Make's error compiling under Linux

[gdauria]

Dear Sr./Mrs,
First of all I would like to thank you so much for the efforts in this project.
I am trying to install it in my Linux
Description: Ubuntu 22.04.3 LTS Release: 22.04 Codename: jammy
I was following the install procedure changing the compilers as described in the Install section. I
mostly I did this for the three lines so the first commented compiler comes in use.

cd src
sed -i "s/= clang #/= /g" Makefile*

Thus, the make all was working until I get this error:

make all
cd src && make -f Makefile_buildMC
make[1]: se entra en el directorio '/MyFolder/GitLab/speciateIT/src'
clang  -c -g -Wall -D__SIM_SSE3 -msse3 -O2 -D_GNU_SOURCE -dynamic -fomit-frame-pointer -funroll-loops -D__AVX -pedantic -Wunused -Wunused-variable -Wunused-value -Wunused-function -Wunused-label -Wredundant-decls -Wreturn-type  -Isrc -o .build/buildMC.o ./buildMC.cc
./buildMC.cc:30:10: fatal error: 'string' file not found
#include <string>
         ^~~~~~~~
1 error generated.
make[1]: *** [Makefile_buildMC:83: .build/buildMC.o] Error 1
make[1]: se sale del directorio '/MyFolder/GitLab/speciateIT/src'
make: *** [Makefile:34: src-make_default] Error 2

I saw also the line saying that: "You may also need to modify LDFLAGS." but I really do not know what I have to do, I am sorry but I am not a programmer.

Thank you in advance for your help.
best regards

Giuseppe

[ravel-lab]

Thanks for your comment. There is no need to cd into src/ and make all Makefiles. Instead, stay in parent directory and perform make -f Makefile. This should compile what you need for classification.

[gdauria]

Hi, thank you for your answer, I think I already did it.
I cleaned and restarted the make -f Makefile from the parent folder. After a while and a lot of compiling messages, I had this error:

g++ .build/buildMC.o .build/IOCUtilities.o .build/IOCppUtilities.o .build/MarkovChains.o .build/CUtilities.o .build/CppUtilities.o .build/strings.o .build/CStatUtilities.o .build/CppStatUtilities.o .build/StatUtilities.o .build/DNAsequence.o .build/Newick.o  -std=c++11 -lc++abi -lstdc++ -o ../bin/buildMC
/usr/bin/ld: no se puede encontrar -lc++abi: No existe el archivo o el directorio
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile_buildMC:80: buildMC] Error 1
make[1]: se sale del directorio '/MyFolder/GitLab/speciateIT/src'
make: *** [Makefile:34: src-make_default] Error 2

Anyway I have the classify executable into the bin folder. Still it does not work, saying that (translated):

bash: /MyFolder/GitLab/speciateIT/bin/classify: can not execute the binary file: Incorrect executable format

I am sorry to bother you again but any help is welcome.

[elscalzarotodoc]

Hi @gdauria, I encountered the same error.
I tried to install the libc++abi-dev library through apt and I was able to correctly compile classify.
I hope it will solve even your problem.