error: package or namespace load failed for 'deseq2 error: package or namespace load failed for '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: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib R version 3.6.3 (2020-02-29) Why is this sentence from The Great Gatsby grammatical? [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 I do know that it works well in qiime2-2020.6. Acidity of alcohols and basicity of amines. 2. Is there a single-word adjective for "having exceptionally strong moral principles"? We've tried this - and can replicate this issue on a completely new install with no existing package installs. Retrying with flexible solve.Solving environment: Found conflicts! Platform: x86_64-apple-darwin13.4.0 (64-bit) [16] phyloseq1.30.0, loaded via a namespace (and not attached): Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) package in your R session. Hello, When an R package depends on a newer package version, the required package is downloaded but not loaded. You are doing something very wrong when installing your packages. package xfun successfully unpacked and MD5 sums checked Installing package(s) 'htmlTable', 'xfun' Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 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. I installed the package successfully with conda, but Rstudio is apparently does not know about it. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. it would be good to hear any speculation you have of how this might have happened). Sign in By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. I hope you can see something I can't see and help me solving this issue. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Just updated my previous R to 4.01 and now I cant load DESeq2. Should I update the Bioconductor to latest version instead? May be the version has problem How can I do ? [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages March 1, 2023, 4:56pm 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'. error: object 'rlang_dots_list' not found Thnaks anyway, Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems, How Intuit democratizes AI development across teams through reusability. Loading required package: GenomeInfoDb [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. 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'. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages To view documentation for the version of this package installed Platform: x86_64-apple-darwin17.0 (64-bit) [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. @artembus Sounds like it was a ton of work! 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 [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Let me confer with the team. Find centralized, trusted content and collaborate around the technologies you use most. "After the incident", I started to be more careful not to trip over things. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' + ), update = TRUE, ask = FALSE) Is there a proper earth ground point in this switch box? This article explains how to resolve the package or namespace loading error. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. 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 [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Please read the posting I was assuming that to be the case. 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. Also make sure that you have RTools.exe installed and working. Bad: conda install -c bioconda bioconductor-deseq2. C:\R\R-3.4.3\library). Is a PhD visitor considered as a visiting scholar? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. there is no package called locfit. 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. Just realize that I need to write the script "library("DESeq2")" before I proceed. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. [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: [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. If you preorder a special airline meal (e.g. Error: package GenomeInfoDb could not be loaded. 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. "4.2") and enter: For older versions of R, please refer to the appropriate (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 . Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Press CTRL-C to abort. Post questions about Bioconductor Policy. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Why do academics stay as adjuncts for years rather than move around? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. That plugin is has not been updated to work with later releases of QIIME 2. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Sounds like you might have an issue with which R Rstudio is running. Why is there a voltage on my HDMI and coaxial cables? One solution is to find all available packages. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Citation (from within R, In install.packages() : Styling contours by colour and by line thickness in QGIS. 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. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Installing Hmisc as suggested above did not solve the issue. This topic was automatically closed 21 days after the last reply. Choose Yes. 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 get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. 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: Content type 'application/zip' length 386703 bytes (377 KB) [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 To learn more, see our tips on writing great answers. 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: Use this. 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). Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") 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. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. 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: Try installing zip, and then loading olsrr. More info about Internet Explorer and Microsoft Edge. Documentation The other option is to download and older version of locfit from the package archive and install manually. Why do many companies reject expired SSL certificates as bugs in bug bounties? [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. 9. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 R version 4.0.1 (2020-06-06) [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 install.packages("BiocManager"), I get this error: [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Feedback I would like to install DESeq2 for DE analysis. privacy statement. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) New replies are no longer allowed. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Whats the grammar of "For those whose stories they are"? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [13] ggplot23.3.0 car3.0-7 carData3.0-3 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. Installing package(s) 'XML' Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Disconnect between goals and daily tasksIs it me, or the industry? You signed in with another tab or window. Use of this site constitutes acceptance of our User Agreement and Privacy [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Content type 'application/zip' length 233860 bytes (228 KB) The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Have a question about this project? So, supposedly the issue is with Hmisc. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Replacing broken pins/legs on a DIP IC package. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 MathJax reference. rev2023.3.3.43278. [69] tidyselect_1.0.0. How can we prove that the supernatural or paranormal doesn't exist? Running under: macOS Sierra 10.12.3, locale: 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). nnet, spatial, survival 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. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : - the incident has nothing to do with me; can I use this this way? Why are physically impossible and logically impossible concepts considered separate in terms of probability? A place where magic is studied and practiced? Follow Up: struct sockaddr storage initialization by network format-string. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Any suggestions would be greatly appreciated. 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. I'm having a similar error, but different package: library("DESeq2") To resolve this error, install the required package as a cluster-installed library. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 binary source needs_compilation I've copied the output below in case it helps with troubleshooting. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. I just figured Id ask. Asking for help, clarification, or responding to other answers. 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"). But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Join us at CRISPR workshops in Koper, Slovenia in 2023. library(DESeq2) I'm trying to reproduce your problem, so being as precise as possible is important. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib I'm running into some bad problems installing and using the DESeq2 package for R. I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7.