in your system, start R and enter: Follow Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) If you have a query related to it or one of the replies, start a new topic and refer back with a link. 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 think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Try installing zip, and then loading olsrr. nnet, spatial, survival so I would try to use BiocManager::install("XML"). "After the incident", I started to be more careful not to trip over things. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Thanks! [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: Making statements based on opinion; back them up with references or personal experience. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Citation (from within R, Warning message: 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. Is a PhD visitor considered as a visiting scholar? New replies are no longer allowed. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. I have tried your suggestion and also updating the packages that command indicates. 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 I hope you can see something I can't see and help me solving this issue. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. I've previously written a blog post about this topic, and I can say from experience that installing R packages through conda can cause lots of headaches. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Just realize that I need to write the script "library("DESeq2")" before I proceed. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Post questions about Bioconductor Solution To resolve this error, install the required package as a cluster-installed library. 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. This can take several minutes. I've copied the output below in case it helps with troubleshooting. Why is there a voltage on my HDMI and coaxial cables? Is there a single-word adjective for "having exceptionally strong moral principles"? That plugin is has not been updated to work with later releases of QIIME 2. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Sorry if I missed this, the question was quite long so I kind of skimmed, but I noticed that early on some of the packages were reported as requiring manual compilation from source. there is no package called locfit. Running under: macOS Sierra 10.12.6. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( [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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Is there anyone the same as mine error while loading library(DESeq2)? (Factorization). LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Not the answer you're looking for? What am I doing wrong here in the PlotLegends specification? 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Press CTRL-C to abort.failedUnsatisfiableError: The following specifications were foundto be incompatible with the existing python installation in your environment:Specifications: It also hung on the solving environment for over an hour. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Sign in The best answers are voted up and rise to the top, Not the answer you're looking for? [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 + "htmlTable", "xfun" Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): I'm trying to reproduce your problem, so being as precise as possible is important. Platform: x86_64-apple-darwin13.4.0 (64-bit) First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). .onLoad failed in loadNamespace() for 'rlang', details: 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. 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. I am running a new install of R (3.5.0) and RStudio (1.1.414). installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Erasmus+ funds available! Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Remember to always click on the red Show me the content on this page notice when navigating these older versions. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. The other option is to download and older version of locfit from the package archive and install manually. You are doing something very wrong when installing your packages. 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!!! Finally After 3-4 manual installations of missing packages everything worked. Did you do that? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? It is working now. 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"). Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Any suggestions would be greatly appreciated. One solution is to find all available packages. Feedback Content type 'application/zip' length 233860 bytes (228 KB) Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Also note, however, that the error you got has been associated in the past with mirror outages. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 After 3-4 manual installs everything worked. R version 3.6.1 (2019-07-05) [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Installation instructions to use this How to notate a grace note at the start of a bar with lilypond? Please try the following steps: Quit all R/Rstudio sessions. If you try loading the DEseq2 library now, that might work. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Find centralized, trusted content and collaborate around the technologies you use most. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. To learn more, see our tips on writing great answers. Connect and share knowledge within a single location that is structured and easy to search. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): To add to this, I have also been using DESeq2 recently and ran into the same problem. install.packages("BiocManager"), I get this error: I even tried BiocManager::install("XML") but all failed as shown below. Content type 'application/zip' length 4255589 bytes (4.1 MB) Also make sure that you have RTools.exe installed and working. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Installing Hmisc as suggested above did not solve the issue. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Content type 'application/zip' length 386703 bytes (377 KB) Citation (from within R, enter citation ("DESeq2") ): Installation To install this package, start R (version "4.2") and enter: if (!require ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") BiocManager::install ("DESeq2") For older versions of R, please refer to the appropriate Bioconductor release . Asking for help, clarification, or responding to other answers. a, There are binary versions available but the source versions are later: BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? binary source needs_compilation 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: As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. [1] stats4 parallel stats graphics grDevices utils @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. So, supposedly the issue is with Hmisc. The error states that the current version is 0.4.5 but 0.4.10 is required. I just figured Id ask. Language(R, Python, SQL) And finally, install the problem packages, perhaps also DESeq2. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Installing DESeq2 Error: no package called GenomeInfoDbData, https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz, https://cran.rstudio.com/bin/macosx/contrib/4.0/RcppArmadillo_0.9.880.1.0.tgz, https://cran.rstudio.com/bin/macosx/contrib/4.0/survival_3.1-12.tgz. Installing package(s) 'GenomeInfoDbData' C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 0 packages out-of-date; 2 packages too new, BiocManager::install(c( 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. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Follow Up: struct sockaddr storage initialization by network format-string. [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]]): there is no package called locfit, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy I tried to download the "locfit" package but I can't find it anywhere. The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. How to use Slater Type Orbitals as a basis functions in matrix method correctly? When you load the package, you can observe this error. Bad: conda install -c bioconda bioconductor-deseq2. Asking for help, clarification, or responding to other answers. Is the God of a monotheism necessarily omnipotent? Bioconductor release. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Use MathJax to format equations. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Use of this site constitutes acceptance of our User Agreement and Privacy Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. How do I align things in the following tabular environment? Already on GitHub? - the incident has nothing to do with me; can I use this this way? to one of the following locations: https://code.bioconductor.org/browse/DESeq2/, https://bioconductor.org/packages/DESeq2/, git clone https://git.bioconductor.org/packages/DESeq2, git clone git@git.bioconductor.org:packages/DESeq2. Why are physically impossible and logically impossible concepts considered separate in terms of probability? I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Platform: x86_64-w64-mingw32/x64 (64-bit) Have you tried install.packages("locfit") ? Is there a proper earth ground point in this switch box? In install.packages() : [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8, attached base packages: "htmlTable", "xfun" Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R 2. library(caret) namespace load failed Object sigma not found caret , . install.packages('
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