error: package or namespace load failed for 'deseq2

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") Then I reinstalled R then Rstudio then RTools. From the console install.packages ("rlang") should fix this. . Bioconductor release. 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. C:\R\R-3.4.3\library). Content type 'application/zip' length 233860 bytes (228 KB) Let me confer with the team. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Is the God of a monotheism necessarily omnipotent? Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. 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. library(DESeq2) 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. library(DESeq2) Styling contours by colour and by line thickness in QGIS. This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. 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. Installing package(s) 'htmlTable', 'xfun' You signed in with another tab or window. Policy. I highly recommend that any R/RStudio version not installed inside conda be removed. 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: By clicking Sign up for GitHub, you agree to our terms of service and When an R package depends on a newer package version, the required package is downloaded but not loaded. Just updated my previous R to 4.01 and now I cant load DESeq2. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Running. [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: The other option is to download and older version of locfit from the package archive and install manually. Solution To resolve this error, install the required package as a cluster-installed library. Connect and share knowledge within a single location that is structured and easy to search. After 3-4 manual installs everything worked. 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. New replies are no longer allowed. nnet, spatial, survival. Also make sure that you have RTools.exe installed and working. Use of this site constitutes acceptance of our User Agreement and Privacy How can we prove that the supernatural or paranormal doesn't exist? What am I doing wrong here in the PlotLegends specification? Language(R, Python, SQL) I tried to download the "locfit" package but I can't find it anywhere. Warning: cannot remove prior installation of package xfun Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 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"). Making statements based on opinion; back them up with references or personal experience. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Give up and run everything from the "permitted" library location (e.g. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 there is no package called data.table 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). Error: package GenomeInfoDb could not be loaded. Disconnect between goals and daily tasksIs it me, or the industry? How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Join us at CRISPR workshops in Koper, Slovenia in 2023. 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. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. 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). Is there a proper earth ground point in this switch box? This topic was automatically closed 21 days after the last reply. "4.2") and enter: For older versions of R, please refer to the appropriate Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Remember to always click on the red Show me the content on this page notice when navigating these older versions. Convince your IT department to relax the permissions for R packages [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Are there tables of wastage rates for different fruit and veg? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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: [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 so I would try to use BiocManager::install("XML"). [7] edgeR_3.16.5 limma_3.30.12 Looking for incompatible packages.This can take several minutes. there is no package called locfit. Whats the grammar of "For those whose stories they are"? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? "htmlTable", "xfun" [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 I'm having a similar error, but different package: library("DESeq2") [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: [7] datasets methods base, other attached packages: In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use, and would ask more Bioconductor-related questions on the Bioconductor support site. I'm trying to reproduce your problem, so being as precise as possible is important. Please read the posting Post questions about Bioconductor If you try loading the DEseq2 library now, that might work. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 [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: there is no package called Hmisc. Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. What is a word for the arcane equivalent of a monastery? Use MathJax to format equations. 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. a, There are binary versions available but the source versions are later: unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': ERROR: lazy loading failed for package Hmisc [a/s/n]: trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 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. Not the answer you're looking for? But I guess you have many problems with your installation, and I'd suggest. When an R package depends on a newer package version, the required package is downloaded but not loaded. 2. This article explains how to resolve the package or namespace loading error. When you load the package, you can observe this error. running multiple versions of the same package, keeping separate libraries for some projects). Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Policy. The best answers are voted up and rise to the top, Not the answer you're looking for? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 1. It is working now. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Connect and share knowledge within a single location that is structured and easy to search. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Why do academics stay as adjuncts for years rather than move around? I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Did you do that? Policy. 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). Thanks for your suggestion. What do I need to do to reproduce your problem? Any other suggestion? Citation (from within R, 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. The package has place the R version constraint. .onLoad failed in loadNamespace() for 'rlang', details: Sorry, I'm newbie. Just realize that I need to write the script "library("DESeq2")" before I proceed. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Is there a single-word adjective for "having exceptionally strong moral principles"? Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. In install.packages() : To learn more, see our tips on writing great answers. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Looking for incompatible packages. 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. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Policy. 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 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 [5] IRanges_2.8.1 S4Vectors_0.12.1 [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 One solution is to find all available packages. If it fails, required operating system facilities are missing. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. A place where magic is studied and practiced? downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' [69] tidyselect_1.0.0. library(caret) namespace load failed Object sigma not found caret , . Feedback What is the output of. Connect and share knowledge within a single location that is structured and easy to search. I have tried your suggestion and also updating the packages that command indicates. - the incident has nothing to do with me; can I use this this way? Thanks for contributing an answer to Bioinformatics Stack Exchange! I would recommend installing an older version of QIIME 2 for this plugin to work. 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. How do you ensure that a red herring doesn't violate Chekhov's gun? I also tried something I found on google: but the installation had errors too, I can write them here if needed. Please try the following steps: Quit all R/Rstudio sessions. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. More info about Internet Explorer and Microsoft Edge. Finally After 3-4 manual installations of missing packages everything worked. Use of this site constitutes acceptance of our User Agreement and Privacy Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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]]) : Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Platform: x86_64-w64-mingw32/x64 (64-bit) 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. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 March 1, 2023, 8:52pm Why is there a voltage on my HDMI and coaxial cables? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. 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. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()'

error: package or namespace load failed for 'deseq2 2023