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Browse other questions tagged, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site. Your best bet would be to download the package source code and change the R version and install manually if you wanted the most recent version of locfit to install on your computer. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Then I reinstalled R then Rstudio then RTools. Making statements based on opinion; back them up with references or personal experience. Solution To resolve this error, install the required package as a cluster-installed library. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Asking for help, clarification, or responding to other answers. Why do many companies reject expired SSL certificates as bugs in bug bounties? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. rev2023.3.3.43278. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Styling contours by colour and by line thickness in QGIS. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Why do academics stay as adjuncts for years rather than move around? [7] datasets methods base, other attached packages: The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. I want to import DESeq2 in Rstudio though and it is giving me a different error when I try importing DESeq2: Error in library("DESeq2") : there is no package called DESeq2. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Now loading the DESeq2 library (Errors): Because I already installed >10 packages by hand I assume the solution is not to keep installing the missing packages because those packages will have more missing packages and more and more and I won't get out of this loop. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Open Source Biology & Genetics Interest Group. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'locfit' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. Old packages: 'RcppArmadillo', 'survival' ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Well occasionally send you account related emails. Finally After 3-4 manual installations of missing packages everything worked. [7] edgeR_3.16.5 limma_3.30.12 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. By clicking Sign up for GitHub, you agree to our terms of service and Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [40] assertthat_0.1 rpart_4.1-10 nnet_7.3-12, It should not be necessary (R should take care of loading dependencies) but try installating data.table also. https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6: https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/PACKAGES', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip', User Agreement and Privacy When an R package depends on a newer package version, the required package is downloaded but not loaded. Is a PhD visitor considered as a visiting scholar? Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. May I know is there any other approach I can try? In install.packages() : BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Why do academics stay as adjuncts for years rather than move around? Connect and share knowledge within a single location that is structured and easy to search. Not the answer you're looking for? As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Is there anything I can do to speed it up? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Sounds like there might be an issue with conda setup? - the incident has nothing to do with me; can I use this this way? Whats the grammar of "For those whose stories they are"? survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in As mentioned above, my institutional IT can replicate this on a laptop with a completely fresh R install and no prior package installations (meaning isn't to do with installing with another version of the package already running). [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. When you install and load some libraries in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. Why are physically impossible and logically impossible concepts considered separate in terms of probability? [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. To resolve this error, install the required package as a cluster-installed library. and then updating the packages that command indicates. It only takes a minute to sign up. How to notate a grace note at the start of a bar with lilypond? Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib now when I tried installing the missing packages they did install. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Please try the following steps: Quit all R/Rstudio sessions. "4.2") and enter: For older versions of R, please refer to the appropriate As such there are two solutions that may be more or less attainable given your own IT system. Join us at CRISPR workshops in Koper, Slovenia in 2023. [13] ggplot23.3.0 car3.0-7 carData3.0-3 I am using the latest stable LAMMPS version (updated 17th Feb 2023) Also I am having troubles with the CMAKE unit testing, in particular for the force styles. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? CRAN: https://mirrors.sjtug.sjtu.edu.cn/cran/, Bioconductor version 3.12 (BiocManager 1.30.17), R 4.0.3 (2020-10-10), Old packages: 'cli', 'dplyr', 'igraph', 'MASS', 'ps', 'RSQLite', 'testthat', 'tibble', package locift is not available for Bioconductor version '3.12', A version of this package for your version of R might be available elsewhere,see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. What is the output of. I installed the package successfully with conda, but Rstudio is apparently does not know about it. I tried to download the "locfit" package but I can't find it anywhere. In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use, and would ask more Bioconductor-related questions on the Bioconductor support site. If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead of the one you've installed via conda. package rlang was built under R version 3.5.1. Please remember to confirm an answer once you've received one. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I highly recommend that any R/RStudio version not installed inside conda be removed. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R "After the incident", I started to be more careful not to trip over things. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR A place where magic is studied and practiced? Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Bioconductor release. to allow custom library locations. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 No error messages are returned. @Tung I've updated my R and RStudio versions (unfortunately I had to first convince my workplace to approve them) and installed the packages through R 3.5.1 however, I'm still getting the same rlang error. I've copied the output below in case it helps with troubleshooting. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. "htmlTable", "xfun" install.packages ("zip") Author: Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd], Maintainer: Michael Love . [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and try to import DESeq2 I am getting the error message: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Thanks for contributing an answer to Stack Overflow! I just figured Id ask. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on.