Error in make command #6
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Could you supply me with the full output of the compilation process;
make clean;make HTSSRC=../htslib/
Den ons. 25. jan. 2023 kl. 10.34 skrev MinLuke ***@***.***>:
… Goodmorning,
After installing htslib as indicated I downloaded the metaDM.cpp.git , I
entered in the folder and execute make HTSSRC = ../htslib/
But I get the following error message and I do not understand why, could
you please help me understanding what to do?
thank you
Crypto library is available to link; adding -lcrypto to LIBS HTSSRC not
defined, assuming systemwide installation -lhts g++ -c -O3 -std=c++11
ngsLCA.cpp ngsLCA.cpp:4:56: fatal error: htslib/hts.h: File o directory non
esistente #include <htslib/hts.h> // for htsFormat, seq_nt16_str ^
compilation terminated.
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Yes of course
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ok, complains that eigen hasnt been installed.
If you are on ubuntu the dependencies can be installed with.
sudo apt install libgsl-dev libeigen3-dev
Den ons. 25. jan. 2023 kl. 11.31 skrev MinLuke ***@***.***>:
… Yes of course
make clean;make HTSSRC=../htslib/ Crypto library is available to link;
adding -lcrypto to LIBS HTSSRC not defined, assuming systemwide
installation -lhts rm -rf metaDMG-cpp *.o *.d version.h test/output Crypto
library is available to link; adding -lcrypto to LIBS HTSSRC defined echo
'#define METADAMAGE_VERSION "0.2-46-gedaf069-dirty"' > version.h g++ -c -O3
-std=c++11 -I/home/minluk/script/metaDMG-core/htslib ngsLCA.cpp ngsLCA.cpp:
In function ‘char2int setlevels(int, char*, int&)’: ngsLCA.cpp:64:51:
warning: deprecated conversion from string constant to ‘std::map<char*,
int, cmp_str>::key_type {aka char*}’ [-Wwrite-strings] char2int::iterator
it = c2i.find("species"); ^ g++ -MM -O3 -std=c++11
-I/home/minluk/script/metaDMG-core/htslib ngsLCA.cpp >ngsLCA.d g++ -c -O3
-std=c++11 -I/home/minluk/script/metaDMG-core/htslib ngsLCA_cli.cpp g++ -MM
-O3 -std=c++11 -I/home/minluk/script/metaDMG-core/htslib ngsLCA_cli.cpp
>ngsLCA_cli.d g++ -c -O3 -std=c++11
-I/home/minluk/script/metaDMG-core/htslib main_pmd.cpp g++ -MM -O3
-std=c++11 -I/home/minluk/script/metaDMG-core/htslib main_pmd.cpp
>main_pmd.d g++ -c -O3 -std=c++11 -I/home/minluk/script/metaDMG-core/htslib
profile.cpp g++ -MM -O3 -std=c++11
-I/home/minluk/script/metaDMG-core/htslib profile.cpp >profile.d g++ -c -O3
-std=c++11 -I/home/minluk/script/metaDMG-core/htslib metaDMG.cpp In file
included from metaDMG.cpp:20:0: regression.h:5:29: fatal error:
eigen3/Eigen/Core: File or directory not exist #include <eigen3/Eigen/Core>
^ compilation terminated. make: *** [metaDMG.o] Error 1
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Alternatively you can install the dependencies using conda/mamba: installation of metaDMG-cpp, by making environment with dependenciesmamba create -n metaDMG-cpp python=3.9 eigen htslib cxx-compiler gsl next activate the conda environmentconda activate metaDMG-cpp install metaDMG-cppgit clone https://github.com/metaDMG-dev/metaDMG-cpp.git Now finally install metaDMG-corepip install metaDMG[all] |
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thanks, is it possible to perform the installation of eigen if im not an administrator? |
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Using mamba command line I get |
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Ok now better but I am getting another error |
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Which system are you trying to install it on.?
It seems your htslib didn’t install probably. Also when you are sending these errors it would be helpful to see the commands too.
From: MinLuke ***@***.***>
Reply to: metaDMG-dev/metaDMG-cpp ***@***.***>
Date: Wednesday, 25 January 2023 at 14.34
To: metaDMG-dev/metaDMG-cpp ***@***.***>
Cc: Mikkel Winther Pedersen ***@***.***>, Comment ***@***.***>
Subject: Re: [metaDMG-dev/metaDMG-cpp] Error in make command (Issue #6)
Ok now better but I am getting another error
Crypto library is available to link; adding -lcrypto to LIBS
HTSSRC not defined, assuming systemwide installation -lhts
echo '#define METADAMAGE_VERSION "0.2-46-gedaf069"' > version.h
/opt/miniconda3/envs/metaDMG-cpp/bin/x86_64-conda-linux-gnu-c++ -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/miniconda3/envs/metaDMG-cpp/include -O3 -std=c++11 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/miniconda3/envs/metaDMG-cpp/lib -Wl,-rpath-link,/opt/miniconda3/envs/metaDMG-cpp/lib -L/opt/miniconda3/envs/metaDMG-cpp/lib ngsLCA.cpp
ngsLCA.cpp: In function 'char2int setlevels(int, char*, int&)':
ngsLCA.cpp:64:42: warning: ISO C++ forbids converting a string constant to 'std::map<char*, int, cmp_str>::key_type' {aka 'char*'} [-Wwrite-strings]
64 | char2int::iterator it = c2i.find("species");
| ^~~~~~~~~
/opt/miniconda3/envs/metaDMG-cpp/bin/x86_64-conda-linux-gnu-c++ -MM -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/miniconda3/envs/metaDMG-cpp/include -O3 -std=c++11 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/miniconda3/envs/metaDMG-cpp/lib -Wl,-rpath-link,/opt/miniconda3/envs/metaDMG-cpp/lib -L/opt/miniconda3/envs/metaDMG-cpp/lib ngsLCA.cpp >ngsLCA.d
/opt/miniconda3/envs/metaDMG-cpp/bin/x86_64-conda-linux-gnu-c++ -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/miniconda3/envs/metaDMG-cpp/include -O3 -std=c++11 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/miniconda3/envs/metaDMG-cpp/lib -Wl,-rpath-link,/opt/miniconda3/envs/metaDMG-cpp/lib -L/opt/miniconda3/envs/metaDMG-cpp/lib ngsLCA_cli.cpp
ngsLCA_cli.cpp: In function 'void pars_free(pars*)':
ngsLCA_cli.cpp:55:9: error: 'sam_hdr_destroy' was not declared in this scope; did you mean 'bam_hdr_destroy'?
55 | sam_hdr_destroy(p->header);
| ^~~~~~~~~~~~~~~
| bam_hdr_destroy
make: *** [ngsLCA_cli.o] Errore 1
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Yes, sorry. Linux p04-64gb 3.10.0-1160.81.1.el7.x86_64 |
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all ok., but the above message must be from trying to install metaDMG-cpp afterwards? No the above command right? |
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then I used: and I get that error message |
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yes, will you htslib is not installed correctly I think or metaDMG cannot find it? try again with the make HTSSRC=../htslib/ and make sure the path points to the htslib folder. |
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Thanks now better but I get another error |
@MinLuke you need to set up the correct order of the conda channels. This error message is related that you are installing an old version. Reinstall htslib but using the one in the bioconda channel. Then it should work. |
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these are my channels in their priority
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` conda config --show channels
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then add first And rerun the installation using conda perhaps in a new environment name. |
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oh and check your channel priority first that it matches the one above. |
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Ok once they are in the right order what do I have to do? |
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I suggest you delete the environment you have and redo the creation of the environment etc. installation of metaDMG-mdmg_cppconda create -n metaDMG-cpp2 python=3.9 eigen htslib cxx-compiler gsl install all dependencies etc. next activate the conda environmentconda activate metaDMG-cpp2 ###install metaDMG-cpp Now finally install metaDMG-corepip install metaDMG[all] |
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Now this should work. |
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it works!! thank you all for this precious support |
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Goodmorning,
After installing htslib as indicated I downloaded the metaDM.cpp.git , I entered in the folder and execute make HTSSRC = ../htslib/
But I get the following message and I do not understand why I am getting this error, could you please help me to understand how to solve it?
Crypto library is available to link; adding -lcrypto to LIBS HTSSRC not defined, assuming systemwide installation -lhts g++ -c -O3 -std=c++11 ngsLCA.cpp ngsLCA.cpp:4:56: fatal error: htslib/hts.h: File o directory not exist #include <htslib/hts.h> // for htsFormat, seq_nt16_str ^ compilation terminated. make: *** [ngsLCA.o] Error 1The text was updated successfully, but these errors were encountered: