So if you still get this error try changing your CRAN mirror. Why is this sentence from The Great Gatsby grammatical? This topic was automatically closed 21 days after the last reply. Any suggestions would be greatly appreciated. March 1, 2023, 4:56pm New replies are no longer allowed. The best answers are voted up and rise to the top, Not the answer you're looking for? and then updating the packages that command indicates. The package has place the R version constraint. Warning: restored xfun, The downloaded binary packages are in Give up and run everything from the "permitted" library location (e.g. From the console install.packages ("rlang") should fix this. Are there tables of wastage rates for different fruit and veg? requires R 4 and running more than a couple of releases behind in R risks multiplying problems. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Making statements based on opinion; back them up with references or personal experience. Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'GenomeInfoDbData' Error: package 'GenomeInfoDb' could not be loaded 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: 1 RR. R https://www.jianshu.com/p/d9ca5a66cb72?v=1676346790161 2 ``` library (tidyverse) Error: package or namespace load failed for 'tidyverse' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'cli' 3.3.0>= 3.4.1 In addition: Warning message: Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. 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. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. 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. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Statistics ; Algorithm(ML, DL,.) Find centralized, trusted content and collaborate around the technologies you use most. I would like to install DESeq2 for DE analysis. Is there anything I can do to speed it up? install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). If you have a query related to it or one of the replies, start a new topic and refer back with a link. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Traffic: 307 users visited in the last hour, I am new to all this! Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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]]): Glad everything is finally working now. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 How can we prove that the supernatural or paranormal doesn't exist? nnet, spatial, survival. Hey, I tried your suggestion and it didn't work as it is but I did figure it out probably with the help of your suggestion. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 If you try loading the DEseq2 library now, that might work. Any other suggestion? there is no package called locfit. privacy statement. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. 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. In file.copy(savedcopy, lib, recursive = TRUE) : I would suggest to install data.table, lme4 and all of the packages denoted in the 2 statements that said Packages which are only available in source form, and may need compilation of C/C++/Fortran: with pacman then re-run the Bioconductor installation of your target package. When an R package depends on a newer package version, the required package is downloaded but not loaded. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? What do I need to do to reproduce your problem? I can download DESeq2 using, User Agreement and Privacy [13] ggplot23.3.0 car3.0-7 carData3.0-3 9. I would recommend installing an older version of QIIME 2 for this plugin to work. 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. Finally After 3-4 manual installations of missing packages everything worked. Fortunately I was able to solve it by doing things from several suggested solutions. 1. @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. How to notate a grace note at the start of a bar with lilypond? Assuming that your conda environment name is renv, try running this in the terminal: This should open up the Rstudio interface, like normal, but using everything defined in your renv environment. 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? To learn more, see our tips on writing great answers. Replacing broken pins/legs on a DIP IC package. May I know is there any other approach I can try? Try installing zip, and then loading olsrr. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. In install.packages() : Well occasionally send you account related emails. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked I hope you can see something I can't see and help me solving this issue. 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). Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. if (!require("BiocManager", quietly = TRUE)) . To view documentation for the version of this package installed [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Making statements based on opinion; back them up with references or personal experience. Thanks! Learn more about Stack Overflow the company, and our products. (I have the most recent version of tidyverse, RStudio, and R.) Error: package or namespace load failed for 'tidyverse': .onAttach failed in attachNamespace() for 'tidyverse', details: call: glue(str, .envir = .envir, .transformer = transformer . [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 I then launched the R application (from the finder, not RStudio) and installed BiocManager. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 [16] phyloseq1.30.0, loaded via a namespace (and not attached): Then I reinstalled R then Rstudio then RTools. Have you tried install.packages("locfit") ? Just realize that I need to write the script "library("DESeq2")" before I proceed. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 installation of package GenomeInfoDbData had non-zero exit status. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? I thought that working in a new environment would help, but it didnt. Error in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]) : there is no package called 'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Connect and share knowledge within a single location that is structured and easy to search. Press CTRL-C to abort. 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'. 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. No error messages are returned. Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Is a PhD visitor considered as a visiting scholar? running multiple versions of the same package, keeping separate libraries for some projects). I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. I guess that means we can finally close this issue. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) failed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: q2-aldex2 -> python=3.6 Your python: python=3.8.15 I've copied the output below in case it helps with troubleshooting. Erasmus+ funds available! [7] datasets methods base, other attached packages: [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Is there a proper earth ground point in this switch box? [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 I noticed that you are trying to install qiime2-2019.4, this may not work as ALDEx2 was made for qiime2-2019.7 as outlined here, up to and including the versions I mentioned earlier. Are you sure the R you're running from the command line is installed through Anaconda as well? 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 'XML' so I would try to use BiocManager::install ("XML"). In addition: Warning message: Convince your IT department to relax the permissions for R packages so I would try to use BiocManager::install("XML"). Does a summoned creature play immediately after being summoned by a ready action? Why are physically impossible and logically impossible concepts considered separate in terms of probability? Connect and share knowledge within a single location that is structured and easy to search. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. How do you ensure that a red herring doesn't violate Chekhov's gun? BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib there is no package called GenomeInfoDbData