Question: Cannot find the package RDRToolbox that has been installed
0
gravatar for sunjoy0102
27 days ago by
sunjoy01020
sunjoy01020 wrote:

Hi there,

I am trying to use the RDRToolbox package to run Isomap model. However, after I installed package by entering:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("RDRToolbox")

I load the library:

library(RDRToolbox)

and got the error message saying that "Error in library(RDRToolbox) : there is no package called ‘RDRToolbox’." Same thing happens when I enter:

library("RDRToolbox")

Here is the message I got when I was installing the package:

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install("RDRToolbox")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'RDRToolbox'
also installing the dependency ‘rgl’

trying URL 'https://cloud.r-project.org/src/contrib/rgl_0.100.19.tar.gz'
Content type 'application/x-gzip' length 2943409 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/RDRToolbox_1.34.0.tar.gz'
Content type 'application/x-gzip' length 237328 bytes (231 KB)
==================================================
downloaded 231 KB

* installing *source* package ‘rgl’ ...
** package ‘rgl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... libraries , headers 
checking GL/gl.h usability... no
checking GL/gl.h presence... no
checking for GL/gl.h... no
checking GL/glu.h usability... no
checking GL/glu.h presence... no
checking for GL/glu.h... no
configure: error: missing required header GL/gl.h
ERROR: configuration failed for package ‘rgl’
* removing ‘/home/zsx0787/R/x86_64-pc-linux-gnu-library/3.6/rgl’
installation of package ‘rgl’ had non-zero exit statusERROR: dependency ‘rgl’ is not available for package ‘RDRToolbox’
* removing ‘/home/zsx0787/R/x86_64-pc-linux-gnu-library/3.6/RDRToolbox’
installation of package ‘RDRToolbox’ had non-zero exit status
The downloaded source packages are in
    ‘/tmp/RtmpDC8HyR/downloaded_packages’
installation path not writeable, unable to update packages: crayon, dbplyr, ellipsis, ergm,
  ggplot2, markdown, memoise, mime, numDeriv, openssl, pbdZMQ, RcppArmadillo, rlang, statnet,
  statnet.common, tergm, tibble, tinytex, tsna, whisker, withr, xfun, littler, class, cluster,
  codetools, foreign, KernSmooth, lattice, Matrix, mgcv, nnet, spatial

Hope someone can help! Thanks.

software error • 83 views
ADD COMMENTlink written 27 days ago by sunjoy01020

RDRToolbox actually did not install correctly because it looks like its dependency "rgl" did not install correctly.

BiocManager::install("rgl")

This will most likely fail with the same ERROR as above - but Could you please show your sessionInfo( ) to indicate your OS? It looks like you might be missing some system dependencies and knowing your OS will assist with providing proper solutions.

ADD REPLYlink modified 27 days ago • written 27 days ago by shepherl ♦♦ 1.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 216 users visited in the last hour