Unable to install nloptr
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729260460 • 0
@729260460-24148
Last seen 12 months ago

Hi, I tried to install nloptr by BiocManager but failed. Here is my installation command lines :

BiocManager::install("nloptr")

The following is the warning report:

libtool: link: ERROR: no information for variable 'AR' cru .libs/libutil.a .libs/mt19937ar.o .libs/sobolseq.o .libs/timer.o .libs/stop.o .libs/redblack.o .libs/qsort_r.o .libs/rescale.o 
../libtool: line 1102: ERROR:: command not found
make[2]: *** [libutil.la] Error 127
make[2]: Leaving directory `/tmp/RtmpCsOsCY/R.INSTALL6c7cbc4c43a4/nloptr/src/nlopt_src/util'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/tmp/RtmpCsOsCY/R.INSTALL6c7cbc4c43a4/nloptr/src/nlopt_src'
make: *** [all] Error 2
ERROR: configuration failed for package 'nloptr'
* removing '/public/home/shipy3/software/R/library/nloptr'

And here is the information of my R session:

R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.0      tools_3.6.0    

Counld anyone please tell me what is going wrong? Thanks a lots!

software error • 2.1k views
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Entering edit mode

I just met the same problem and solved it bysudo yum install nlopt-devel. I think this could help you with your problem https://stackoverflow.com/questions/37425509/trouble-installing-nloptr-package-on-r-3-3-0

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@james-w-macdonald-5106
Last seen 4 hours ago
United States

You need to upgrade to R-4.0.x and the current version of Bioconductor. While we are able to ensure that the Bioconductor packages installed for a given version of R are compatible, we cannot do the same (just yet) for CRAN packages, and apparently nloptr on CRAN needs R-4.0.x

Which you should note I figured out by googling your error, and which you could have done yourself as well. Not a bad 'skill' to have.

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lea.urpa ▴ 10
@user-25092
Last seen 6 months ago

Actually, in contrast to James' answer, I was able to get nloptr without upgrading my R (I am on a virtual machine that for reasons can't use the latest R version).

The nloptr package is an R interface for the NLOpt C library. The problem is that when nloptr installs, it tries to download the NLOpt library from a link. In older versions of R, the corresponding nloptr version tries to install NLOpt from a broken link (see the github issue here for more info: https://github.com/jyypma/nloptr/issues/40). You can fix this by upgrading your R version, and therefore your nloptr package version- or you can donwload the NLOptr package yourself.

I was able to fix this problem on a Debian GNU/Linux 10 (buster) system with sudo apt-get install libnlopt-dev, as per the github issue comments linked above.

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