I also checked BiocManager::valid() and everything seems to be OK (TRUE). Installing package into ‘/home/R/x8664-pc-linux-gnu-library/4. Loaded via a namespace (and not attached): stats graphics grDevices utils datasets methods base to return zero if the program finished successfully, or a nonzero exit status if something. LC_MONETARY=English_United States.utf8 LC_NUMERIC=C and that r is the value that the reference r refers to. LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 Running under: Windows 10 圆4 (build 18363) Installation of package ‘38.knownGene’ had non-zero exit statusĪnd here is the sessionInfo(): R version 4.2.0 ( ucrt) ‘C:\Users\AppData\Local\Temp\RtmpKWfcYV\downloaded_packages’ Installing the source package ‘38.knownGene’Ĭontent type 'application/x-gzip' length 44812729 bytes (42.7 MB) Here is the error message again: Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 ( ucrt) GetOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 ( ucrt) Installing package(s) '38.knownGene' installing the source package ‘38.knownGene’ trying URL ' ' Content type 'application/x-gzip' length 44812729 bytes (42.7 MB) downloaded 42.7 MB The downloaded source packages are in ‘C:\Users\AppData\Local\Temp\RtmpsPAYMJ\downloaded_packages’ Warning message: In install.packages(.) : installation of package ‘38.knownGene’ had non-zero exit status Any ideas how I can install the package? Thanks!īiocManager::install("38.knownGene") Unfortunately, the error message is not so helpful. Once confirmed, you can run the install.package('rJava') command.I'm trying to install 38.knownGene package but I fail. If that ran correctly, you should now see both files in /usr/lib64 path: rstats r statistics If this does not work for you, some friend says he solved it through installing the 'Rcpp' package and 'gsl' package. Which should be located at /usr/lib/gcc/x86_64-amazon-linux/4.8.5/libgomp.spec - if so, you can manually create symlinks to fix this: $ sudo ln -s /usr/lib/gcc/x86_64-amazon-linux/4.8.5/libgomp.spec /usr/lib64/ It looks like the installation is requiring libgomp.spec/libgomp.a files, so you can first find that file: $ sudo yum install -y R-java-devel.x86_64Īnd finally, install the necessary XML libraries to support the XML package in R:Īfter which you can then open R (either as root user.) Instead, from a prompt, install R + the necessary development files for later installation of R packages: may be valid for another distro of Linux, but does not appear to be available in the yum repos - running yum search 'r-cran-rjava' returned no results 2) root) for that command 1īut I don't believe that package exists in the available repos (ie. Which will allow you to impersonate the superuser (ie. Is there a way that I can still install these packages?įor Amazon SageMaker notebook Instances, you have the ability to assume root privileges, so instead of: XML is a dependency for multiple R libraries (as is rJava). This issue wasn't reproducible on a local RStudio environment. However, I don't have root access and cannot install as I get the message "You need to be root to perform this command." So this workaround hasn't been possible.Īfter checking the documentation for rJava and XML, I am running the requirements for JDK and other system requirements in SageMaker. Which involves commands such as: yum install r-cran-rjava I found a workaround that could work if I had root access, which is installing via the command line in a terminal. XML is the second package that I have run into this issue with. I have had no issues for the past 6 months whilst using it on my work laptop but since yesterday this has been an issue. “installation of package ‘XML’ had non-zero exit status”Updating HTML index of packages in '.Library' Non-zero exit status issues Having real issues when trying to install ggplot2 package with non-zero exit status for both ‘lifecycle’ and ‘scales’. I've come across two different libraries that result in the following error: Warning message in install.packages("XML", repos = ""): Hi all, I'm having an issue with an R kernel/Jupyter notebook.
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