I am installing Julia packages in Linux system. The error message is below. There are three kinds of error message. I don't know how to fix it. I have already tried pkg> update. It didn't help. The julia version is Version 1.0.0 (2018-08-08).
Related
I need to install few packages that should be installed with remotes::install_github() like
"acidgenomics/basejump" or "satijalab/seurat".
During the installation, it need to upgrade few other packages version. The BiocManager::install program cannot find those versions and I had to install those dependencies packages version with:
R CMD INSTALL IRanges_2.20.2.tar.gz
Then other packages, that use the same packages stop working. like DESeq2,
I get the error:
Error: package or namespace load failed for ‘DESeq2’:
objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:S4Vectors'
I found few answers that say it happen (like url)
remotes::install_github() isn't picking up the correct Bioconductor
devel repos, whereas installing with BiocManager::install() does work
as expected.
we have the R 3.6.0 installed as a module and a lot of users uses the same R version. I need all packages to work for everyone.
How can I make all variety packages versions to work?
Finally, I install new version of R 3.6.3 with Bioconductor 3.10 and all the packages install right.
After upgrading to R 3.6.2 I am getting a series of errors about earlier versions of libraries being used :
Error: package ‘stringi’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Execution halted
I have worked through several of these via
install.packages('stringi')
but that just leads down the rabbit hole to the next mismatched library. What I'd like to do is en-masse upgrade the existing libraries. Here is a suggestion to use:
lib_loc <- "<old R library path"
to_install <- unname(installed.packages(lib.loc = lib_loc)[, "Package"])
to_install
install.packages(pkgs = to_install)
However - where is the <old R library path> on ubuntu?
Update Based on suggestion from #RuiBarradas I ran:
update.packages(ask=FALSE)
But the "different internals" errors shown above still happens for many packages. So I am still looking for an answer to how to upgrade the ones installed on the older version of R (3.4.4)
Following did the trick - thanks to #RuiBarradas for the pointer to update.packages:
update.packages(checkBuilt=TRUE, ask=FALSE)
I would like to install the R Package JuliaCall, to use Julia from R. I have installed Julia via snap and installed the JuliaCall R package form the Cran.
I received the following error when trying to use the setup function of JuliaCall.
library(JuliaCall)
julia <- julia_setup()
Julia version 1.0.4 at location /snap/julia/13/bin will be used.
Error in dyn.load(.julia$dll_file) :
unable to load shared object '/snap/julia/13/bin/../lib/libjulia.so.1':
/snap/julia/13/bin/../lib/libjulia.so.1: wrong ELF class: ELFCLASS32
Show Traceback
Rerun with Debug
Error in juliacall_initialize(.julia$dll_file) :
/snap/julia/13/bin/../lib/libjulia.so.1 - /snap/julia/13/bin/../lib/libjulia.so.1: wrong ELF class: ELFCLASS32
Julia is installed:
XRJulia::findJulia()
[1] "/snap/bin/julia"
I have tried some suggestions found in
https://github.com/Non-Contradiction/JuliaCall/issues/72
and even report my problems, but I'm not sure if this is an issue to open on Github or a problem with my installation.
The same error occurs
My system specifications are:
Ubuntu 18.04,
Rstudio 1.1.456,
R 3.5.1,
Julia installed via snap
Thanks for any help you could provide
Actually, the developer of JuliaCall answered my question.
I have installed Julia using snap without noticing that a 32bits version was used. Installing Julia from the .tar.gz archive and choosing the correct 64 bits version solve this problem.
Many Thanks to #Non-Contradiction.
I receive the following error from Travis after doing a git push:
Installing R packages from GitHub: jimhester/covr
$ Rscript -e 'devtools::install_github(c("jimhester/covr"),
build_vignettes = FALSE)'
Error: package ‘devtools’ was installed by an R version with different
internals; it needs to be reinstalled for use with this R version
Execution halted
More information you can find here:
https://travis-ci.org/bozmik/genomation/jobs/315357710#L1125
Do you have any idea how to solve this issue?
You can add
r_packages:
- devtools
before
r_github_packages:
- jimhester/covr
This solve my problem.
I've encountering this issue separately and unfortunately Chaoran's solution didn't work for me.
The problem is that the devtools binary being called from the package cache was built under a different version of R than the one that Travis is using.
I was able to fix this by adding
r: devel
to my .travis.yml, forcing Travis to use the development version of R instead of the release channel. The devtools binary that's causing the problem has been compiled on this devel channel.
I know there are a few similar questions out there, particularly this one:
How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?
The answer is bit overwhelming to me, frankly, since I'm not quite familiar with R settings/installation etc. I tried some solutions, but didn't get it work yet.
What I want to do is to install some bioconductor packages from here:
https://www.bioconductor.org/packages/release/BiocViews.html#___CopyNumberVariation
for example "CNVPanelizer", but I got the following error message:
> biocLite("CNVPanelizer")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.3), R version 3.2.1.
Installing package(s) 'CNVPanelizer'
Old packages: 'PSCBS', 'rgl'
Update all/some/none? [a/s/n]: #--- I tried 'a' and 'n', neither working
Warning message:
package ‘CNVPanelizer’ is not available (for R version 3.2.1) #--- this is the error message I got, as shown in my topic title
For all packages in bioconductor/dnacopy web page, I got the same error message.
Anyone has a simple solution? A step by step guidance will be highly appreciated!
TIA
Try to clarify here (as to answer comments below)
I tried both "a" and "n" options when asked "Update all/some/none? [a/s/n]:". Neither works.
> library("CNVPanelizer")
Error in library("CNVPanelizer") :
there is no package called ‘CNVPanelizer’
How to install an old version of Bioconductor? I'll google meanwhile...
Thanks.
Update:
I tried upgrade R, Bioconductor, biocinstaller. This works for some packages listed on this page:
https://www.bioconductor.org/packages/release/BiocViews.html#___CopyNumberVariation
such as exomeCopy. some installed with warnings; some with errors, such as CNVPanelizer. and one common error is
Old packages: 'rgl'
I saw this 'rgl' before I upgrade R/Bioconductor. And sometime I see messages saying removing 'rgl' and 'rgl' reinstalled. Don't know what this 'rgl' thing is......
You are running Bioconductor 3.1 but according to the landing page for CNVPanelizer, it was introduced in Bioconductor 3.2. So you should upgrade:
library(BiocInstaller)
biocLite("BiocUpgrade")
Then you should be able to install CNVPanelizer:
biocLite("CNVPanelizer")
And actually after upgrading you should upgrade all your existing packages by calling biocLite() without arguments.