now I'm trying to build sra-tools. 2017-12-04 17:34 GMT+01:00 Gábor Boskovits <boskov...@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 <boskov...@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 <boskov...@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 <boskov...@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 <boskov...@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 <boskov...@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 <boskov...@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 <boskov...@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 <boskov...@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 <boskov...@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 <boskov...@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 <boskov...@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 <cmmarus...@gmail.com >>>>>>>>>>>> >: >>>>>>>>>>>> >>>>>>>>>>>>> Gábor Boskovits <boskov...@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 >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
