Installation error

[m-waqas]

I am trying to install biokanga on ubuntu 18.0.4 and getting the following error at make install stage:

waqas@waqas-Inspiron-5521:~/biokanga$ make install
Making install in libbiokanga
make[1]: Entering directory '/home/waqas/biokanga/libbiokanga'
make[2]: Entering directory '/home/waqas/biokanga/libbiokanga'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/waqas/biokanga/libbiokanga'
make[1]: Leaving directory '/home/waqas/biokanga/libbiokanga'
Making install in libBKPLPlot
make[1]: Entering directory '/home/waqas/biokanga/libBKPLPlot'
make[2]: Entering directory '/home/waqas/biokanga/libBKPLPlot'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/waqas/biokanga/libBKPLPlot'
make[1]: Leaving directory '/home/waqas/biokanga/libBKPLPlot'
Making install in genhyperconserved
make[1]: Entering directory '/home/waqas/biokanga/genhyperconserved'
g++ -g -O2 -o genhyperconserved genhyperconserved.o ../libbiokanga/libbiokanga.a ../libbiokanga/zlib/libz.a -lrt -ldl -lpthread
/usr/bin/ld: ../libbiokanga/zlib/libz.a(crc32.o): relocation R_X86_64_32 against .rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../libbiokanga/zlib/libz.a(deflate.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../libbiokanga/zlib/libz.a(inflate.o): relocation R_X86_64_32S against hidden symbol zcfree' can not be used when making a PIE object /usr/bin/ld: ../libbiokanga/zlib/libz.a(inftrees.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../libbiokanga/zlib/libz.a(trees.o): relocation R_X86_64_32S against hidden symbol _length_code' can not be used when making a PIE object /usr/bin/ld: ../libbiokanga/zlib/libz.a(zutil.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../libbiokanga/zlib/libz.a(compress.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../libbiokanga/zlib/libz.a(gzlib.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../libbiokanga/zlib/libz.a(gzread.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../libbiokanga/zlib/libz.a(gzwrite.o): relocation R_X86_64_32S against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../libbiokanga/zlib/libz.a(inffast.o): relocation R_X86_64_32S against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:338: recipe for target 'genhyperconserved' failed
make[1]: *** [genhyperconserved] Error 1
make[1]: Leaving directory '/home/waqas/biokanga/genhyperconserved'
Makefile:371: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1

Any help will be highly appreciated.

[kit4b]

Looks like there is a library version incompatibility issue on your machine with an outdated copy of libz.a being installed with the current biokanga source release.
You could find the system wide release of libz installed on your machine and copy that into ../libbiokanga/zlib/ which should then resolve the incompatibility issue.

An alternative is to use 'kit4b' (https://github.com/kit4b/kit4b) which is a clone of 'biokanga' with improved functionality and capabilities. The 'libz' release incompatibility issue is resolved in 'kit4b' by removing all dependencies on 'libz' versions - when you build 'kit4b' , '../kit4b/libzlib'/source is compiled and linked into all 'kit4b' dependent modules.

[jimie0311]

Looks like there is a library version incompatibility issue on your machine with an outdated copy of libz.a being installed with the current biokanga source release. You could find the system wide release of libz installed on your machine and copy that into ../libbiokanga/zlib/ which should then resolve the incompatibility issue.

An alternative is to use 'kit4b' (https://github.com/kit4b/kit4b) which is a clone of 'biokanga' with improved functionality and capabilities. The 'libz' release incompatibility issue is resolved in 'kit4b' by removing all dependencies on 'libz' versions - when you build 'kit4b' , '../kit4b/libzlib'/source is compiled and linked into all 'kit4b' dependent modules.

Hi,
I met the same error when make install of biokanga.
As you suggested, I have installed kit4b, but where can I find the documentation of kit4b?
If I want to use kit4b to run the command as biokanga, what should I do
biokanga index --threads=4 -i genome -o biokanga_index -r gene_mapping
biokanga blitz --sensitivity=2 --mismatchscore=1 --threads=4 -o GeneMapping.txt --in=gene --sfx=biokanga_index

Thanks

[kit4b]

‘kit4b’ contains a ‘./Doc’ directory which details the parameterisations for most of the ‘ngskit4b’ toolkit modules – ‘blitz’: ‘ngskit4b.blitz.txt’ and ‘index’ : ‘ngskit4b.index.txt’. Documentation is becoming outdated, with many modules having additional parameters. You can view current (latest) parameters with the ‘ngskit4b <module_name> -h’ command. With ‘blitz’ for example, you can now also align PE readsets. -i, --in=<file> input sequences to align from this file (or PE1 if PE processing when SAM output format mode) -u, --inpe2=<file> PE2 input sequences to align from this file if PE processing with SAM output format mode Looking at the parameters quoted as being used for ‘biokanga’ then these will map onto ‘ngskit4b’ without modification. I note the lack of file name extensions, maybe the quoted file name parameters are prototype file names?. From: Junmin Liang ***@***.***> Sent: Monday, 4 July 2022 7:31 PM To: csiro-crop-informatics/biokanga ***@***.***> Cc: Stuart Stephen ***@***.***>; Comment ***@***.***> Subject: Re: [csiro-crop-informatics/biokanga] Installation error (#32) Looks like there is a library version incompatibility issue on your machine with an outdated copy of libz.a being installed with the current biokanga source release. You could find the system wide release of libz installed on your machine and copy that into ../libbiokanga/zlib/ which should then resolve the incompatibility issue. An alternative is to use 'kit4b' (https://github.com/kit4b/kit4b) which is a clone of 'biokanga' with improved functionality and capabilities. The 'libz' release incompatibility issue is resolved in 'kit4b' by removing all dependencies on 'libz' versions - when you build 'kit4b' , '../kit4b/libzlib'/source is compiled and linked into all 'kit4b' dependent modules. Hi, I met the same error when make install of biokanga. As you suggested, I have installed kit4b, but where can I find the documentation of kit4b? If I want to use kit4b to run the command as biokanga, what should I do biokanga index --threads=4 -i genome -o biokanga_index -r gene_mapping biokanga blitz --sensitivity=2 --mismatchscore=1 --threads=4 -o GeneMapping.txt --in=gene --sfx=biokanga_index Thanks — Reply to this email directly, view it on GitHub<#32 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAWBIGE6V5UKAARTAZQFP6DVSKVN5ANCNFSM4LPIGCYA>. You are receiving this because you commented.Message ID: ***@***.******@***.***>>