Processed: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
Processing commands for cont...@bugs.debian.org:
reopen 679180
Bug #679180 {Done: Dirk Eddelbuettel e...@debian.org} [r-base-core] arm*
builds fail: SHLIB_LIBADD: No such file or directory
'reopen' may be inappropriate when a bug has been closed with a version;
all fixed versions will be cleared, and you may need to re-add them.
Bug reopened
No longer marked as fixed in versions r-base/2.15.1-2.
notfixed 679180 2.15.1-2
Bug #679180 [r-base-core] arm* builds fail: SHLIB_LIBADD: No such file or
directory
There is no source info for the package 'r-base-core' at version '2.15.1-2'
with architecture ''
Unable to make a source version for version '2.15.1-2'
Ignoring request to alter fixed versions of bug #679180 to the same values
previously set
thanks
Stopping processing here.
Please contact me if you need assistance.
--
679180: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=679180
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--
To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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 Description: Binary data
Processed: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
Processing commands for cont...@bugs.debian.org:
reopen 679180
Bug #679180 {Done: Dirk Eddelbuettel e...@debian.org} [r-base-core] arm*
builds fail: SHLIB_LIBADD: No such file or directory
'reopen' may be inappropriate when a bug has been closed with a version;
all fixed versions will be cleared, and you may need to re-add them.
Bug reopened
No longer marked as fixed in versions r-base/2.15.1-3.
notfixed 679180 2.15.1-3
Bug #679180 [r-base-core] arm* builds fail: SHLIB_LIBADD: No such file or
directory
There is no source info for the package 'r-base-core' at version '2.15.1-3'
with architecture ''
Unable to make a source version for version '2.15.1-3'
Ignoring request to alter fixed versions of bug #679180 to the same values
previously set
thanks
Stopping processing here.
Please contact me if you need assistance.
--
679180: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=679180
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--
To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org
with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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 | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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 -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Processed: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
Processing commands for cont...@bugs.debian.org: reassign 679180 r-base-core Bug #679180 [src:raschsampler] FTBFS on arm*: SHLIB_LIBADD: No such file or directory Bug reassigned from package 'src:raschsampler' to 'r-base-core'. No longer marked as found in versions raschsampler/0.8-5-1. Ignoring request to alter fixed versions of bug #679180 to the same values previously set retitle 679180 arm* builds fail: SHLIB_LIBADD: No such file or directory Bug #679180 [r-base-core] FTBFS on arm*: SHLIB_LIBADD: No such file or directory Changed Bug title to 'arm* builds fail: SHLIB_LIBADD: No such file or directory' from 'FTBFS on arm*: SHLIB_LIBADD: No such file or directory' found 679180 2.15.1-1 Bug #679180 [r-base-core] arm* builds fail: SHLIB_LIBADD: No such file or directory Marked as found in versions r-base/2.15.1-1. thanks Stopping processing here. Please contact me if you need assistance. -- 679180: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=679180 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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 Description: Binary data
Processed: Re: Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
Processing commands for cont...@bugs.debian.org: tags 679180 + patch Bug #679180 [r-base-core] arm* builds fail: SHLIB_LIBADD: No such file or directory Added tag(s) patch. thanks Stopping processing here. Please contact me if you need assistance. -- 679180: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=679180 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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 machinelogin max x86_64unknown 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 | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
2012/7/14 Dirk Eddelbuettel e...@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. -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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 Description: Digital signature
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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 | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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 -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
2012/6/27 Julian Gilbey jul...@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. -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
On Wed, Jun 27, 2012 at 12:10:29PM +0200, Luca Falavigna wrote: 2012/6/27 Julian Gilbey jul...@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 -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#679180: FTBFS on arm*: SHLIB_LIBADD: No such file or directory
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=raschsamplerarch=armelver=0.8-5-1stamp=1338782046 https://buildd.debian.org/status/fetch.php?pkg=raschsamplerarch=armhfver=0.8-5-1stamp=1332118956 -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
