I'm a totally fresh man in bioinformatics and this is my first time to ask for help in english language web. When I tried to install 'BioPerl' in my MacBookPro BigSur 11.5.2, something strange happened.
Firstly, when doing cpan install BioPerl, it failed and told to me that
one dependency not OK (Graph::Directed); additionally test harness failed
Secondly, I tried to install Graph::Directed, and ...
Result: FAIL
Failed 63/84 test programs. 11/740 subtests failed.
make: *** [test_dynamic] Error 255
ETJ/Graph-0.9724.tar.gz
one dependency not OK (Set::Object); additionally test harness failed
/usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports ETJ/Graph-0.9724.tar.gz
Thirdly, I installed Set::Object, this failed again...
cc -c -g -pipe -fno-strict-aliasing -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -Os -DVERSION=\"1.41\" -DXS_VERSION=\"1.41\" -iwithsysroot "/System/Library/Perl/5.30/darwin-thread-multi-2level/CORE" Object.c
Object.xs:5:10: fatal error: 'EXTERN.h' file not found
#include "EXTERN.h"
^~~~~~~~~~
1 error generated.
make: *** [Object.o] Error 1
RURBAN/Set-Object-1.41.tar.gz
/usr/bin/make -- NOT OK
After that, I find some answers ("Fatal error: 'EXTERN.h' file not found" while installing Perl modules1) but not work, my perl is 5.30.2 (result of 'perl -v' in terminal) while '/Library/Developer/CommandLineTools/SDKs' just including 'MacOSX10.14.sdk' and 'MacOSX10.15.sdk' (no 'MacOSX11sdk') and when I use
find /Library/Developer/CommandLineTools -name EXTERN.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/EXTERN.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Perl/5.28/darwin-thread-multi-2level/CORE/EXTERN.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/EXTERN.h
Versions in my Mac maybe in chaos? so I have no idea to solve this question now. That is very upsetting to a new man but I will never give up...
After the failure of all the above, I look for perl 5.30.2 file, and it is in "usr/perl" and "sys/lib", compared with which i "find"(sys/lib/developer/), the "CORE" file is empty and cannot be edited (I want to copy the absent file from 5.28 but failed and does not work). That is the results to those errors. While, I cannot fix it...