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HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework
https://github.com/HenrikBengtsson/aroma.seq
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TIPCC: sequenza 3.0.0 fails to install on TIPCC #49

Open HenrikBengtsson opened 5 years ago

HenrikBengtsson commented 5 years ago

Issue

The new sequenza 3.0.0 depends on seqminer, which fails to install on TIPCC. We get installation errors such as:

> install.packages("seqminer")
...
/tmp/henrik/ccjlyQXx.s: Assembler messages:
/tmp/henrik/ccjlyQXx.s:460: Error: no such instruction: `shlx %r11,%r9,%r9'
/tmp/henrik/ccjlyQXx.s:488: Error: no such instruction: `shlx %r10,%rcx,%rcx'
/tmp/henrik/ccjlyQXx.s:533: Error: no such instruction: `shrx %rcx,%r9,%r9'
/tmp/henrik/ccjlyQXx.s:620: Error: no such instruction: `shlx %rsi,%rcx,%rcx'
/tmp/henrik/ccjlyQXx.s:648: Error: no such instruction: `shlx %rax,%rsi,%rax'
/tmp/henrik/ccjlyQXx.s:673: Error: no such instruction: `shlx %r13,%rsi,%rsi'
/tmp/henrik/ccjlyQXx.s:691: Error: no such instruction: `shlx %r10,%rsi,%rsi'
/tmp/henrik/ccjlyQXx.s:753: Error: no such instruction: `shrx %rsi,%rcx,%r9'
/tmp/henrik/ccjlyQXx.s:771: Error: no such instruction: `shlx %rsi,%rcx,%rcx'
make: *** [zstd/lib/compress/huf_compress.o] Error 1
ERROR: compilation failed for package 'seqminer'

Troubleshooting

This falls under TIPCC is outdated.

Workaround

I've attempted various suggestions adding compiler flags such as

PKG_CFLAGS += -mno-fma -mno-avx2 -march=bdver1
PKG_CPPFLAGS += -mno-fma -mno-avx2 -march=bdver1

to R-specific ~/.R/Makevars file but it made no difference.

A workaround is to install an older version of seqminer. The following works on TIPCC with R 3.6.1;

install.packages("https://cran.r-project.org/src/contrib/Archive/seqminer/seqminer_6.1.tar.gz")

After installing that, 

install.packages("sequenza")

works.