szpiech
commented
3 months ago Hi,
Does your cluster run MacOS on arm (eg M-series) architecture? Looks like this is trying to link to gsl static libraries compiled for MacOS arm. My guess is it’s a Linux system. I think there should be a makefile for Linux, hopefully called Makefile.lin, which you can run with make -f Makefile.lin.
Let me know if this works,
Zachary
Le mer. 3 juil. 2024 à 16:22, Tania Guerrero @.***> a écrit :
Hi, Thank you so much for this software. I was trying to install with make, but I get the following error: Sorry is very long. I wonder if I have to change something on the makefile but not sure where to begin. I am trying to do this in a cluster, and run the make command while inside a conda environment I specifically created for selscan. Thank you so much!
g++ -O3 -m64 -mmmx -msse -msse2 -o norm norm.o param_t.o ../lib/macos-arm/libgsl.a ../lib/macos-arm/libgslcblas.a /usr/bin/ld: norm.o: in function analyzeIHH12BPWindows(std::cxx11::basic_string<char, std::char_traits
, std::allocator cxx11::basic_string<char, std::char_traits, std::allocator >, int, int, int, int, int)': norm.cpp:(.text+0x6bd6): undefined reference to gsl_sort2' /usr/bin/ld: norm.cpp:(.text+0x6c43): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x6d5f): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text+0x6d77): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x6e02): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x703f): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text+0x7057): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x70e5): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.o: in function analyzeXPEHHBPWindows(std::__cxx11::basic_string<char, std::char_traits>, int, int, int, int, int)': norm.cpp:(.text+0x4947): undefined reference to gsl_sort2' /usr/bin/ld: norm.cpp:(.text+0x49af): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x4acc): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text+0x4ae4): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x4b6f): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x4da4): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text+0x4dbc): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x4e4c): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.o: in function analyzeIHSBPWindows(std:: , std::allocator >, int, int, int, int, int)': norm.cpp:(.text+0x92d9): undefined reference to gsl_sort2' /usr/bin/ld: norm.cpp:(.text+0x92f3): undefined reference to gsl_sort2' /usr/bin/ld: norm.cpp:(.text+0x9376): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9399): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x94fb): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text+0x9513): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x959a): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x97dd): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text+0x97f5): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9881): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9bdc): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text+0x9bf6): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9c6f): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9e8c): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text+0x9ea4): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9f23): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.o: in function main': norm.cpp:(.text.startup+0x20d1): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text.startup+0x2569): undefined reference to gsl_sort' /usr/bin/ld: norm.cpp:(.text.startup+0x29af): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text.startup+0x29cf): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text.startup+0x2ad1): undefined reference to gsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text.startup+0x2af1): undefined reference to gsl_stats_quantile_from_sorted_data' collect2: error: ld returned 1 exit status make: *** [Makefile:51: norm] Error 1 — Reply to this email directly, view it on GitHub https://github.com/szpiech/selscan/issues/118, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQU77GWURCEE5MU3OG3ZKRMORAVCNFSM6AAAAABKKIJ6L2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4DSNBQGM4DGNY . You are receiving this because you are subscribed to this thread.Message ID: @.***>
TaniaPGue
Hi, Thank you so much for this software. I was trying to install with make, but I get the following error: Sorry is very long. I wonder if I have to change something on the makefile but not sure where to begin. I am trying to do this in a cluster, and run the make command while inside a conda environment I specifically created for selscan. Thank you so much!
g++ -O3 -m64 -mmmx -msse -msse2 -o norm norm.o param_t.o ../lib/macos-arm/libgsl.a ../lib/macos-arm/libgslcblas.a /usr/bin/ld: norm.o: in function, std::allocator >, int, int, int, int, int)':
norm.cpp:(.text+0x6bd6): undefined reference to cxx11::basic_string<char, std::char_traits, std::allocator >, int, int, int, int, int)':
norm.cpp:(.text+0x92d9): undefined reference to
analyzeIHH12BPWindows(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int*, int, int, int, int)': norm.cpp:(.text+0x4947): undefined reference togsl_sort2' /usr/bin/ld: norm.cpp:(.text+0x49af): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x4acc): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text+0x4ae4): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x4b6f): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x4da4): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text+0x4dbc): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x4e4c): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.o: in functionanalyzeIHSBPWindows(std::cxx11::basic_string<char, std::char_traitsgsl_sort2' /usr/bin/ld: norm.cpp:(.text+0x6c43): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x6d5f): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text+0x6d77): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x6e02): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x703f): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text+0x7057): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x70e5): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.o: in function `analyzeXPEHHBPWindows(std::gsl_sort2' /usr/bin/ld: norm.cpp:(.text+0x92f3): undefined reference togsl_sort2' /usr/bin/ld: norm.cpp:(.text+0x9376): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9399): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x94fb): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text+0x9513): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x959a): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x97dd): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text+0x97f5): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9881): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9bdc): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text+0x9bf6): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9c6f): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9e8c): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text+0x9ea4): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text+0x9f23): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.o: in functionmain': norm.cpp:(.text.startup+0x20d1): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text.startup+0x2569): undefined reference togsl_sort' /usr/bin/ld: norm.cpp:(.text.startup+0x29af): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text.startup+0x29cf): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text.startup+0x2ad1): undefined reference togsl_stats_quantile_from_sorted_data' /usr/bin/ld: norm.cpp:(.text.startup+0x2af1): undefined reference to `gsl_stats_quantile_from_sorted_data' collect2: error: ld returned 1 exit status make: *** [Makefile:51: norm] Error 1