/bin not created

[dblyons]

hello and thanks for the software-- am running ubuntu 18.04; after I perform ./configure and make -nogzip I enter make copy -nogzip which appears to work fine, but no /bin directory is created, so I cannot use any of the tools thanks for any help you can offer. here is output from make copy -nogzip:

g++ ./src/calmeth.cpp -o ./src/calmeth -m64 -I./src/samtools-0.1.18/ -L./src/samtools-0.1.18/ -lbam -lz g++ ./src/splitSam.cpp -o ./src/splitSam -m64 -I./src/samtools-0.1.18/ -L./src/samtools-0.1.18/ -lbam -lz -pthread if [ -d "bin" ]; then echo bin exists; else mkdir bin; fi g++ -o ./scripts/BatMeth2 ./scripts/BatMeth2.cpp -lpthread g++ ./scripts/report2html.cpp -o ./scripts/report2html cp ./scripts/BatMeth2 ./bin/batmeth2 cp scripts/strip.pl bin cp scripts/report2html bin cp scripts/b2c.pl bin cp scripts/build_complement bin cp scripts/filter.pl bin cp scripts/build_indexX bin cp scripts/build_all bin cp scripts/ann2loc.pl bin cp scripts/build_location.pl bin cp scripts/build_revcmp bin cp scripts/complement.pl bin cp scripts/ReverseComplteFQ bin cp src/bwtformatdb bin cp src/reverse bin cp src/penguin bin cp src/penguin-a bin cp src/calmeth bin cp src/batmethindex bin cp src/filter bin cp bwtformatdb.ini bin cp src/splitSam bin cp src/methyGff bin cp src/methyPlot bin cp src/.r bin cp scripts/.r bin cp src/DMCannotation bin cp scripts/GeneMethHeatmap ./bin/ cp scripts/chrLenExtract ./bin cp scripts/combined.element bin cp scripts/batmeth2-align bin cp scripts/BatMeth2 bin cp scripts/build_ann_location.pl bin cp scripts/preGenome bin cp src/batDMR/batDMR ./bin cp src/genome_filter bin cp src/build_index_rrbs bin

[ZhouQiangwei]

Please check the current directory. The ./bin folder should be in the current directory. In addition, we suggest you use the ’git clone' to get the latest version of batmeth2. We have removed the -nogzip parameter. Thank you for your use.

[stepondust]

@dblyons Actually, in some advanced versions of Ubuntu like Ubuntu 18.04, the problem will be reported when executing the command make copy, resulting in failure of installing batmeth2 and generating /bin directory. Because from Ubuntu 16.10, gcc enables the config --enable-default-pie to enable PIE by default when compiling. However, some libraries don't support PIE, resulting in errors. Therefore, we need to modify MakeFile manually.

Find the following two lines in MakeFile: g++ ./src/calmeth.cpp -o ./src/calmeth -m64 -I./src/samtools-0.1.18/ -L./src/samtools-0.1.18/ -lbam -lz g++ ./src/splitSam.cpp -o ./src/splitSam -m64 -I./src/samtools-0.1.18/ -L./src/samtools-0.1.18/ -lbam -lz -pthread

Add -no-pie for them: g++ ./src/calmeth.cpp -o ./src/calmeth -m64 -I./src/samtools-0.1.18/ -L./src/samtools-0.1.18/ -lbam -lz -no-pie g++ ./src/splitSam.cpp -o ./src/splitSam -m64 -I./src/samtools-0.1.18/ -L./src/samtools-0.1.18/ -lbam -lz -pthread -no-pie

After that, re-execute the command make copy to generate /bin directory.