Install issues

[slschnorr]

Expected Behavior

I'm having issues installing plass using all options. I work in CentOS 8 x86_64

Current Behavior

1. Install from bioconda appears to succeed but then the plass executable does not exist

2. Install from the static file results in:
   --2022-01-14 09:04:13-- https://mmseqs.com/plass/plass-static_sse41.tar.gz
   Resolving mmseqs.com (mmseqs.com)... 141.5.100.26
   Connecting to mmseqs.com (mmseqs.com)|141.5.100.26|:443... connected.
   HTTP request sent, awaiting response... 404 Not Found
   2022-01-14 09:04:14 ERROR 404: Not Found.

3. Install from git clone errors during make with:
   make -j 4 && make install
   Consolidate compiler generated dependencies of target microtar
   Consolidate compiler generated dependencies of target ksw2
   Consolidate compiler generated dependencies of target cacode
   Consolidate compiler generated dependencies of target alp
   [ 2%] Built target microtar
   [ 2%] Built target ksw2
   [ 2%] Built target cacode
   [ 7%] Built target alp
   [ 7%] Building C object lib/mmseqs/lib/tinyexpr/CMakeFiles/tinyexpr.dir/tinyexpr.c.o
   [ 7%] Generating ../generated/VTML80.out.h
   [ 7%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/entropy_common.c.o
   [ 7%] Generating ../generated/assemble.sh.h
   : invalid option
   make[2]: *** [lib/mmseqs/data/CMakeFiles/generated.dir/build.make:159: lib/mmseqs/generated/VTML80.out.h] Error 1
   make[1]: *** [CMakeFiles/Makefile2:803: lib/mmseqs/data/CMakeFiles/generated.dir/all] Error 2
   make[1]: *** Waiting for unfinished jobs....
   : invalid option
   make[2]: *** [data/CMakeFiles/local-generated.dir/build.make:81: generated/assemble.sh.h] Error 1
   make[2]: *** Waiting for unfinished jobs....
   [ 7%] Generating ../generated/nuclassemble.sh.h
   [ 7%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/fse_decompress.c.o
   : invalid option
   make[2]: *** [data/CMakeFiles/local-generated.dir/build.make:97: generated/nuclassemble.sh.h] Error 1
   make[1]: *** [CMakeFiles/Makefile2:861: data/CMakeFiles/local-generated.dir/all] Error 2
   [ 8%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/threading.c.o
   [ 8%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/pool.c.o
   [ 8%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/zstd_common.c.o
   [ 9%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/error_private.c.o
   [ 9%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/hist.c.o
   [ 9%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/common/xxhash.c.o
   [ 10%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/fse_compress.c.o
   [ 11%] Linking C static library libtinyexpr.a
   [ 11%] Built target tinyexpr
   [ 11%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/huf_compress.c.o
   [ 12%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_compress.c.o
   [ 12%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstdmt_compress.c.o
   [ 12%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_fast.c.o
   [ 13%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_double_fast.c.o
   [ 13%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_lazy.c.o
   [ 13%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_opt.c.o
   [ 14%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/compress/zstd_ldm.c.o
   [ 14%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/decompress/huf_decompress.c.o
   [ 14%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/decompress/zstd_decompress.c.o
   [ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/decompress/zstd_decompress_block.c.o
   [ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/decompress/zstd_ddict.c.o
   [ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/dictBuilder/cover.c.o
   [ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/dictBuilder/fastcover.c.o
   [ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/dictBuilder/divsufsort.c.o
   [ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/dictBuilder/zdict.c.o
   [ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/deprecated/zbuff_common.c.o
   [ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/deprecated/zbuff_compress.c.o
   [ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir////lib/deprecated/zbuff_decompress.c.o
   [ 18%] Linking C static library libzstd.a
   [ 18%] Built target libzstd_static
   make: *** [Makefile:136: all] Error 2

Context

lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 48
On-line CPU(s) list: 0-47
Thread(s) per core: 2
Core(s) per socket: 12
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 62
Model name: Intel(R) Xeon(R) CPU E5-2697 v2 @ 2.70GHz
Stepping: 4
CPU MHz: 3500.000
CPU max MHz: 3500.0000
CPU min MHz: 1200.0000
BogoMIPS: 5387.14
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 30720K
NUMA node0 CPU(s): 0-11,24-35
NUMA node1 CPU(s): 12-23,36-47

[milot-mirdita]

We changed the naming scheme of the files on the download server and forgot to update the readme:

You can find the SSE4.1 Linux binary at:
https://mmseqs.com/plass/plass-linux-sse41.tar.gz

To compile from source you need to have either xxd (usually from a system package like vim-common) or if that doesn't exist then it will fall back to a perl script.

[slschnorr]

Hi
Thanks that worked and I got it installed.
But I do have xxd, so I'm confused why compiling from source failed, especially if it should fall back to a perl script.

[milot-mirdita]

If you have the cmake build directory still could you show the output of the following files:

cat CMakeFiles/CMakeOutput.log CMakeFiles/CMakeError.log

[slschnorr]

plass_CMakelogs.txt

[milot-mirdita]

Hm that didn't help much, could you make a new build folder, run cmake again from this fresh build folder and post its output? I can't reproduce the issue :/

[slschnorr]

Sure :)
plass_CMakelogs2.txt