error: package or namespace load failed for 'deseq2

Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): From the console install.packages ("rlang") should fix this. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Thanks for your suggestion. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Styling contours by colour and by line thickness in QGIS. Error when installing Aldex2 - Community Plugin Support - Open Source Sounds like you might have an issue with which R Rstudio is running. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': library(DESeq2) A place where magic is studied and practiced? installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat [13] ggplot23.3.0 car3.0-7 carData3.0-3 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") [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Connect and share knowledge within a single location that is structured and easy to search. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 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. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Disconnect between goals and daily tasksIs it me, or the industry? Statistics ; Algorithm(ML, DL,.) C:\R\R-3.4.3\library). It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. 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. So, supposedly the issue is with Hmisc. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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. Replacing broken pins/legs on a DIP IC package. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Installing package(s) 'XML' Sounds like there might be an issue with conda setup? When an R package depends on a newer package version, the required package is downloaded but not loaded. Choose Yes. 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. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 @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. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Finally After 3-4 manual installations of missing packages everything worked. Acidity of alcohols and basicity of amines. Use MathJax to format equations. package rlang was built under R version 3.5.1. Sign in It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. there is no package called Hmisc. Just to add on -- do you require an old version of Bioconductor for your current project? Policy. Content type 'application/zip' length 233860 bytes (228 KB) [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Making statements based on opinion; back them up with references or personal experience. @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. 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. it would be good to hear any speculation you have of how this might have happened). [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 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. Policy. What is a word for the arcane equivalent of a monastery? May I know is there any other approach I can try? Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Why do academics stay as adjuncts for years rather than move around? [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Warning: cannot remove prior installation of package xfun 4. [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. 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). By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Any suggestions would be greatly appreciated. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 ERROR: lazy loading failed for package Hmisc Sorry, I'm newbie. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. library(caret) namespace load failed Object sigma not found caret , . Loading required package: GenomicRanges Thanks! When an R package depends on a newer package version, the required package is downloaded but not loaded. rev2023.3.3.43278. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. If not fixed, Try removing remove.packages (rlang) then. [69] tidyselect_1.0.0. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Surly Straggler vs. other types of steel frames. [7] datasets methods base, other attached packages: "htmlTable", "xfun" ()library(DESeq2):Error in loadNamespace: no package called ""s [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Why is there a voltage on my HDMI and coaxial cables? 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. if (!require("BiocManager", quietly = TRUE)) (Factorization). 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. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 How can we prove that the supernatural or paranormal doesn't exist? Making statements based on opinion; back them up with references or personal experience. When you load the package, you can observe this error. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. 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). I would recommend installing an older version of QIIME 2 for this plugin to work. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Running under: Windows 10 x64 (build 18362), locale: [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Content type 'application/zip' length 4255589 bytes (4.1 MB) We've tried this - and can replicate this issue on a completely new install with no existing package installs. vegan) just to try it, does this inconvenience the caterers and staff? Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or? By clicking Sign up for GitHub, you agree to our terms of service and [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 To learn more, see our tips on writing great answers. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [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: Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? I need help installing a package "DESeq2" having - RStudio Community Is a PhD visitor considered as a visiting scholar? Asking for help, clarification, or responding to other answers. Connect and share knowledge within a single location that is structured and easy to search. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Update all/some/none? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Find centralized, trusted content and collaborate around the technologies you use most. Bad: conda install -c bioconda bioconductor-deseq2. Platform: x86_64-apple-darwin17.0 (64-bit) This can take several minutes. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Start R to confirm they are gone. 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. Why are physically impossible and logically impossible concepts considered separate in terms of probability? package xfun successfully unpacked and MD5 sums checked After 3-4 manual installs everything worked.

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