From kasperdanielhansen at gmail.com  Fri Feb 15 19:32:25 2013
From: kasperdanielhansen at gmail.com (Kasper Daniel Hansen)
Date: Fri, 15 Feb 2013 13:32:25 -0500
Subject: [Rd] Matrix does not build with R trunk since Oct.
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On Fri, Feb 15, 2013 at 1:25 PM, Joshua Ulrich <josh.m.ulrich at gmail.com> wrote:
> On Fri, Feb 15, 2013 at 12:19 PM, Kasper Daniel Hansen
> <kasperdanielhansen at gmail.com> wrote:
>> I build from svn daily and I have not had this problem.  I build in a
>> tree separate from the source tree.
>>
>> I do think Hin-Tak has a point about clearly specifying that this is
>> how you should do it, in the manual (if that has not already
>> happened).  As a casual user, I would expect make clean to clean out
>> any stale files, but perhaps that is not happening.  Anyway, seems
>> more to be a possible documentation problem.
>>
> It's already in the R Installation and Administration Manual:
> http://cran.r-project.org/doc/manuals/R-admin.html#Simple-compilation
>
> See the second-to-last paragraph.  It recommends you do not build in
> the top-level source directory, particularly when you work with a
> version of R from Subversion.

Ok, this certainly recommends doing it in another build tree, so I
think it is quite clearly documented.

Kasper

> Best,
> Josh
>
>> Kasper
>>
>> On Fri, Feb 15, 2013 at 1:08 PM, Simon Urbanek
>> <simon.urbanek at r-project.org> wrote:
>>> On Feb 15, 2013, at 11:36 AM, Hin-Tak Leung wrote:
>>>
>>>> --- On Fri, 15/2/13, Simon Urbanek <simon.urbanek at r-project.org> wrote:
>>>>
>>>>> On Feb 15, 2013, at 9:11 AM, Hin-Tak
>>>>> Leung wrote:
>>>>>
>>>>>> Somebody else had written separately about this before,
>>>>> and so have I a couple of months ago. I assumed this will be
>>>>> fixed before the next R. Since R 3.0 is supposedly only 6
>>>>> weeks away, even if it is fixed now it doesn't leave much
>>>>> room for testing.
>>>>>>
>>>>>> Anyway neither Matrix 1.0-11 (current) nor 1.0-9 (sept
>>>>> 2012) build with current R trunk.  The  last time
>>>>> it did was 1. 0-9 on 3rd october over 4 months ago. So it
>>>>> appears to be due to change inside r trunk in sept or early
>>>>> oct.
>>>>>>
>>>>>
>>>>> No problem here - Matrix 1.0-11 and R-devel build just fine
>>>>> with your flags (tested on Ubuntu 12.10, x86_64).
>>>>>
>>>>> If in doubt, please remove R-devel and checkout a fresh
>>>>> copy. Also FWIW it's a bad practice to build inside the
>>>>> sources - it often causes all sorts of problems when you try
>>>>> to track the sources and stale files are probably what's
>>>>> hitting you.
>>>>>
>>>>> FWIW: This is likely not the problem you're mentioning, but
>>>>> some recent gcc versions break and LTO is also known to
>>>>> cause issues depending on the compiler version, so tread
>>>>> lightly on the cutting edge.
>>>>
>>>>
>>>> Here is a fairly similar post:
>>>> http://r.789695.n4.nabble.com/Build-from-Source-fails-on-Loading-required-package-Matrix-td4640371.html
>>>>
>>>> The eventual "solution" of that thread seems to be building from tar ball, which is quite beside the whole point of building from svn trunk.
>>>>
>>>
>>> And how is that relevant to what I said? Did you follow the advice I sent? If you did and still have an issue, post *exact* details on what you did, what system and tools you are using.
>>>
>>>
>>>> FWIW, it is very unproductive to talk about "bad practice" - in a hand-waving undocumented/unsubstantiated manner
>>>
>>> Building in sources has two problems: a) the content of the source tree can change so subsequent builds can be different from the clean one - you cannot undo that and b) if you update the sources stale files from previous builds can break the build.
>>>
>>> If solving your problems is "unproductive" then I'm not surprised you have them for 4 moths now.
>>>
>>>
>>>> - and options that might or might not work. If "--enable-lto" (or any other options, or build within the dev directory) does not work reliably, it should be either disabled/removed, or documented, or both.
>>>
>>> R cannot test all aspects of a compiler and detect all its bugs. It is *your* responsibility to provide a working compiler - if you are unwilling to do that, R cannot do anything about that.
>>>
>>>
>>>> Anyway, it has not been working for over 4 months.
>>>>
>>>
>>> That is not true, obviously, and I have presented a counter-example. It may not have been working for *you* and it's likely a problem in your setup (given your lack of cooperation there is no way to tell for sure). We cannot prevent user errors. We can try to point people in the right direction, but if they refuse to listen it's on their head.
>>>
>>>
>>>> You have about 6 weeks before this becomes a big problem - "big" as in "wide-spread".
>>>>
>>>
>>> You are yet to show that this is a problem in R at all. You failed to follow the basic instructions in the FAQ.
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>
>>>>> Cheers,
>>>>> Simon
>>>>>
>>>>>
>>>>>>
>>>>>> ----------------
>>>>>> Loading required package: Matrix
>>>>>> Error in namespaceExport(ns, exports) : undefined
>>>>> exports: .M.classEnv
>>>>>> Error : require(Matrix) is not TRUE
>>>>>> ERROR: installing package indices failed
>>>>>> * removing ?/svn-loc/R/library/Matrix?
>>>>>> * restoring previous ?/svn-loc/R/library/Matrix?
>>>>>> make[2]: *** [Matrix.ts] Error 1
>>>>>> make[2]: Leaving directory
>>>>> `/svn-loc/R/src/library/Recommended'
>>>>>> make[1]: *** [recommended-packages] Error 2
>>>>>> make[1]: Leaving directory
>>>>> `/svn-loc/R/src/library/Recommended'
>>>>>> make: *** [stamp-recommended] Error 2
>>>>>> ----------------
>>>>>>
>>>>>> If it matters, here is what r trunk built with:
>>>>>> ./configure --enable-memory-profiling
>>>>> --enable-strict-barrier --enable-byte-compiled-packages
>>>>> --with-valgrind-instrumentation=2 --enable-lto
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-devel at r-project.org
>>>>> mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>>>
>>>>
>>>>
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
> --
> Joshua Ulrich  |  about.me/joshuaulrich
> FOSS Trading  |  www.fosstrading.com
>
> R/Finance 2013: Applied Finance with R  | www.RinFinance.com



[Rd] Matrix does not build with R trunk since Oct.
Kasper Daniel Hansen