library(caret) namespace load failed Object sigma not found caret , . Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Content type 'application/zip' length 233860 bytes (228 KB) (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 . im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. The package has place the R version constraint. What do I need to do to reproduce your problem? 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: But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () 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. And finally, install the problem packages, perhaps also DESeq2. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 I installed the package successfully with conda, but Rstudio is apparently does not know about it. Warning: cannot remove prior installation of package xfun install.packages("BiocManager"), I get this error: I was assuming that to be the case. Thanks! nnet, spatial, survival. Why do academics stay as adjuncts for years rather than move around? Thank you @hharder. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. 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? Statistics ; Algorithm(ML, DL,.) Why is this sentence from The Great Gatsby grammatical? /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages library(DESeq2) The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). call: dots_list() sessionInfo() Solving environment: Found conflicts! Acidity of alcohols and basicity of amines. [16] phyloseq1.30.0, loaded via a namespace (and not attached): [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 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 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. If it fails, required operating system facilities are missing. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) + ), update = TRUE, ask = FALSE) Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? if (!require("BiocManager", quietly = TRUE)) Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. 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 . Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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. Connect and share knowledge within a single location that is structured and easy to search. Installing package(s) 'GenomeInfoDbData' This article explains how to resolve the package or namespace loading error. Making statements based on opinion; back them up with references or personal experience. In file.copy(savedcopy, lib, recursive = TRUE) : [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Surly Straggler vs. other types of steel frames. Disconnect between goals and daily tasksIs it me, or the industry? Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. MathJax reference. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 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. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide, You can try installing packages in R (which comes with R 3.5.1, not RStudio). 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!!! It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Start R to confirm they are gone. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Does a summoned creature play immediately after being summoned by a ready action? How to use Slater Type Orbitals as a basis functions in matrix method correctly? ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: 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. 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. 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: 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: Is a PhD visitor considered as a visiting scholar? This includes any installed libraries. I tried to download the "locfit" package but I can't find it anywhere. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. I would like to install DESeq2 for DE analysis. I just figured Id ask. package in your R session. I tried again and again was met with missing packages BUT!!! Thanks for contributing an answer to Stack Overflow! How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. data . Warning message: 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. Asking for help, clarification, or responding to other answers. Policy. If not fixed, Try removing remove.packages (rlang) then. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 How do I align things in the following tabular environment? [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 so I would try to use BiocManager::install("XML"). install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. ERROR: dependency Hmisc is not available for package DESeq2 [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 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. It only takes a minute to sign up. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Looking for incompatible packages. Sign in Making statements based on opinion; back them up with references or personal experience. Update all/some/none? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . I'm having a similar error, but different package: library("DESeq2") [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Styling contours by colour and by line thickness in QGIS. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. This can take several minutes. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Post questions about Bioconductor Installing package(s) 'XML' Is there a proper earth ground point in this switch box? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc package rlang was built under R version 3.5.1. Not the answer you're looking for? Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Installation instructions to use this - the incident has nothing to do with me; can I use this this way? 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 [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 to allow custom library locations. 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). 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. Language(R, Python, SQL) As such there are two solutions that may be more or less attainable given your own IT system. Retrying with flexible solve.Solving environment: Found conflicts! To add to this, I have also been using DESeq2 recently and ran into the same problem. Running under: macOS Catalina 10.15.3, Matrix products: default and then updating the packages that command indicates. Join us at CRISPR workshops in Koper, Slovenia in 2023. [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 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Bioconductor release. You are doing something very wrong when installing your packages. 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. Learn more about Stack Overflow the company, and our products. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Just realize that I need to write the script "library("DESeq2")" before I proceed. What am I doing wrong here in the PlotLegends specification? [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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"). March 1, 2023, 3:25pm Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): it would be good to hear any speculation you have of how this might have happened). in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Not the answer you're looking for? Platform: x86_64-apple-darwin17.0 (64-bit) there is no package called data.table Just to add on -- do you require an old version of Bioconductor for your current project? there is no package called Hmisc. [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: [7] edgeR_3.16.5 limma_3.30.12 Running under: Windows 10 x64 (build 18362), locale: Have a question about this project? Citation (from within R, Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Installing package(s) 'htmlTable', 'xfun' I would recommend installing an older version of QIIME 2 for this plugin to work. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Follow Up: struct sockaddr storage initialization by network format-string. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: If you try loading the DEseq2 library now, that might work. there is no package called Hmisc. Loading required package: GenomicRanges Use of this site constitutes acceptance of our User Agreement and Privacy Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat [a/s/n]: Well occasionally send you account related emails. (Factorization). Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I am using R 3.6.1 and Rstudio 1.2. technocrat August 27, 2020, 10:15pm #2 RedRabbit: DESeq2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Warning message: 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 . New replies are no longer allowed. How can we prove that the supernatural or paranormal doesn't exist? 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. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Please read the posting March 1, 2023, 4:56pm [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Is there a single-word adjective for "having exceptionally strong moral principles"? How do you ensure that a red herring doesn't violate Chekhov's gun? Hello, I tried installing DESeq2 using: but it run into a lot of errors (some missing packages for some dependency packages etc) Then I tried installing all the missing packages manually by downloading from CREN and installing the missing packages from .zip files. there is no package called locfit. Platform: x86_64-apple-darwin15.6.0 (64-bit) Platform: x86_64-w64-mingw32/x64 (64-bit) 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. What is the output of. To learn more, see our tips on writing great answers. Any other suggestion? 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. More info about Internet Explorer and Microsoft Edge. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Whats the grammar of "For those whose stories they are"? Making statements based on opinion; back them up with references or personal experience. 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]]): 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. From the console install.packages ("rlang") should fix this. Running. 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"). Also note, however, that the error you got has been associated in the past with mirror outages. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. [5] IRanges_2.8.1 S4Vectors_0.12.1 Sorry, I'm newbie. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. 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. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. 9. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Thanks for contributing an answer to Stack Overflow! Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. R version 3.6.3 (2020-02-29) Why do many companies reject expired SSL certificates as bugs in bug bounties? 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. binary source needs_compilation The other option is to download and older version of locfit from the package archive and install manually. Let me confer with the team. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages R version 4.0.1 (2020-06-06) Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Choose Yes. Sounds like there might be an issue with conda setup? installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat When you load the package, you can observe this error. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. rev2023.3.3.43278. R version 3.6.1 (2019-07-05) Is there anything I can do to speed it up? ERROR: lazy loading failed for package Hmisc [69] tidyselect_1.0.0. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Loading required package: GenomeInfoDb