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error: package or namespace load failed for 'deseq2

to your account. [69] tidyselect_1.0.0. Not the answer you're looking for? Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . While a notebook is attached to a cluster, the R namespace cannot be refreshed. 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. Open Source Biology & Genetics Interest Group. Installing package(s) 'GenomeInfoDbData' there is no package called locfit. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. 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. Just updated my previous R to 4.01 and now I cant load DESeq2. Warning: restored xfun, The downloaded binary packages are in Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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. Have a question about this project? Sounds like there might be an issue with conda setup? 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: [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Already on GitHub? [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? I guess that means we can finally close this issue. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 When an R package depends on a newer package version, the required package is downloaded but not loaded. Installing Hmisc as suggested above did not solve the issue. Please try reinstalling rlang on a fresh session. there is no package called GenomeInfoDbData [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 I even tried BiocManager::install("XML") but all failed as shown below. Choose Yes. [5] IRanges_2.8.1 S4Vectors_0.12.1 Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Thanks! To add to this, I have also been using DESeq2 recently and ran into the same problem. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Why do many companies reject expired SSL certificates as bugs in bug bounties? What is the output of. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Then I reinstalled R then Rstudio then RTools. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. 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. Press CTRL-C to abort. March 1, 2023, 3:25pm How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? The best answers are voted up and rise to the top, Not the answer you're looking for? Why do academics stay as adjuncts for years rather than move around? [13] ggplot23.3.0 car3.0-7 carData3.0-3 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Running under: macOS Sierra 10.12.6. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Making statements based on opinion; back them up with references or personal experience. 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 Policy. I do know that it works well in qiime2-2020.6. Surly Straggler vs. other types of steel frames. Policy. vegan) just to try it, does this inconvenience the caterers and staff? You signed in with another tab or window. privacy statement. Connect and share knowledge within a single location that is structured and easy to search. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Disconnect between goals and daily tasksIs it me, or the industry? The error states that the current version is 0.4.5 but 0.4.10 is required. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. This article explains how to resolve the package or namespace loading error. Documentation Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 guide. I would like to install DESeq2 for DE analysis. You are doing something very wrong when installing your packages. "htmlTable", "xfun" [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Policy. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. As such there are two solutions that may be more or less attainable given your own IT system. Find centralized, trusted content and collaborate around the technologies you use most. 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'. Find centralized, trusted content and collaborate around the technologies you use most. Thanks for contributing an answer to Bioinformatics Stack Exchange! It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. enter citation("DESeq2")): To install this package, start R (version [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: Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). 9. One solution is to find all available packages. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages biocLite(), install.packages() (and the devtools equivalent?) [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 So if you still get this error try changing your CRAN mirror. Whats the grammar of "For those whose stories they are"? rev2023.3.3.43278. I would recommend installing an older version of QIIME 2 for this plugin to work. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Are you sure the R you're running from the command line is installed through Anaconda as well? Why are physically impossible and logically impossible concepts considered separate in terms of probability? When you load the package, you can observe this error. [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 also tried something I found on google: but the installation had errors too, I can write them here if needed. 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. Use of this site constitutes acceptance of our User Agreement and Privacy [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 [7] edgeR_3.16.5 limma_3.30.12 I tried to download the "locfit" package but I can't find it anywhere. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. No error messages are returned. Policy. @artembus Sounds like it was a ton of work! I tried again and again was met with missing packages BUT!!! Sounds like you might have an issue with which R Rstudio is running. I'm having a similar error, but different package: library("DESeq2") [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Acidity of alcohols and basicity of amines. package rlang was built under R version 3.5.1. Solution To resolve this error, install the required package as a cluster-installed library. nnet, spatial, survival. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Is it suspicious or odd to stand by the gate of a GA airport watching the planes? We've tried this - and can replicate this issue on a completely new install with no existing package installs. Use MathJax to format equations. I highly recommend that any R/RStudio version not installed inside conda be removed. Is a PhD visitor considered as a visiting scholar? [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. I have tried your suggestion and also updating the packages that command indicates. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Sign in Give up and run everything from the "permitted" library location (e.g. Did you do that? 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. This can take several minutes. Use this. 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. After 3-4 manual installs everything worked. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 sessionInfo() Surly Straggler vs. other types of steel frames. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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. install.packages("BiocManager"), I get this error: - the incident has nothing to do with me; can I use this this way? Do I need a thermal expansion tank if I already have a pressure tank? downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Please read the posting Replacing broken pins/legs on a DIP IC package. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. 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 Platform: x86_64-w64-mingw32/x64 (64-bit) so I would try to use BiocManager::install("XML"). [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 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. Bioconductor release. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Use of this site constitutes acceptance of our User Agreement and Privacy To subscribe to this RSS feed, copy and paste this URL into your RSS reader. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. To resolve this error, install the required package as a cluster-installed library. Let me confer with the team. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 How to use Slater Type Orbitals as a basis functions in matrix method correctly? [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 binary source needs_compilation Feedback Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Not the answer you're looking for? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I can download DESeq2 using, User Agreement and Privacy [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 March 1, 2023, 8:52pm 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. 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. running multiple versions of the same package, keeping separate libraries for some projects). "After the incident", I started to be more careful not to trip over things. 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'. Hello, Warning: cannot remove prior installation of package xfun Retrying with flexible solve.Solving environment: Found conflicts! Installing package(s) 'htmlTable', 'xfun' I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 and then updating the packages that command indicates. rev2023.3.3.43278. 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: Loading required package: GenomicRanges [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Sorry, I'm newbie. Looking for incompatible packages.This can take several minutes. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 library(caret) namespace load failed Object sigma not found caret , . To view documentation for the version of this package installed By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. 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 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. 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) Is there a single-word adjective for "having exceptionally strong moral principles"? . C:\R\R-3.4.3\library). 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!!! 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 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Statistics ; Algorithm(ML, DL,.) March 1, 2023, 4:56pm - the incident has nothing to do with me; can I use this this way? I tried following the instructions for 2019.7 as well and I am getting the same error. 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. 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). When an R package depends on a newer package version, the required package is downloaded but not loaded. March 1, 2023, 7:31pm Bad: conda install -c bioconda bioconductor-deseq2. If you have a query related to it or one of the replies, start a new topic and refer back with a link. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat 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. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). sessionInfo() 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. Post questions about Bioconductor Platform: x86_64-apple-darwin13.4.0 (64-bit) 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. Use of this site constitutes acceptance of our User Agreement and Privacy [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [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: What do I need to do to reproduce your problem? Join us at CRISPR workshops in Koper, Slovenia in 2023. Traffic: 307 users visited in the last hour, I am new to all this! @Tung I've updated my R and RStudio versions (unfortunately I had to first convince my workplace to approve them) and installed the packages through R 3.5.1 however, I'm still getting the same rlang error. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I thought that working in a new environment would help, but it didnt. That plugin is has not been updated to work with later releases of QIIME 2. it would be good to hear any speculation you have of how this might have happened). [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Also note, however, that the error you got has been associated in the past with mirror outages. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 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. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. (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 . If it fails, required operating system facilities are missing. Thanks for contributing an answer to Stack Overflow! [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 But I guess you have many problems with your installation, and I'd suggest. Warning message: :), BiocManager::install("locift") [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 .onLoad failed in loadNamespace() for 'rlang', details: 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. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Does a summoned creature play immediately after being summoned by a ready action? Styling contours by colour and by line thickness in QGIS.

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error: package or namespace load failed for 'deseq2

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