make: *** [ShortRead.so] Error 1
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mictadlo • 0
@mictadlo-10885
Last seen 2.7 years ago

Hi,

I got this error  `make: *** [ShortRead.so] Error 1`  while installing ShortRead in the following way:

> source("http://bioconductor.org/biocLite.R")
> biocLite( "ShortRead" )
...
 -lz -fopenmp -L/usr/lib64/R/lib -lR
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.6/libgomp.a(env.o): relocation R_X86_64_32 against `gomp_global_icv' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-linux-gnu/4.6/libgomp.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [ShortRead.so] Error 1
ERROR: compilation failed for package ‘ShortRead’
* removing ‘/home/waterhouse/R/x86_64-pc-linux-gnu-library/3.2/ShortRead’

The downloaded source packages are in
    ‘/tmp/Rtmpagckv6/downloaded_packages’
Old packages: 'boot', 'MASS', 'Matrix', 'nlme', 'spatial', 'survival'
Update all/some/none? [a/s/n]: a

What did I do wrong?

Thank you in advance.

Best wishes,

Mic

shortread • 839 views
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The error seems to be saying that libgomp.a was built as a static library, whereas R has been built (probably implicitly. configure has argument --enable-static with [default=no]) as a shared library. I think this type of error should have occurred when R itself was built, unless the compiler / some other part of the build toolchain has been updated in the mean time. How was R installed?.

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