error: package or namespace load failed for 'deseq2

[9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Platform: x86_64-w64-mingw32/x64 (64-bit) to allow custom library locations. 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. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): As such there are two solutions that may be more or less attainable given your own IT system. :), BiocManager::install("locift") Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Are there tables of wastage rates for different fruit and veg? Old packages: 'RcppArmadillo', 'survival' The error states that the current version is 0.4.5 but 0.4.10 is required. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? @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. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 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 downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: If you preorder a special airline meal (e.g. May be the version has problem How can I do ? 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. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat ERROR: lazy loading failed for package Hmisc library(DESeq2) Why is this sentence from The Great Gatsby grammatical? You are doing something very wrong when installing your packages. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): [7] datasets methods base, other attached packages: [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 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. there is no package called locfit. 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). Convince your IT department to relax the permissions for R packages Use MathJax to format equations. 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. Do I need a thermal expansion tank if I already have a pressure tank? Any suggestions would be greatly appreciated. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. 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. Connect and share knowledge within a single location that is structured and easy to search. 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. 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. Please remember to confirm an answer once you've received one. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Sign in it would be good to hear any speculation you have of how this might have happened). I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Should I update the Bioconductor to latest version instead? [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 So if you still get this error try changing your CRAN mirror. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. What do I need to do to reproduce your problem? (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 . What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' privacy statement. 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 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. 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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Policy. 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!!! Is there a proper earth ground point in this switch box? 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. Solving environment: Found conflicts! After 3-4 manual installs everything worked. I would recommend installing an older version of QIIME 2 for this plugin to work. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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 enter citation("DESeq2")): To install this package, start R (version Why do many companies reject expired SSL certificates as bugs in bug bounties? Then I reinstalled R then Rstudio then RTools. 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. there is no package called Hmisc. This article explains how to resolve the package or namespace loading error. March 1, 2023, 3:25pm 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, spatial, survival /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages installation of package GenomeInfoDbData had non-zero exit status. Let me confer with the team. Is there a single-word adjective for "having exceptionally strong moral principles"? No error messages are returned. Is a PhD visitor considered as a visiting scholar? [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib 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 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. Replacing broken pins/legs on a DIP IC package. Also make sure that you have RTools.exe installed and working. Traffic: 307 users visited in the last hour, https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz', https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 I installed the package successfully with conda, but Rstudio is apparently does not know about it. What is the output of. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Press CTRL-C to abort. Find centralized, trusted content and collaborate around the technologies you use most. Why do academics stay as adjuncts for years rather than move around? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 [69] tidyselect_1.0.0. .onLoad failed in loadNamespace() for 'rlang', details: How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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"). Content type 'application/zip' length 4255589 bytes (4.1 MB) I would like to install DESeq2 for DE analysis. In install.packages() : Installing package(s) 'htmlTable', 'xfun' if (!require("BiocManager", quietly = TRUE)) ERROR: dependency Hmisc is not available for package DESeq2 0 packages out-of-date; 2 packages too new, BiocManager::install(c( 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. Then I reinstalled R then Rstudio then RTools. 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. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. 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 Powered by Discourse, best viewed with JavaScript enabled, DESeq2: Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Error: package GenomeInfoDb could not be loaded. 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. error: object 'rlang_dots_list' not found "After the incident", I started to be more careful not to trip over things. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Running under: macOS Catalina 10.15.3, Matrix products: default C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Surly Straggler vs. other types of steel frames. Making statements based on opinion; back them up with references or personal experience. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Installing Hmisc as suggested above did not solve the issue. I guess that means we can finally close this issue. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Sorry, I'm newbie. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Installing package(s) 'XML' [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Retrying with flexible solve.Solving environment: Found conflicts! Following successful installation of backports BiocManager::install ("DESeq2") will succeed under requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Disconnect between goals and daily tasksIs it me, or the industry? I then launched the R application (from the finder, not RStudio) and installed BiocManager. I am running a new install of R (3.5.0) and RStudio (1.1.414). 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]]): Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) 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 I also tried something I found on google: but the installation had errors too, I can write them here if needed. [5] IRanges_2.8.1 S4Vectors_0.12.1 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): library ("DESeq2") 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 'Hmisc' Installing Hmisc as suggested above did not solve the issue.