installation failed when trying msa
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akp • 0
@akp-8846
Last seen 5.2 years ago
I am trying to install "MSA" as,

source("https://bioconductor.org/biocLite.R")
biocLite("msa")

 - but I fece the following erorrs,
g++: error: ./libgc.a: No such file or directory
g++: error: ./libClustalW.a: No such file or directory
g++: error: ./libClustalOmega.a: No such file or directory
g++: error: ./libMuscle.a: No such file or directory
make[2]: *** [libMuscle.so] Error 1
make[2]: Leaving directory `/tmp/Rtmp1PL5FI/R.INSTALLdc0965fbf450/msa/src/Muscle'
make[1]: Leaving directory `/tmp/Rtmp1PL5FI/R.INSTALLdc0965fbf450/msa/src/Muscle'
make[1]: *** [muscle] Error 1
make: *** [build_muscle] Error 2
ERROR: compilation failed for package ‘msa’
* removing ‘/home/djf482/R/x86_64-pc-linux-gnu-library/3.3/msa’

 

the following is my RsessionInfo

> sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE 13.1 (Bottle) (x86_64)

msa • 856 views
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UBodenhofer ▴ 270
@ubodenhofer-5425
Last seen 4 weeks ago
University of Applied Sciences Upper Au…

Sorry that you are encountering troubles! I am happy to help where I can. However, the information you provided is not sufficient to spot the source of the problem. Maybe you are missing some libraries, let's see. Please try the installation again, dump the entire output to a plain text file, and send it to us by e-mail (msa@bioinf.jku.at).

Cheers, Ulrich  (package maintainer)

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UBodenhofer ▴ 270
@ubodenhofer-5425
Last seen 4 weeks ago
University of Applied Sciences Upper Au…

Thanks for sending the output of your installation procedure! I now found out what the problem is: it seems that, unlike on Ubuntu, the PKG_LIBS variable seems to carry over to make child processes on your openSUSE system. I do not have an immediate solution. I will discuss the subject on the bioc-devel mailing list and keep you posted about possible solutions and updates. Sorry for any inconveniences

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Thanks, no worries; I look forward to hearing from you :-)

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