Re: java: switch to icedtea-8 as default JDK

["Gábor Boskovits" <boskovits@gmail.com>]

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now I'm trying to build sra-tools.

2017-12-04 17:34 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:

> New branch name is: change-default-icedtea-8-wip
> <https://github.com/Boskovits/guix/tree/change-default-icedtea-8-wip>
> I left the original intact, but that does not have the needed fixes.
>
> Guix refresh shows the following on current core updates:
> Building the following 39 packages would ensure 202 dependent packages are
> rebuilt: sra-tools@2.8.2-1 minced@0.2.0 r-seurat@1.4.0.12-1.fccb77d
> ant@1.10.1 java-htsjdk@1.129 java-osgi-service-jdbc@1.0.0
> java-plexus-interpolation@1.23 java-commons-cli@1.2 f-seq@1.1-1.6ccded3
> java-commons-net@3.6 java-commons-lang@2.6 tuxguitar@1.4 antlr3@3.5.2
> java-commons-daemon@1.0.15 java-jdom@1.1.3 java-commons-beanutils@1.9.3
> java-httpcomponents-httpcore-ab@4.4.6 java-httpcomponents-httpcore-
> nio@4.4.6 java-commons-collections4@4.1 java-jgit@4.7.0.201704051617-r
> java-jmh@1.17.5 java-javax-mail@1.5.6 clojure@1.8.0
> java-osgi-service-resolver@1.0.1 java-osgi-service-packageadmin@1.2.0
> java-osgi-util-tracker@1.5.1 java-osgi-service-cm@1.5.0
> java-httpcomponents-httpmime@4.5.3 java-eclipse-team-core@3.8.0
> java-plexus-container-default@1.7.1 kodi@18.0_alpha-6-f22d62d
> hdf-java@3.3.2 ruby-atoulme-antwrap@0.7.5 plantuml@8048 icedtea-web@1.6.2
> java-guice-servlet@4.1 java-eclipse-jetty-servlet@9.2.22
> java-eclipse-jetty-servlet@9.4.6 axoloti-patcher@1.0.12
>
>
> 2017-12-04 16:44 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>
>> Now that this problem around glibc is resolved, I think I will do some
>> history rewrite, so that these reverts, reverting the revert.... does not
>> show up.
>> I 'm also willing to rename the branch to have wip in the name, as this
>> seems to be standard for longer runnig parts. WDYT?
>>
>> 2017-12-04 15:19 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>>
>>> Ok, so it seems, that the latest glibc update was made to fix the icu4c
>>> thing.
>>> It just broke the locales.
>>> Fix for that has just been pushed, making core-updates usable again.
>>> I pushed to my icedtea branch also.
>>> I'm now building it to see what we have now.
>>>
>>> 2017-12-04 13:59 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>>>
>>>> Upstream corrected the issue in commit 6913ad65e00bb32417ad39c41d292b
>>>> 976171e27e.
>>>>
>>>> It is not yet included in 2.26.
>>>>
>>>> The patch is basically the same as I proposed.
>>>>
>>>> I think we should get the upstream version.
>>>>
>>>> 2017-12-04 13:33 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>>>>
>>>>> I think it should look like this:
>>>>>
>>>>> --- cdefs.h 2017-12-04 13:27:55.640000000 +0100
>>>>> +++ cdefs.new.h 2017-12-04 13:31:53.820000000 +0100
>>>>> @@ -1,4 +1,4 @@
>>>>> -/* Copyright (C) 1992-2017 Free Software Foundation, Inc.
>>>>> +y/* Copyright (C) 1992-2017 Free Software Foundation, Inc.
>>>>>     This file is part of the GNU C Library.
>>>>>
>>>>>     The GNU C Library is free software; you can redistribute it and/or
>>>>> @@ -471,10 +471,10 @@
>>>>>     testing __STDC_VERSION__ for generic selection support.
>>>>>     On the other hand, Clang also defines __GNUC__, so a clang-specific
>>>>>     check is required to enable the use of generic selection.  */
>>>>> -#if __GNUC_PREREQ (4, 9) \
>>>>> +#if !defined __cplusplus && (__GNUC_PREREQ (4, 9)   \
>>>>>      || __glibc_clang_has_extension (c_generic_selections) \
>>>>>      || (!defined __GNUC__ && defined __STDC_VERSION__ \
>>>>> - && __STDC_VERSION__ >= 201112L)
>>>>> + && __STDC_VERSION__ >= 201112L))
>>>>>  # define __HAVE_GENERIC_SELECTION 1
>>>>>  #else
>>>>>  # define __HAVE_GENERIC_SELECTION 0
>>>>>
>>>>>
>>>>> 2017-12-04 13:21 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>>>>>
>>>>>> We also have this in bits/floatn.h, but this seems right.
>>>>>>
>>>>>> #if (defined __x86_64__
>>>>>>    \
>>>>>>      ? __GNUC_PREREQ (4, 3)
>>>>>>    \
>>>>>>      : (defined __GNU__ ? __GNUC_PREREQ (4, 5) : __GNUC_PREREQ (4,
>>>>>> 4)))
>>>>>> # define __HAVE_FLOAT128 1
>>>>>> #else
>>>>>> # define __HAVE_FLOAT128 0
>>>>>> #endif
>>>>>>
>>>>>> /* Defined to 1 if __HAVE_FLOAT128 is 1 and the type is ABI-distinct
>>>>>>
>>>>>>
>>>>>>    from the default float, double and long double types in this
>>>>>> glibc.  */
>>>>>> #if __HAVE_FLOAT128
>>>>>> # define __HAVE_DISTINCT_FLOAT128 1
>>>>>> #else
>>>>>> # define __HAVE_DISTINCT_FLOAT128 0
>>>>>> #endif
>>>>>>
>>>>>> I think the problem is caused by HAVE_GENERIC_SELECTION defined when
>>>>>> we are in C++.
>>>>>>
>>>>>>
>>>>>> 2017-12-04 13:18 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>>>>>>
>>>>>>> We have this in cdefs.h:
>>>>>>> #if __GNUC_PREREQ (4, 9) \
>>>>>>>     || __glibc_clang_has_extension (c_generic_selections) \
>>>>>>>     || (!defined __GNUC__ && defined __STDC_VERSION__ \
>>>>>>>         && __STDC_VERSION__ >= 201112L)
>>>>>>> # define __HAVE_GENERIC_SELECTION 1
>>>>>>> #else
>>>>>>> # define __HAVE_GENERIC_SELECTION 0
>>>>>>> #endif
>>>>>>>
>>>>>>> This does not seem right.
>>>>>>>
>>>>>>> We should not have this defined when compiling c++.
>>>>>>> WDYT?
>>>>>>>
>>>>>>> 2017-12-04 13:03 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>>>>>>>
>>>>>>>> This minimal file reproduces the problem in icu4c 60.1 in guix
>>>>>>>> environment icu4c on current core-updates.
>>>>>>>>
>>>>>>>> #include <cmath>
>>>>>>>>
>>>>>>>> int main(int argc, char **argv)
>>>>>>>> {
>>>>>>>>   std::signbit(1);
>>>>>>>>   return 0;
>>>>>>>> }
>>>>>>>>
>>>>>>>> It seems, that it is some problem with cmath.h
>>>>>>>>
>>>>>>>> /gnu/store/2wzijwwgpcdb1msmn3wgq9zmrbrkpx2h-gcc-5.5.0/includ
>>>>>>>> e/c++/cmath:44:0
>>>>>>>>
>>>>>>>> The definition is in glibc 2.26 math.h, looks like this:
>>>>>>>>
>>>>>>>> #elif __HAVE_DISTINCT_FLOAT128
>>>>>>>> # if __HAVE_GENERIC_SELECTION
>>>>>>>> #  define __MATH_TG(TG_ARG, FUNC, ARGS)         \
>>>>>>>>      _Generic ((TG_ARG),                        \
>>>>>>>>        float: FUNC ## f ARGS,           \
>>>>>>>>                default: FUNC ARGS,              \
>>>>>>>>                long double: FUNC ## l ARGS,     \
>>>>>>>>                _Float128: FUNC ## f128 ARGS)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 2017-12-03 23:25 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>>>>>>>>
>>>>>>>>> It seems, that the fix is already included in the 60.1 release for
>>>>>>>>> the xlocal problem. I think we can ignore that.
>>>>>>>>>
>>>>>>>>> 2017-12-03 23:20 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>>>>>>>>>
>>>>>>>>>> It seems, that they issued that already:
>>>>>>>>>> http://bugs.icu-project.org/trac/changeset/40603
>>>>>>>>>>
>>>>>>>>>> 2017-12-03 23:08 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>:
>>>>>>>>>>
>>>>>>>>>>> Ok, I found this one:
>>>>>>>>>>> https://sourceware.org/glibc/wiki/Release/2.26#Removal_of_.2
>>>>>>>>>>> 7xlocale.h.27
>>>>>>>>>>>
>>>>>>>>>>> It seems, that xlocale.h should not be used as an include, and
>>>>>>>>>>> glibc removed that.
>>>>>>>>>>>
>>>>>>>>>>> So this is ok.
>>>>>>>>>>>
>>>>>>>>>>> The question is if this issue was addressed by icu4c, so we can
>>>>>>>>>>> just go to the next step, or should we do something about this.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> 2017-12-03 23:04 GMT+01:00 Gábor Boskovits <boskovits@gmail.com>
>>>>>>>>>>> :
>>>>>>>>>>>
>>>>>>>>>>>> I've found that simply reverting the update to icu4c 60 commit
>>>>>>>>>>>> brings up the issue you just mentioned, with missing xlocale.h.
>>>>>>>>>>>> So it seems, that the one you found introduced the xlocale
>>>>>>>>>>>> problem, while 4e080fbb0bb73e4444181599676f4e1ef5fdc2ba
>>>>>>>>>>>> introduces the new error.
>>>>>>>>>>>> I think we should deal with the one you find first, the see
>>>>>>>>>>>> what's with this newer one.
>>>>>>>>>>>>
>>>>>>>>>>>> We also have a long running discussion on a bug introduced by a
>>>>>>>>>>>> later glibc update, ee3ebf1a357bd4eb36a2fa1790a7b549cffb305a
>>>>>>>>>>>> which broke a lot of packages. Might these be somehow related?
>>>>>>>>>>>> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=29537
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 2017-12-03 22:46 GMT+01:00 Chris Marusich <cmmarusich@gmail.com
>>>>>>>>>>>> >:
>>>>>>>>>>>>
>>>>>>>>>>>>> Gábor Boskovits <boskovits@gmail.com> writes:
>>>>>>>>>>>>>
>>>>>>>>>>>>> > Any news on this icu4c thing?
>>>>>>>>>>>>>
>>>>>>>>>>>>> After about 2 days of running git bisect, my computer has
>>>>>>>>>>>>> informed me
>>>>>>>>>>>>> that the first bad commit is 67d527e35e367c9e9e89ec01cda2ce
>>>>>>>>>>>>> 32cabd2d89.
>>>>>>>>>>>>> This is the first commit where icu4c fails to build on
>>>>>>>>>>>>> core-updates.
>>>>>>>>>>>>> The build failure at this commit is as follows:
>>>>>>>>>>>>>
>>>>>>>>>>>>> --8<---------------cut here---------------start------
>>>>>>>>>>>>> ------->8---
>>>>>>>>>>>>>    g++   ...  decimfmt.cpp
>>>>>>>>>>>>>    g++   ...  decimalformatpattern.cpp
>>>>>>>>>>>>>    g++   ...  dcfmtsym.cpp
>>>>>>>>>>>>>    g++   ...  digitlst.cpp
>>>>>>>>>>>>>    g++   ...  fmtable_cnv.cpp
>>>>>>>>>>>>> digitlst.cpp:67:24: fatal error: xlocale.h: No such file or
>>>>>>>>>>>>> directory
>>>>>>>>>>>>> compilation terminated.
>>>>>>>>>>>>> *** Failed compilation command follows:
>>>>>>>>>>>>> ----------------------------------------------------------
>>>>>>>>>>>>> g++ -D_REENTRANT -DU_HAVE_ELF_H=1 -DU_HAVE_ATOMIC=1
>>>>>>>>>>>>> -DU_HAVE_STRTOD_L=1 -I. -I../common -DU_ATTRIBUTE_DEPRECATED=
>>>>>>>>>>>>> -DU_I18N_IMPLEMENTATION -O2 -W -Wall -pedantic -Wpointer-arith
>>>>>>>>>>>>> -Wwrite-strings -Wno-long-long --std=c++0x -c -DPIC -fPIC -o digitlst.o
>>>>>>>>>>>>> digitlst.cpp
>>>>>>>>>>>>> --- ( rebuild with "make VERBOSE=1 all" to show all parameters
>>>>>>>>>>>>> ) --------
>>>>>>>>>>>>> make[1]: *** [../config/mh-linux:51: digitlst.o] Error 1
>>>>>>>>>>>>> make[1]: *** Waiting for unfinished jobs....
>>>>>>>>>>>>> make[1]: Leaving directory '/tmp/guix-build-icu4c-58.2.dr
>>>>>>>>>>>>> v-0/icu/source/i18n'
>>>>>>>>>>>>> make: *** [Makefile:143: all-recursive] Error 2
>>>>>>>>>>>>> phase `build' failed after 59.0 seconds
>>>>>>>>>>>>> builder for `/gnu/store/mdd6glhc0dg65y4wd11y0b7sbky9cwv6-icu4c-58.2.drv'
>>>>>>>>>>>>> failed with exit code 1
>>>>>>>>>>>>> @ build-failed /gnu/store/mdd6glhc0dg65y4wd11y0b7sbky9cwv6-icu4c-58.2.drv
>>>>>>>>>>>>> - 1 builder for `/gnu/store/mdd6glhc0dg65y4wd11y0b7sbky9cwv6-icu4c-58.2.drv'
>>>>>>>>>>>>> failed with exit code 1
>>>>>>>>>>>>> guix build: error: build failed: build of
>>>>>>>>>>>>> `/gnu/store/mdd6glhc0dg65y4wd11y0b7sbky9cwv6-icu4c-58.2.drv'
>>>>>>>>>>>>> failed
>>>>>>>>>>>>> --8<---------------cut here---------------end--------
>>>>>>>>>>>>> ------->8---
>>>>>>>>>>>>>
>>>>>>>>>>>>> Note that this is NOT the same error as the one that occurs at
>>>>>>>>>>>>> commit
>>>>>>>>>>>>> d6adba786cf2ab1b26ff083928b64262281ff106 (which is the commit
>>>>>>>>>>>>> on
>>>>>>>>>>>>> core-updates from which Gábor's branch
>>>>>>>>>>>>> change-default-icedtea-8 branch
>>>>>>>>>>>>> begins).  That error is:
>>>>>>>>>>>>>
>>>>>>>>>>>>> --8<---------------cut here---------------start------
>>>>>>>>>>>>> ------->8---
>>>>>>>>>>>>>    g++   ...  number_decimalquantity.cpp
>>>>>>>>>>>>>    g++   ...  number_decimfmtprops.cpp
>>>>>>>>>>>>> number_decimalquantity.cpp: In member function
>>>>>>>>>>>>> ‘icu_60::number::impl::DecimalQuantity&
>>>>>>>>>>>>> icu_60::number::impl::DecimalQuantity::setToDouble(double)’:
>>>>>>>>>>>>> number_decimalquantity.cpp:333:9: error: ‘_Generic’ is not a
>>>>>>>>>>>>> member of ‘std’
>>>>>>>>>>>>>      if (std::signbit(n) != 0) {
>>>>>>>>>>>>>          ^
>>>>>>>>>>>>> In file included from /gnu/store/nz2m4gdvgzcrkqa4xwv
>>>>>>>>>>>>> 360iskh7syj7i-gcc-5.5.0/include/c++/cmath:44:0,
>>>>>>>>>>>>>                  from number_decimalquantity.cpp:9:
>>>>>>>>>>>>> number_decimalquantity.cpp:333:14: error: expected
>>>>>>>>>>>>> primary-expression before ‘float’
>>>>>>>>>>>>>      if (std::signbit(n) != 0) {
>>>>>>>>>>>>>               ^
>>>>>>>>>>>>> number_decimalquantity.cpp:333:14: error: expected
>>>>>>>>>>>>> primary-expression before ‘default’
>>>>>>>>>>>>>      if (std::signbit(n) != 0) {
>>>>>>>>>>>>>               ^
>>>>>>>>>>>>> number_decimalquantity.cpp:333:14: error: expected
>>>>>>>>>>>>> primary-expression before ‘long’
>>>>>>>>>>>>>      if (std::signbit(n) != 0) {
>>>>>>>>>>>>>               ^
>>>>>>>>>>>>> number_decimalquantity.cpp:333:14: error: expected
>>>>>>>>>>>>> primary-expression before ‘:’ token
>>>>>>>>>>>>>      if (std::signbit(n) != 0) {
>>>>>>>>>>>>>               ^
>>>>>>>>>>>>> number_decimalquantity.cpp:337:9: error: ‘__builtin_isnan’ is
>>>>>>>>>>>>> not a member of ‘std’
>>>>>>>>>>>>>      if (std::isnan(n) != 0) {
>>>>>>>>>>>>>          ^
>>>>>>>>>>>>> number_decimalquantity.cpp:337:9: note: suggested alternative:
>>>>>>>>>>>>> <built-in>: note:   ‘__builtin_isnan’
>>>>>>>>>>>>> number_decimalquantity.cpp:339:16: error:
>>>>>>>>>>>>> ‘__builtin_isfinite’ is not a member of ‘std’
>>>>>>>>>>>>>      } else if (std::isfinite(n) == 0) {
>>>>>>>>>>>>>                 ^
>>>>>>>>>>>>> number_decimalquantity.cpp:339:16: note: suggested
>>>>>>>>>>>>> alternative:
>>>>>>>>>>>>> <built-in>: note:   ‘__builtin_isfinite’
>>>>>>>>>>>>> *** Failed compilation command follows:
>>>>>>>>>>>>> ----------------------------------------------------------
>>>>>>>>>>>>> g++ -D_REENTRANT -DU_HAVE_ELF_H=1 -DU_HAVE_ATOMIC=1
>>>>>>>>>>>>> -DU_HAVE_STRTOD_L=1 -DU_HAVE_XLOCALE_H=0 -I. -I../common
>>>>>>>>>>>>> -DU_ATTRIBUTE_DEPRECATED= -DU_I18N_IMPLEMENTATION -O2 -W -Wall -pedantic
>>>>>>>>>>>>> -Wpointer-arith -Wwrite-strings -Wno-long-long -std=c++11 -c -DPIC -fPIC -o
>>>>>>>>>>>>> number_decimalquantity.o number_decimalquantity.cpp
>>>>>>>>>>>>> --- ( rebuild with "make VERBOSE=1 all" to show all parameters
>>>>>>>>>>>>> ) --------
>>>>>>>>>>>>> make[1]: *** [../config/mh-linux:51: number_decimalquantity.o]
>>>>>>>>>>>>> Error 1
>>>>>>>>>>>>> make[1]: *** Waiting for unfinished jobs....
>>>>>>>>>>>>> make[1]: Leaving directory '/tmp/guix-build-icu4c-60.1.dr
>>>>>>>>>>>>> v-0/icu/source/i18n'
>>>>>>>>>>>>> make: *** [Makefile:149: all-recursive] Error 2
>>>>>>>>>>>>> phase `build' failed after 122.2 seconds
>>>>>>>>>>>>> builder for `/gnu/store/8s6q5cll4knh7y0wfrbjqs2dai0x4sm2-icu4c-60.1.drv'
>>>>>>>>>>>>> failed with exit code 1
>>>>>>>>>>>>> @ build-failed /gnu/store/8s6q5cll4knh7y0wfrbjqs2dai0x4sm2-icu4c-60.1.drv
>>>>>>>>>>>>> - 1 builder for `/gnu/store/8s6q5cll4knh7y0wfrbjqs2dai0x4sm2-icu4c-60.1.drv'
>>>>>>>>>>>>> failed with exit code 1
>>>>>>>>>>>>> guix build: error: build failed: build of
>>>>>>>>>>>>> `/gnu/store/8s6q5cll4knh7y0wfrbjqs2dai0x4sm2-icu4c-60.1.drv'
>>>>>>>>>>>>> failed
>>>>>>>>>>>>> --8<---------------cut here---------------end--------
>>>>>>>>>>>>> ------->8---
>>>>>>>>>>>>>
>>>>>>>>>>>>> The fact that these errors are different suggests that more
>>>>>>>>>>>>> than one
>>>>>>>>>>>>> problem may have been introduced...
>>>>>>>>>>>>>
>>>>>>>>>>>>> I haven't tried any more recent commits on core-updates.  I am
>>>>>>>>>>>>> not sure
>>>>>>>>>>>>> what the best way is to debug this, so I would appreciate any
>>>>>>>>>>>>> advice
>>>>>>>>>>>>> anyone has.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I hope that information helps.  Hopefully, together, we can
>>>>>>>>>>>>> untangle
>>>>>>>>>>>>> this!
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Chris
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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