error: package or namespace load failed for 'deseq2
-error: package or namespace load failed for 'deseq2
error: object 'rlang_dots_list' not found [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. 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"). It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so I even tried BiocManager::install("XML") but all failed as shown below. Why do academics stay as adjuncts for years rather than move around? Citation (from within R, Is there anyone the same as mine error while loading library(DESeq2)? downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Does anyone know why I'm getting the following message when I load tidyverse in a new session. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. there is no package called data.table Making statements based on opinion; back them up with references or personal experience. Policy. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I tried again and again was met with missing packages BUT!!! [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Old packages: 'RcppArmadillo', 'survival' Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. 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. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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). [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Is there anything I can do to speed it up? library(DESeq2) + ), update = TRUE, ask = FALSE) MathJax reference. I tried following the instructions for 2019.7 as well and I am getting the same error. To add to this, I have also been using DESeq2 recently and ran into the same problem. sessionInfo() Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Loading required package: GenomicRanges binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 That plugin is has not been updated to work with later releases of QIIME 2. Policy. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Finally After 3-4 manual installations of missing packages everything worked. Error: package GenomeInfoDb could not be loaded. R version 4.0.1 (2020-06-06) It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Language(R, Python, SQL) Installing package(s) 'htmlTable', 'xfun' So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. package in your R session. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. I'm trying to reproduce your problem, so being as precise as possible is important. When an R package depends on a newer package version, the required package is downloaded but not loaded. While a notebook is attached to a cluster, the R namespace cannot be refreshed. "After the incident", I started to be more careful not to trip over things. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 [16] phyloseq1.30.0, loaded via a namespace (and not attached): Installation instructions to use this I was assuming that to be the case. I hope you can see something I can't see and help me solving this issue. If it fails, required operating system facilities are missing. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Asking for help, clarification, or responding to other answers. Warning message: Is a PhD visitor considered as a visiting scholar? 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: or install using BiocManager that will also install CRAN packages BiocManager::install('locfit'), I couldn't intall locfit but somehow, i did so many different things and it worked. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Do I need a thermal expansion tank if I already have a pressure tank? - the incident has nothing to do with me; can I use this this way? Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? A place where magic is studied and practiced? Not the answer you're looking for? Use of this site constitutes acceptance of our User Agreement and Privacy [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( "After the incident", I started to be more careful not to trip over things. In addition: Warning message: install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 + "htmlTable", "xfun" - the incident has nothing to do with me; can I use this this way? May I know is there any other approach I can try? 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. enter citation("DESeq2")): To install this package, start R (version When you load the package, you can observe this error. Policy. Sounds like you might have an issue with which R Rstudio is running. 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. Thanks! I just figured Id ask. The error states that the current version is 0.4.5 but 0.4.10 is required. [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: Warning message: I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. This article explains how to resolve the package or namespace loading error. 1. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Running under: macOS Catalina 10.15.3, Matrix products: default Find centralized, trusted content and collaborate around the technologies you use most. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in to your account. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Why are physically impossible and logically impossible concepts considered separate in terms of probability? rev2023.3.3.43278. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? I would recommend installing an older version of QIIME 2 for this plugin to work. 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. March 1, 2023, 7:31pm Not the answer you're looking for? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) library(caret) namespace load failed Object sigma not found caret , . [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Warning: cannot remove prior installation of package xfun R version 3.6.3 (2020-02-29) Please try reinstalling rlang on a fresh session. [a/s/n]: Sign in I have tried your suggestion and also updating the packages that command indicates. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Connect and share knowledge within a single location that is structured and easy to search. 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 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Did you do that? install.packages ("zip") How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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. Loading required package: GenomeInfoDb Does a summoned creature play immediately after being summoned by a ready action? privacy statement. To learn more, see our tips on writing great answers. Press CTRL-C to abort. 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 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. Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in If you try loading the DEseq2 library now, that might work. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Choose Yes. Just updated my previous R to 4.01 and now I cant load DESeq2. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 0 packages out-of-date; 2 packages too new, BiocManager::install(c( As such there are two solutions that may be more or less attainable given your own IT system. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Why is there a voltage on my HDMI and coaxial cables? Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Running under: Windows 10 x64 (build 18362), locale: I installed the package successfully with conda, but Rstudio is apparently does not know about it. Use of this site constitutes acceptance of our User Agreement and Privacy biocLite(), install.packages() (and the devtools equivalent?) Styling contours by colour and by line thickness in QGIS. Statistics ; Algorithm(ML, DL,.) Looking for incompatible packages. Should I update the Bioconductor to latest version instead? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. so I would try to use BiocManager::install("XML"). Find centralized, trusted content and collaborate around the technologies you use most. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under rev2023.3.3.43278. Then I reinstalled R then Rstudio then RTools. I highly recommend that any R/RStudio version not installed inside conda be removed. 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. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Sorry, I'm newbie. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? @KonradRudolph It's pacman (not packman) and you are correct in that it's basically just a wrapper for, Thanks for your suggestion, I tried doing this step by step as you said but the biocLite command still did throw errors for missing packages. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Solving environment: Found conflicts! How can we prove that the supernatural or paranormal doesn't exist? downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Whats the grammar of "For those whose stories they are"? What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 So if you still get this error try changing your CRAN mirror. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Thanks for contributing an answer to Stack Overflow! Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. sessionInfo() More info about Internet Explorer and Microsoft Edge. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 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. How to use Slater Type Orbitals as a basis functions in matrix method correctly? there is no package called locfit. 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]]): You are doing something very wrong when installing your packages. there is no package called Hmisc. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. package xfun successfully unpacked and MD5 sums checked 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. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) You signed in with another tab or window. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Asking for help, clarification, or responding to other answers. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 How do I align things in the following tabular environment? Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. 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. to allow custom library locations. Platform: x86_64-apple-darwin13.4.0 (64-bit) Warning: restored xfun, The downloaded binary packages are in [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 It only takes a minute to sign up. Sounds like there might be an issue with conda setup? Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. (Factorization). running multiple versions of the same package, keeping separate libraries for some projects). [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 (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 . By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Solution To resolve this error, install the required package as a cluster-installed library. CRAN: https://mirrors.sjtug.sjtu.edu.cn/cran/, Bioconductor version 3.12 (BiocManager 1.30.17), R 4.0.3 (2020-10-10), Old packages: 'cli', 'dplyr', 'igraph', 'MASS', 'ps', 'RSQLite', 'testthat', 'tibble', package locift is not available for Bioconductor version '3.12', A version of this package for your version of R might be available elsewhere,see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. 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 Please remember to confirm an answer once you've received one. Connect and share knowledge within a single location that is structured and easy to search. "htmlTable", "xfun" Erasmus+ funds available! If you preorder a special airline meal (e.g. 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. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. 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 [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: Also make sure that you have RTools.exe installed and working. 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. March 1, 2023, 4:56pm 2. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? "4.2") and enter: For older versions of R, please refer to the appropriate Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' March 1, 2023, 3:25pm I guess that means we can finally close this issue. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 To resolve this error, install the required package as a cluster-installed library. there is no package called GenomeInfoDbData What do I need to do to reproduce your problem? 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.