Xingyu-Liao
commented
2 years ago Hi,
Thanks for creating such great programmes!
I have a problem when trying to install the software, it stops at the Minimap2 installation, which I have anyway installed locally using conda before.
Please see the installation log here:
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC main.c -o main.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kthread.c -o kthread.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kalloc.c -o kalloc.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC misc.c -o misc.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC bseq.c -o bseq.o
Not sure what is the problem actually. Hopefully you can help.
Thanks!
Hi，
Thanks for your feedback. When minimap2 is successfully installed, the log should look like this.
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC main.c -o main.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kthread.c -o kthread.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kalloc.c -o kalloc.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC misc.c -o misc.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC bseq.c -o bseq.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sketch.c -o sketch.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sdust.c -o sdust.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC options.c -o options.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC index.c -o index.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC lchain.c -o lchain.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC align.c -o align.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC hit.c -o hit.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC seed.c -o seed.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC map.c -o map.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC format.c -o format.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC pe.c -o pe.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC esterr.c -o esterr.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC splitidx.c -o splitidx.o cc -c -g -Wall -O2 -Wc++-compat -msse2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o cc -c -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o cc -c -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o cc -c -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o cc -g -Wall -O2 -Wc++-compat main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread
To install minimap2, you need to have a C compiler, GNU make and zlib development files installed. Maybe these conditions are met in your conda environment, but not on your system (outside of conda ).
I will test the full steps of LongRepMarker installation in conda as soon as possible and provide a solution to the problem. Thank you very much!
Best,
Xingyu Liao
Hypecoum
Hi,
Thanks for creating such great programmes!
I have a problem when trying to install the software, it stops at the Minimap2 installation, which I have anyway installed locally using conda before.
Please see the installation log here:
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC main.c -o main.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kthread.c -o kthread.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kalloc.c -o kalloc.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC misc.c -o misc.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC bseq.c -o bseq.o
Not sure what is the problem actually. Hopefully you can help.
Thanks!