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gpertea / gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
MIT License
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make: *** [Makefile:61: ../gclib] Error 127 #57

Closed yejilee-biostat closed 4 years ago

yejilee-biostat commented 4 years ago

Hello,

I tried to install gffcompare on centos from source codes on the github, and it gave me the following message :

===================

make release remote: Enumerating objects: 31, done. remote: Counting objects: 100% (31/31), done. remote: Compressing objects: 100% (22/22), done. remote: Total 1171 (delta 14), reused 24 (delta 9), pack-reused 1140 Receiving objects: 100% (1171/1171), 840.29 KiB | 340.00 KiB/s, done. Resolving deltas: 100% (777/777), done. Cloning into 'gclib'... make: Cloning: Command not found make: *** [Makefile:61: ../gclib] Error 127

I'm trying to use the pre-compiled version for now, but I'm still curious about this issue. Could you help me to solve this issue? Thank you.

-Yeji

gpertea commented 4 years ago

Ouch, there was indeed a mistake in the Makefile that seemed to not cause problems on newer Linux distros but failed on CentOS. I corrected that and re-released v0.11.7 source with that simple Makefile fix. Could you try again with the updated Makefile?

Thank you for pointing out this build problem.

yejilee-biostat commented 4 years ago

Sorry for not replying for so long - I have been using the pre-compiled version and forgot about this issue. I have tried to compile the updated version, and now it gives me the new kind of errors

==== ... /home/tools/yejilee/miniconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -O3 -DNDEBUG -std=c++0x -Wall -Wextra -I../gclib -D_REENTRANT -fno-exceptions -fno-rtti -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/tools/yejilee/miniconda3/include -c gffcompare.cpp -o gffcompare.o g++ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath /home/tools/yejilee/miniconda3/lib -Wl,-rpath-link,/home/tools/miniconda3/lib -L /home/tools/yejilee/miniconda3/lib -o gffcompare ../gclib/GFastaIndex.o ../gclib/GFaSeqGet.o ../gclib/gff.o ../gclib/gdna.o ../gclib/codons.o ../gclib/GBase.o ../gclib/GStr.o ../gclib/GArgs.o gtf_tracking.o gffcompare.o /usr/bin/ld: ../gclib/gff.o: unrecognized relocation (0x29) in section `.text._ZN5GPVecI7GffExonE15DefaultFreeProcEPv[_ZN5GPVecI7GffExonE15DefaultFreeProcEPv]' /usr/bin/ld: final link failed: Bad value collect2: error: ld returned 1 exit status make: *** [Makefile:68: gffcompare] Error 1

I am not sure it is a problem caused by my local setting or source codes. But the pre-compiled version seems working well for me, so I will probably not dig into this issue any further. Still, thank you for your kind reply!