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. Sounds like there might be an issue with conda setup? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 "After the incident", I started to be more careful not to trip over things. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? MathJax reference. Then I reinstalled R then Rstudio then RTools. This includes any installed libraries. Why are physically impossible and logically impossible concepts considered separate in terms of probability? Traffic: 307 users visited in the last hour, https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz', https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'. Give up and run everything from the "permitted" library location (e.g. Why do many companies reject expired SSL certificates as bugs in bug bounties? Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, sessionInfo() Well occasionally send you account related emails. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Whats the grammar of "For those whose stories they are"? In install.packages() : 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. Not the answer you're looking for? I then launched the R application (from the finder, not RStudio) and installed BiocManager. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I tried to get a whole new environment and install an old version of Qiime but I still got a ton of conflicts and it didnt install. Policy. To view documentation for the version of this package installed [7] edgeR_3.16.5 limma_3.30.12 I installed the package successfully with conda, but Rstudio is apparently does not know about it. If you preorder a special airline meal (e.g. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Replacing broken pins/legs on a DIP IC package. there is no package called data.table I'm running into some bad problems installing and using the DESeq2 package for R. I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7. By clicking Sign up for GitHub, you agree to our terms of service and Following successful installation of backports BiocManager::install ("DESeq2") will succeed under I'm trying to reproduce your problem, so being as precise as possible is important. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. How do you ensure that a red herring doesn't violate Chekhov's gun? When an R package depends on a newer package version, the required package is downloaded but not loaded. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. I was assuming that to be the case. How to use Slater Type Orbitals as a basis functions in matrix method correctly? I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! 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: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. 2. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Error in R: (Package which is only available in source form, and may need compilation of C/C++/Fortran), Loading BioConductor library "GO.db" fails, Installing R packages from a local repo (all .tar.gz files have been downloaded there), Cannot remove prior installation of package, but package not found, I can't seem to install the 'ecospat' package on R studio for windows, I am unable to install ggplot, there occurs some error. Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. To learn more, see our tips on writing great answers. Do I need a thermal expansion tank if I already have a pressure tank? While a notebook is attached to a cluster, the R namespace cannot be refreshed. I've copied the output below in case it helps with troubleshooting. Just updated my previous R to 4.01 and now I cant load DESeq2. Running under: Windows 10 x64 (build 18362), locale: Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Convince your IT department to relax the permissions for R packages ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 9. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): I have tried your suggestion and also updating the packages that command indicates. Asking for help, clarification, or responding to other answers. Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or? In addition: Warning message: Is a PhD visitor considered as a visiting scholar? Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? This is the beauty of installing QIIME 2 via conda, you can have many different versions of QIIME 2 on your system at the same time and activate the version you want to use. Looking for incompatible packages.This can take several minutes. vegan) just to try it, does this inconvenience the caterers and staff? What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. This topic was automatically closed 21 days after the last reply. Content type 'application/zip' length 4255589 bytes (4.1 MB) rev2023.3.3.43278. Installing packages directly into that location fixes the issue but is not desirable for all the reasons that people might want to use custom locations (e.g. but when I go to load the libraries I get this error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : Have a question about this project? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Warning message: What is the output of. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Find centralized, trusted content and collaborate around the technologies you use most. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? nnet, spatial, survival By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Bad: conda install -c bioconda bioconductor-deseq2. I tried to install Python 3.6 and got 1000s of lines of conflicts, and python version still returns 3.8. when I switch back to my Qiime environment to install Aldex2, I get an error. Warning message: [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Policy. What do I need to do to reproduce your problem? [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 Does anyone know why I'm getting the following message when I load tidyverse in a new session. Does a summoned creature play immediately after being summoned by a ready action? [5] IRanges_2.8.1 S4Vectors_0.12.1 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Sounds like you might have an issue with which R Rstudio is running. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Thanks for contributing an answer to Stack Overflow! [69] tidyselect_1.0.0. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Should I update the Bioconductor to latest version instead? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed.
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