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INSTALL report for Rhisat2 on taxco

This page was generated on 2021-01-31 03:53:36 -0500 (Sun, 31 Jan 2021).

These are experimental builds on Apple's new arm64 arch. See here for more information.
To the developers/maintainers of the Rhisat2 package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1493/1938HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhisat2 1.7.0
Charlotte Soneson
Snapshot Date: 2021-01-30 14:40:03 -0500 (Sat, 30 Jan 2021)
URL: https://git.bioconductor.org/packages/Rhisat2
Branch: master
Last Commit: 12dbbf5
Last Changed Date: 2020-10-27 11:41:46 -0500 (Tue, 27 Oct 2020)
taxcomacOS 11.0.1 Big Sur / arm64  ERROR    NA    NA  

Summary

Package: Rhisat2
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhisat2
StartedAt: 2021-01-30 18:17:35 -0500 (Sat, 30 Jan 2021)
EndedAt: 2021-01-30 18:17:54 -0500 (Sat, 30 Jan 2021)
EllapsedTime: 19.1 seconds
RetCode: 1
Status:   ERROR  

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhisat2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library’
* installing *source* package ‘Rhisat2’ ...
** using staged installation
** libs
** arch - 
/usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
	-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \
	 -I third_party \
	-o hisat2-build-s hisat2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
	-lpthread 
In file included from hisat2_build.cpp:35:
In file included from ./gfm.h:61:
In file included from ./processor_support.h:17:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:11:2: error: this header is for x86 only
#error this header is for x86 only
 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:271:5: error: invalid output constraint '=a' in asm
    __cpuid(__leaf, __eax, __ebx, __ecx, __edx);
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:236:11: note: expanded from macro '__cpuid'
        : "=a"(__eax), "=r" (__ebx), "=c"(__ecx), "=d"(__edx) \
          ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:286:5: error: invalid output constraint '=a' in asm
    __cpuid(__leaf, *__eax, *__ebx, *__ecx, *__edx);
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:236:11: note: expanded from macro '__cpuid'
        : "=a"(__eax), "=r" (__ebx), "=c"(__ecx), "=d"(__edx) \
          ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:300:5: error: invalid output constraint '=a' in asm
    __cpuid_count(__leaf, __subleaf, *__eax, *__ebx, *__ecx, *__edx);
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:243:11: note: expanded from macro '__cpuid_count'
        : "=a"(__eax), "=r" (__ebx), "=c"(__ecx), "=d"(__edx) \
          ^
4 errors generated.
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:61:
In file included from ./processor_support.h:17:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:11:2: error: this header is for x86 only
#error this header is for x86 only
 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:271:5: error: invalid output constraint '=a' in asm
    __cpuid(__leaf, __eax, __ebx, __ecx, __edx);
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:236:11: note: expanded from macro '__cpuid'
        : "=a"(__eax), "=r" (__ebx), "=c"(__ecx), "=d"(__edx) \
          ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:286:5: error: invalid output constraint '=a' in asm
    __cpuid(__leaf, *__eax, *__ebx, *__ecx, *__edx);
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:236:11: note: expanded from macro '__cpuid'
        : "=a"(__eax), "=r" (__ebx), "=c"(__ecx), "=d"(__edx) \
          ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:300:5: error: invalid output constraint '=a' in asm
    __cpuid_count(__leaf, __subleaf, *__eax, *__ebx, *__ecx, *__edx);
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:243:11: note: expanded from macro '__cpuid_count'
        : "=a"(__eax), "=r" (__ebx), "=c"(__ecx), "=d"(__edx) \
          ^
4 errors generated.
In file included from gfm.cpp:21:
In file included from ./gfm.h:61:
In file included from ./processor_support.h:17:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:11:2: error: this header is for x86 only
#error this header is for x86 only
 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:271:5: error: invalid output constraint '=a' in asm
    __cpuid(__leaf, __eax, __ebx, __ecx, __edx);
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:236:11: note: expanded from macro '__cpuid'
        : "=a"(__eax), "=r" (__ebx), "=c"(__ecx), "=d"(__edx) \
          ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:286:5: error: invalid output constraint '=a' in asm
    __cpuid(__leaf, *__eax, *__ebx, *__ecx, *__edx);
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:236:11: note: expanded from macro '__cpuid'
        : "=a"(__eax), "=r" (__ebx), "=c"(__ecx), "=d"(__edx) \
          ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:300:5: error: invalid output constraint '=a' in asm
    __cpuid_count(__leaf, __subleaf, *__eax, *__ebx, *__ecx, *__edx);
    ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/12.0.0/include/cpuid.h:243:11: note: expanded from macro '__cpuid_count'
        : "=a"(__eax), "=r" (__ebx), "=c"(__ecx), "=d"(__edx) \
          ^
4 errors generated.
make: *** [hisat2-build-s] Error 1
ERROR: compilation failed for package ‘Rhisat2’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhisat2’