I would like to install the package GeoXp, but R doesn't let me...see the error below...
>install.packages("GeoXp")
...
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’
* removing ‘/home/****/R/x86_64-pc-linux-gnu-library/3.0/rgl’
Warning in install.packages :
installation of package ‘rgl’ had non-zero exit status
ERROR: dependency ‘rgl’ is not available for package ‘GeoXp’
* removing ‘/home/******/R/x86_64-pc-linux-gnu-library/3.0/GeoXp’
Warning in install.packages :
installation of package ‘GeoXp’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpAbblyJ/downloaded_packages’
> library("GeoXp")
Error in library("GeoXp") : there is no package called ‘GeoXp’
Well, there seems to be a problem with the dependencies...but installing rgl does not work either...
Here my session info:
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] spacetime_1.1-3 sp_1.0-17
loaded via a namespace (and not attached):
[1] grid_3.0.2 intervals_0.15.0 lattice_0.20-29
tools_3.0.2 xts_0.9-7 zoo_1.7-11
What can I do?
GeoXp has a dependency on rgl, tries to install that first, but fails there. rgl needs to have the X11 development libraries, as well as the (open source) OpenGL development and run-time libraries (mesa). For Ubuntu, you need to install the system packages libgl1-mesa-dev and libglu1-mesa-dev first (with apt-get or sth similar), then install in R package rgl, then GeoXp.
I think the problem is that you have to install X library and gl
Ops, sorry #Pascal, I did not see your comment.
Related
I'm currently trying to use readFastq with the ShortRead library. I have specified the version of Bioconductor I need (3.14) in order to run it in R version 4.1 (which is the one I'm currently using). I keep getting an error message saying:
> library(ShortRead)
Error in library(Shortread) : there is no package called 'ShortRead'
and also:
ln: failed to create symbolic link 'libhts.so.2': Operation not supported
make: *** [Makevars:28: populate-usrlib-dir] Error 1
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/Rhtslib’
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/GenomicAlignments’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’, ‘Rhtslib’ are not available for package ‘ShortRead’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/ShortRead’
and
ERROR: configuration failed for package ‘textshaping’
* removing ‘/opt/conda/envs/r/lib/R/library/textshaping’
* restoring previous ‘/opt/conda/envs/r/lib/R/library/textshaping’
* installing *source* package ‘ragg’ ...
** package ‘ragg’ successfully unpacked and MD5 sums checked
** using staged installation
and lastly
ERROR: configuration failed for package ‘ragg’
* removing ‘/opt/conda/envs/r/lib/R/library/ragg’
* restoring previous ‘/opt/conda/envs/r/lib/R/library/ragg’
The downloaded source packages are in
‘/tmp/RtmpgByRyT/downloaded_packages’
I would really appreciate som help with troubleshooting this or a "smarter" way to convert fastq.gz files to fasta files
The commands I've run so far are:
#Installing ShortRead package containing the readFastq function
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version="3.14")
BiocManager::install("GenomeInfoDbData")
BiocManager::install("GenomeInfoDb")
BiocManager::install("ShortRead")
#Loading the library
library(ShortRead)
Some extra session information:
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS/LAPACK: /opt/conda/envs/r/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.19
loaded via a namespace (and not attached):
[1] compiler_4.1.1 fastmap_1.1.0 cli_3.4.1 htmltools_0.5.3 tools_4.1.1
[6] rstudioapi_0.14 yaml_2.3.6 rmarkdown_2.17 knitr_1.40 xfun_0.34
[11] digest_0.6.30 rlang_1.0.6 evaluate_0.17
I do not understand why it won't install. I would it expect it to work when I have made sure to use the correct version
I am pretty desperate to install.packages("devtools").
However it allways fails with this error
Error: .onLoad failed in loadNamespace() for 'pkgload', details:
call: readRDS(nsInfoFilePath)
error: error reading from connection
Execution halted
ERROR: lazy loading failed for package ‘devtools’
* removing ‘/home/bjoern/R/x86_64-pc-linux-gnu-library/3.6/devtools’
Things I tried to fix this:
Add the dependencies = T argument
Following a suggestion by hadley wickham on github -> update rlang package
Try to run install.packages("pkgload") resulting in nearly exactly the same error (see below)
Completely removing R and reinstalling it
Additionally installing package following packages:
r-base-dev
r-cran-devtools
r-recommended
Updated all packages update.packages(ask = FALSE, checkBuilt = TRUE)
Error of install.packages("pkgload")
Error: package or namespace load failed for ‘pkgload’:
.onLoad failed in loadNamespace() for 'pkgload', details:
call: readRDS(nsInfoFilePath)
error: error reading from connection
Error: loading failed
Execution halted
ERROR: loading failed
I digged even deeper to the pkgload (which at least I hope is the only reason for the problem). I will check if manually (re)installing all imports and suggests from the CRAN page of pkgload does solve it.
Imports: desc, methods, pkgbuild, rlang, rprojroot, rstudioapi,
utils, withr Suggests: bitops, covr, Rcpp, testthat
My sessionInfo() output:
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3
I still refuse to belief that it is impossibe to install devtools on ubuntu20
However at this point I take any straw
Solution Edit:
In short what fixed the issue for me was installing testthat package before. Thanks to comment by rui-barradas
install.packages("testthat")
install.packages("pkgload")
install.packages("devtools")
I am also on Ubuntu 20.04 but running R 4.0.0.
When trying to install a package, if it depends on another that was installed prior to R 4.0.0 I get an error message and the installation fails. This happens even if I set dependencies = TRUE in the call to install.packages.
Example: The command was
install.packages('pkgload')
I omit the first output lines, saying that the file was downloaded. Then, the relevant part.
installing source package ‘pkgload’ ...
** package ‘rcmdcheck’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading Error: package ‘testthat’ was installed before R 4.0.0: please re-install it
Execution halted ERROR: lazy loading failed for package ‘pkgload’
removing ‘/usr/local/lib/R/site-library/pkgload’
restoring previous ‘/usr/local/lib/R/site-library/pkgload’ Warning in install.packages : installation of package ‘pkgload’ had
non-zero exit status The downloaded source packages are in
‘/tmp/RtmpVxpbs0/downloaded_packages’
Correct way.
The right way of installing package pkgload was to run the sequence
install.packages('testthat')
install.packages('pkgload')
and the problem was solved.
Note that with other packages, it already happened to see this be a recursive issue. Imagine that package testthat depended (which it does not) on another package installed prior to R 4.0.0.
Annoying but solvable.
sessionInfo()
#R version 4.0.0 (2020-04-24)
#Platform: x86_64-pc-linux-gnu (64-bit)
#Running under: Ubuntu 20.04 LTS
#
#Matrix products: default
#BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#
#locale:
# [1] LC_CTYPE=pt_PT.UTF-8 LC_NUMERIC=C
#[3] LC_TIME=pt_PT.UTF-8 LC_COLLATE=pt_PT.UTF-8
# [5] LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8
# [7] LC_PAPER=pt_PT.UTF-8 LC_NAME=C
# [9] LC_ADDRESS=C LC_TELEPHONE=C
#[11] LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C
#
#attached base packages:
#[1] stats graphics grDevices utils datasets
#[6] methods base
#
#other attached packages:
#[1] rvest_0.3.5 xml2_1.3.2 data.table_1.12.8
#
#loaded via a namespace (and not attached):
I had the same problems, and the solution was, at least in my case, Ubuntu 20.04.1 LTS (Focal Fossa) + R 4.0.2:
First (from terminal), install:
Step 1: sudo apt-get update -y
Step 2: sudo apt-get install -y libxml2-dev
Then from RStudio (setRepositories first, and choose 8 repositories) and install both packages:
Install xml2 package
install devtools
And works for me.
Trying to install package "caret" on R 3.1.0 (Ubuntu 14.04.01 LTS) and running into a build error.
> install.packages('caret')
[...]
* installing *source* package ‘BradleyTerry2’ ...
** package ‘BradleyTerry2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : object ‘brglm’ is not exported by 'namespace:brglm'
ERROR: lazy loading failed for package ‘BradleyTerry2’
* removing ‘/home/br00t/R/x86_64-pc-linux-gnu-library/3.1/BradleyTerry2’
Warning in install.packages :
installation of package ‘BradleyTerry2’ had non-zero exit status
ERROR: dependency ‘BradleyTerry2’ is not available for package ‘caret’
* removing ‘/home/br00t/R/x86_64-pc-linux-gnu-library/3.1/caret’
Warning in install.packages :
installation of package ‘caret’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp7pWmvr/downloaded_packages’
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sp_1.0-16
loaded via a namespace (and not attached):
[1] grid_3.1.0 lattice_0.20-29 tools_3.1.0
Wasn't able to find anything helpful on the interwebs. Not sure if this is an issue with the BradleyTerry2 package or brglm... help?
Thanks,
br00t
If you are running a version of the brglm package greater than 0.5-9, uninstall and install brglm package version 0.5-9
I was able to get over the issue too by installing the dependencies. You may want to select your answer as the right one.
When I tried git-hub install, using:
install_github('slidify', 'ramnathv')
But I got the follwing message:
> install_github('slidify', 'ramnathv')
Installing github repo slidify/master from ramnathv
Downloading master.zip from https://github.com/ramnathv/slidify/archive/master.zip
Installing package from C:\Users\6E86~1\AppData\Local\Temp\RtmpYD4xRM/master.zip
Installing slidify
"C:/PROGRA~1/R/R-31~1.0/bin/i386/R" --vanilla CMD INSTALL "C:\Users\ \
ע\AppData\Local\Temp\RtmpYD4xRM\devtools1f901f6d4e5e\slidify-master" \
--library="C:/Program Files/R/R-3.1.0/library" --install-tests
Warning: invalid package 'C:\Users\ע\AppData\Local\Temp\RtmpYD4xRM\devtools1f901f6d4e5e\slidify-master'
Error: ERROR: no packages specified
Error: Command failed (1)
I also tried downlowding "slidify-master.zip" and installing it localy using:
install.packages("c:/r/packages/slidify-master.zip", repos = NULL, type="source")
but nothing seems to happen, and the package is not installed:
> library(slidify)
Error in library(slidify) : there is no package called ‘slidify’
my sessionInfo() is:
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Hebrew_Israel.1255 LC_CTYPE=Hebrew_Israel.1255
[3] LC_MONETARY=Hebrew_Israel.1255 LC_NUMERIC=C
[5] LC_TIME=Hebrew_Israel.1255
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_1.5
loaded via a namespace (and not attached):
[1] digest_0.6.4 evaluate_0.5.5 httr_0.3 memoise_0.2.1 parallel_3.1.0
[6] RCurl_1.95-4.1 stringr_0.6.2 tools_3.1.0 whisker_0.3-2
any ideas?
The problem presisted when I tried to install other packages from Github.
Seems it has to do ith the user name, and the directory where the downloads are stored.
I created a new user in windows with a simple name (no spaces, no special characters) and the installation succeeded !
I am unable to install e1071 on my ubuntu machine.
I tried using:
sudo apt-get install r-cran-e1071
gives an error message:
Warning messages:
1: In open.connection(con, "r") :
unable to connect to 'cran.r-project.org' on port 80.
2: E: Unable to locate package r-cran-e1071
and
install.packages("e1071", dep = TRUE, type = "source")
gives an error message:
package ‘e1071’ is not available (for R version 2.15.2)
sessionInfo() gives:
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tcltk_2.15.2 tools_2.15.2
The package e1071 depends on package class. The package class depends on R (≥ 3.0.0). Hence, you should update to a more recent R version.
Like #SvenHohenstein already said, the package needs a different version of R. What you can do is get an old version of the package from its archives, but you'll probably have to install older versions of other packages. In addition, you'll have to build the old version of the package from source as no binary versions are archived. Simply updating to a new R version is much easier...