make issue

[klahmers1]

I am attempting to 'make' 1.0.4 and receive this (truncated):

./multikey_qsort.h:490:16: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned long') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion] size_t upto = OFF_MASK)

./btypes.h:25:18: note: expanded from macro 'OFF_MASK'
#define OFF_MASK 0xffffffffffffffff
                 ^~~~~~~~~~~~~~~~~~
In file included from centrifuge_build.cpp:27:
In file included from ./bt2_idx.h:62:
In file included from ./processor_support.h:17:
third_party/cpuid.h:162:3: error: invalid output constraint '=a' in asm
  __cpuid (__ext, __eax, __ebx, __ecx, __edx);
  ^
third_party/cpuid.h:104:7: note: expanded from macro '__cpuid'
           : "=a" (a), "=b" (b), "=c" (c), "=d" (d)     \
             ^
third_party/cpuid.h:185:3: error: invalid output constraint '=a' in asm
  __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx);
  ^
third_party/cpuid.h:104:7: note: expanded from macro '__cpuid'
           : "=a" (a), "=b" (b), "=c" (c), "=d" (d)     \
             ^
In file included from centrifuge_build.cpp:27:
In file included from ./bt2_idx.h:44:
In file included from ./blockwise_sa.h:29:
In file included from ./diff_sample.h:26:
./multikey_qsort.h:348:17: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned long') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion]
        size_t upper = OFF_MASK)

I can't seem to decipher this on stack overflow.  Any suggestions would be appreciated.

[mourisl]

Which gcc version you use and which architecture is your system? Is it ARM?

[klahmers1]

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1

Apple clang version 12.0.5 (clang-1205.0.22.11)

Target: arm64-apple-darwin20.6.0

On Wed, Aug 18, 2021 at 11:57 AM Li Song @.***> wrote:

Which gcc version you use and which architecture is your system? Is it ARM?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DaehwanKimLab/centrifuge/issues/217#issuecomment-901232743, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGBIB327GQV5I5YSR4FPGF3T5PJ7JANCNFSM5CK5J2OQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

-- Kevin K. Lahmers, DVM, PhD, DACVP Associate Professor, Clinical track Associate Laboratory Director, Virginia Tech Animal Laboratory Services (ViTALS) Virginia Maryland College of Veterinary Medicine @.***

[mourisl]

Does the bioconda installation work? https://bioconda.github.io/recipes/centrifuge/README.html

[klahmers1]

No, but I think that is because I am using python 3.8. Could that have been this issue with the source install?

[mourisl]

No. Centrifuge does not rely on python. I think it might be the ARM architecture. Is your apple system using M1 chip?

[klahmers1]

Yes, it is an M1 chip.

This is what I get with conda install centrifuge

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

• centrifuge -> python[version='2.7.|3.5.|3.6.|<3|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=2.7,<2.8.0a0|3.4.']

Your python: python=3.8

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

[klahmers1]

I made a conda env with py3.6 and it installed. Thanks for your help