Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

make STAR error and unable to install gcc using homebrew #2124

Open
mahek3012 opened this issue Apr 25, 2024 · 0 comments
Open

make STAR error and unable to install gcc using homebrew #2124

mahek3012 opened this issue Apr 25, 2024 · 0 comments

Comments

@mahek3012
Copy link

So I'm analysing RNA-seq data of data available from NCBI and I'm very novice in this area. Im using Mac M1-arm 64 architecture. I have prepare pipeline for preprocessing of this dataset which contains 30 samples using SNAKEMAKE. I'm stuck in aligning the reads.

  1. Firstly I used bwa-mem for alignment, the rule was working but it was taking a lot of time. and when I went back to literature, I saw STAR is the best aligner tool for human genome.
  2. So, I used Miniconda and tried to install star. but it says there is no STAR package available. so I installed to my working directory and was trying to make STAR. but it threw this error:

(star) mahek@ snakemake-data % cd STAR-2.7.11b/source
(star) mahek@. source % make STAR-2.7.11b
date: illegal option -- -
usage: date [-jnRu] [-I[date|hours|minutes|seconds]] [-f input_fmt]
[-r filename|seconds] [-v[+|-]val[y|m|w|d|H|M|S]]
[[[[mm]dd]HH]MM[[cc]yy][.SS] | new_date] [+output_fmt]
make: *** No rule to make target `STAR-2.7.11b'. Stop.
(star) mahek@ source % make STAR
date: illegal option -- -
usage: date [-jnRu] [-I[date|hours|minutes|seconds]] [-f input_fmt]
[-r filename|seconds] [-v[+|-]val[y|m|w|d|H|M|S]]
[[[[mm]dd]HH]MM[[cc]yy][.SS] | new_date] [+output_fmt]
c++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=" :/Users/mahek/snakemake-data/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra systemFunctions.cpp
clang: error: unsupported option '-fopenmp'
make: *** [systemFunctions.o] Error 1

Then I tried to download homebrew without sudo. and tried to follow the steps from the manual that I need gcc to install. but it threw me this error:
./configure --prefix=/Users/mahek/snakemake-data/STAR-2.7.11b/source/homebr
==> make
Last 15 lines from /Users/mahek/Library/Logs/Homebrew/gcc/02.make:
In file included from ../../gcc/system.h:233:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/vector:321:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/locale:202:
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__locale:813:5: error: expected expression
return std::use_facet<ctype<_CharT> >(__loc).is(ctype_base::cntrl, __c);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[3]: *** [cp/module.o] Error 1
rm gcc.pod
make[2]: *** [all-stage1-gcc] Error 2
make[1]: *** [stage1-bubble] Error 2
make: *** [all] Error 2

Do not report this issue to Homebrew/brew or Homebrew/homebrew-core!

These open issues may also help:
gcc: error in catching C++ exceptions Homebrew/homebrew-core#162714
Do not report this issue: you are running in an unsupported configuration.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant