I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Did you do that? 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. 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): So, supposedly the issue is with Hmisc. 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. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Policy. library(DESeq2) Sounds like there might be an issue with conda setup? ()library(DESeq2):Error in loadNamespace: no package called ""s I thought that working in a new environment would help, but it didnt. This topic was automatically closed 21 days after the last reply. How do you ensure that a red herring doesn't violate Chekhov's gun? 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. running multiple versions of the same package, keeping separate libraries for some projects). Any other suggestion? Sounds like you might have an issue with which R Rstudio is running. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Warning message: 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. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Find centralized, trusted content and collaborate around the technologies you use most. [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. Resolving package or namespace loading error Is it suspicious or odd to stand by the gate of a GA airport watching the planes? New replies are no longer allowed. Is there a proper earth ground point in this switch box? @artembus Sounds like it was a ton of work! Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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. Open Source Biology & Genetics Interest Group. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Have you tried install.packages("locfit") ? sessionInfo() I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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 . Thanks for contributing an answer to Bioinformatics Stack Exchange! downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked You are doing something very wrong when installing your packages. [13] ggplot23.3.0 car3.0-7 carData3.0-3 [7] edgeR_3.16.5 limma_3.30.12 to allow custom library locations. Asking for help, clarification, or responding to other answers. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : I'm trying to reproduce your problem, so being as precise as possible is important. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Thnaks anyway, Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems, How Intuit democratizes AI development across teams through reusability. Are you sure the R you're running from the command line is installed through Anaconda as well? Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R 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 As such there are two solutions that may be more or less attainable given your own IT system. Making statements based on opinion; back them up with references or personal experience. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Use MathJax to format equations. 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. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in 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. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 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: DESeq2: Error: package or namespace load failed for 'DESeq2': objects How to use Slater Type Orbitals as a basis functions in matrix method correctly? However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. [16] phyloseq1.30.0, loaded via a namespace (and not attached): What is a word for the arcane equivalent of a monastery? so I would try to use BiocManager::install("XML"). privacy statement. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: vegan) just to try it, does this inconvenience the caterers and staff? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? March 1, 2023, 8:52pm Is the God of a monotheism necessarily omnipotent? [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Thanks for contributing an answer to Stack Overflow! 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 Is there anyone the same as mine error while loading library(DESeq2)? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. library(caret) namespace load failed Object sigma not In install.packages() : More info about Internet Explorer and Microsoft Edge. Then I reinstalled R then Rstudio then RTools. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Thanks! ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 [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: there is no package called GenomeInfoDbData Finally After 3-4 manual installations of missing packages everything worked. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Error when installing Aldex2 - Community Plugin Support - Open Source [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: 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]]) : [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Use of this site constitutes acceptance of our User Agreement and Privacy 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: Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Running under: macOS Sierra 10.12.6. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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. "After the incident", I started to be more careful not to trip over things. I'd take a look at need, to see if there are any insights to be had, so that you can correct the root problem rather than having to do this procedure with other packages. MathJax reference. If you try loading the DEseq2 library now, that might work. DESeq2_2301_76497647-CSDN To learn more, see our tips on writing great answers. How can I fix error with loading package in R ? | ResearchGate By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Thanks for contributing an answer to Stack Overflow! Press CTRL-C to abort. Running under: macOS Catalina 10.15.3, Matrix products: default Making statements based on opinion; back them up with references or personal experience. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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. That plugin is has not been updated to work with later releases of QIIME 2. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 When an R package depends on a newer package version, the required package is downloaded but not loaded. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Hello, R version 3.6.3 (2020-02-29) May be the version has problem How can I do ? To resolve this error, install the required package as a cluster-installed library. Bioconductor - DESeq2 [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 I then launched the R application (from the finder, not RStudio) and installed BiocManager. I would like to install DESeq2 for DE analysis. Not the answer you're looking for? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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 it would be good to hear any speculation you have of how this might have happened). [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) If I run install.packages(GenomeInfoDb) from R console, it is telling me that the package is not available for R version 3.5.1. rev2023.3.3.43278. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 there is no package called Hmisc. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Citation (from within R, How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Then I reinstalled R then Rstudio then RTools. 9. Let me confer with the team. Learn more about Stack Overflow the company, and our products. The other option is to download and older version of locfit from the package archive and install manually. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [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: downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' To add to this, I have also been using DESeq2 recently and ran into the same problem. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages So if you still get this error try changing your CRAN mirror. biocLite(), install.packages() (and the devtools equivalent?) Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. One solution is to find all available packages. R| - 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: Error: package GenomeInfoDb could not be loaded. Join us at CRISPR workshops in Koper, Slovenia in 2023. Have a question about this project? 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. Is a PhD visitor considered as a visiting scholar? Platform: x86_64-apple-darwin17.0 (64-bit) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): nnet, spatial, survival. March 1, 2023, 3:25pm - the incident has nothing to do with me; can I use this this way? error: object 'rlang_dots_list' not found [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: The best answers are voted up and rise to the top, Not the answer you're looking for? Is there a single-word adjective for "having exceptionally strong moral principles"? rev2023.3.3.43278. and then updating the packages that command indicates. Traffic: 307 users visited in the last hour, I am new to all this! Styling contours by colour and by line thickness in QGIS. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 problem copying C:\Users\ASUS\Documents\R\win-library\3.6\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\ASUS\Documents\R\win-library\3.6\xfun\libs\x64\xfun.dll: Permission denied, BiocManager::install("XML") Running under: Windows 10 x64 (build 18362), locale: Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). 0 packages out-of-date; 2 packages too new, BiocManager::install(c( DESeq2 - I can't get the library to load - Bioconductor Why do academics stay as adjuncts for years rather than move around? [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 But I guess you have many problems with your installation, and I'd suggest. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open You signed in with another tab or window. How to use Slater Type Orbitals as a basis functions in matrix method correctly? The error states that the current version is 0.4.5 but 0.4.10 is required. If it fails, required operating system facilities are missing. Looking for incompatible packages.This can take several minutes. [5] IRanges_2.8.1 S4Vectors_0.12.1 ERROR: dependency Hmisc is not available for package DESeq2 A place where magic is studied and practiced? in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE installation of package GenomeInfoDbData had non-zero exit status. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages This includes any installed libraries. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages I was assuming that to be the case. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 now when I tried installing the missing packages they did install. I just figured Id ask. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. I also tried something I found on google: but the installation had errors too, I can write them here if needed. install.packages ("zip") May I know is there any other approach I can try? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Installing Hmisc as suggested above did not solve the issue. Whats the grammar of "For those whose stories they are"? I have tried your suggestion and also updating the packages that command indicates. data . Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Use of this site constitutes acceptance of our User Agreement and Privacy check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Making statements based on opinion; back them up with references or personal experience. 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 [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 . I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. 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). enter citation("DESeq2")): To install this package, start R (version Please read the posting Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) I again tried the installation with biocLite but was met with errors of missing packages (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors) so I changed the CRAN mirror in RStudio. Sign in This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. to your account. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. guide. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. "After the incident", I started to be more careful not to trip over things. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 I am also encountering a set of similar (although possible totally unrelated) issue with other packages, RStudio provides the following warning every startup, library(devtools) gives the following errors, Someone on twitter asked for the results of packageDescription("rlang"). How do I align things in the following tabular environment? It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Use this. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 install.packages("BiocManager"), I get this error: Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Installing package(s) 'GenomeInfoDbData' 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 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Also make sure that you have RTools.exe installed and working. 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. Feedback Error: package or namespace load failed, object not found 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 If you preorder a special airline meal (e.g. [1] stats4 parallel stats graphics grDevices utils I'm having a similar error, but different package: library("DESeq2") Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. R DESeq2 - Policy. 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 In addition: Warning message: Policy. package xfun successfully unpacked and MD5 sums checked Install DESeq2 through anaconda - Bioinformatics Stack Exchange What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? I guess that means we can finally close this issue. 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. Also note, however, that the error you got has been associated in the past with mirror outages.
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