hisat2 error: Symbol not found ... libstdc++.6.dylib

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4.0 years ago

axolootle • 0

I have a trouble in running hisat2(2.1.0).

machine: Mac OS 10.15.4 hisat2(2.1.0) was installed via 1) bioconda, 2)docker, 3)binary but all of these suffered from the same error related with libstdc++.6.dylib as below:

% hisat2
dyld: Symbol not found: __ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEED1Ev
Referenced from: /usr/local/bin/../Cellar/hisat2/2.1.0/bin/hisat2-align-s
Expected in: /usr/lib/libstdc++.6.dylib
in /usr/local/bin/../Cellar/hisat2/2.1.0/bin/hisat2-align-s
(ERR): Description of arguments failed!
Exiting now ...

Similar problem was also argued in hisat2 was not worked

They say it can be fixed it by deleting /usr/lib/libstdc++.6.0.9.dylib via Finder (Mac). But I could not remove libstdc++.6.0.9.dylib, even from Finder. Additionally, deleting such a file manually from library is a bit scary to me...

Please help me.

hisat2 libstdc RNA-Seq dylib • 2.1k views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 4.0 years ago by axolootle • 0

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https://stackoverflow.com/questions/23015152/git-command-line-on-mac-os-error-dyld-symbol-not-found-strlcpy-chk

Probably missing XCode, see link.

ADD REPLY • link 4.0 years ago by ATpoint 81k

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