I tried to install nloptr by BiocManager but failed. Here is my installation command lines :
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: *** [libutil.la] Error 127
make: Leaving directory `/tmp/RtmpCsOsCY/R.INSTALL6c7cbc4c43a4/nloptr/src/nlopt_src/util'
make: *** [all-recursive] Error 1
make: 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
attached base packages:
 stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
 BiocManager_1.30.10 compiler_3.6.0 tools_3.6.0
Counld anyone please tell me what is going wrong? Thanks a lots!
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.
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.