error: package or namespace load failed for 'deseq2

By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Bad: conda install -c bioconda bioconductor-deseq2. @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. data . Author: Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd], Maintainer: Michael Love . Also make sure that you have RTools.exe installed and working. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Looking for incompatible packages. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 [69] tidyselect_1.0.0. [13] ggplot23.3.0 car3.0-7 carData3.0-3 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. I can download DESeq2 using, User Agreement and Privacy Loading required package: GenomicRanges Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Does anyone know why I'm getting the following message when I load tidyverse in a new session. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. You signed in with another tab or window. Are there tables of wastage rates for different fruit and veg? 1. Language(R, Python, SQL) March 1, 2023, 4:56pm If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Have a question about this project? ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: I highly recommend that any R/RStudio version not installed inside conda be removed. Running under: macOS Catalina 10.15.3, Matrix products: default In install.packages() : Remember to always click on the red Show me the content on this page notice when navigating these older versions. The package has place the R version constraint. Press CTRL-C to abort. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Give up and run everything from the "permitted" library location (e.g. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. This includes any installed libraries. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Installing package(s) 'XML' ()library(DESeq2):Error in loadNamespace: no package called ""s Is there a single-word adjective for "having exceptionally strong moral principles"? Policy. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Glad everything is finally working now. Is there anything I can do to speed it up? Resolving package or namespace loading error What do I need to do to reproduce your problem? Acidity of alcohols and basicity of amines. 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 That plugin is has not been updated to work with later releases of QIIME 2. Content type 'application/zip' length 233860 bytes (228 KB) I'm trying to reproduce your problem, so being as precise as possible is important. I am running a new install of R (3.5.0) and RStudio (1.1.414). Try again and choose No. R DESeq2 - Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Feedback binary source needs_compilation Looking for incompatible packages.This can take several minutes. installation of package GenomeInfoDbData had non-zero exit status. Asking for help, clarification, or responding to other answers. If not fixed, Try removing remove.packages (rlang) then. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 2. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Should I update the Bioconductor to latest version instead? I tried to download the "locfit" package but I can't find it anywhere. 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. 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. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? And finally, install the problem packages, perhaps also DESeq2. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. 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. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR When an R package depends on a newer package version, the required package is downloaded but not loaded. Whats the grammar of "For those whose stories they are"? Sign in in your system, start R and enter: Follow Use of this site constitutes acceptance of our 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. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Bioconductor release. vegan) just to try it, does this inconvenience the caterers and staff? Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, - the incident has nothing to do with me; can I use this this way? More info about Internet Explorer and Microsoft Edge. How to notate a grace note at the start of a bar with lilypond? Asking for help, clarification, or responding to other answers. Why do academics stay as adjuncts for years rather than move around? Find centralized, trusted content and collaborate around the technologies you use most. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. 9. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Platform: x86_64-w64-mingw32/x64 (64-bit) I do know that it works well in qiime2-2020.6. Try installing zip, and then loading olsrr. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE A place where magic is studied and practiced? rev2023.3.3.43278. Policy. library(caret) namespace load failed Object sigma not install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Are you sure the R you're running from the command line is installed through Anaconda as well? It only takes a minute to sign up. @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. After 3-4 manual installs everything worked. library(caret) namespace load failed Object sigma not found caret , . rstudio - Error: package or namespace load failed for 'tidyverse [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 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. Rload failed - dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext You are doing something very wrong when installing your packages. it would be good to hear any speculation you have of how this might have happened). "After the incident", I started to be more careful not to trip over things. R| - 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). there is no package called GenomeInfoDbData im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) (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 . I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. but when I go to load the libraries I get this error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, "After the incident", I started to be more careful not to trip over things. Solution To resolve this error, install the required package as a cluster-installed library. 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 This topic was automatically closed 21 days after the last reply. Retrying with flexible solve.Solving environment: Found conflicts! 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. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Please remember to confirm an answer once you've received one. When you load the package, you can observe this error. When you load the package, you can observe this error. 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). call: dots_list() Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in The best answers are voted up and rise to the top, Not the answer you're looking for? Warning: restored xfun, The downloaded binary packages are in Policy. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 ERROR: dependency Hmisc is not available for package DESeq2 But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Does a summoned creature play immediately after being summoned by a ready action? Policy. Use of this site constitutes acceptance of our User Agreement and Privacy So, supposedly the issue is with Hmisc. + "htmlTable", "xfun" Fortunately I was able to solve it by doing things from several suggested solutions. By clicking Sign up for GitHub, you agree to our terms of service and Thank you @hharder. I would recommend installing an older version of QIIME 2 for this plugin to work. I installed the package successfully with conda, but Rstudio is apparently does not know about it. 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. March 1, 2023, 8:52pm [a/s/n]: Sorry, I'm newbie. 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"). It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Connect and share knowledge within a single location that is structured and easy to search. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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. Thanks! there is no package called Hmisc. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: DESeq2_2301_76497647-CSDN /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. MathJax reference. 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. Citation (from within R, 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. Is a PhD visitor considered as a visiting scholar? Install DESeq2 through anaconda - Bioinformatics Stack Exchange Not the answer you're looking for? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). there is no package called locfit. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Also note, however, that the error you got has been associated in the past with mirror outages. so I would try to use BiocManager::install("XML"). 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 Content type 'application/zip' length 4255589 bytes (4.1 MB) Making statements based on opinion; back them up with references or personal experience. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 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). 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. 4. 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") [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: [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. biocLite(), install.packages() (and the devtools equivalent?) Connect and share knowledge within a single location that is structured and easy to search. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. 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. Surly Straggler vs. other types of steel frames. Join us at CRISPR workshops in Koper, Slovenia in 2023. To resolve this error, install the required package as a cluster-installed library. I would like to install DESeq2 for DE analysis. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Thanks for contributing an answer to Stack Overflow! Is a PhD visitor considered as a visiting scholar? The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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. Surly Straggler vs. other types of steel frames. To learn more, see our tips on writing great answers. Sounds like you might have an issue with which R Rstudio is running. While a notebook is attached to a cluster, the R namespace cannot be refreshed. One solution is to find all available packages. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Thanks for contributing an answer to Stack Overflow! Thanks for your suggestion. Is there a proper earth ground point in this switch box? Convince your IT department to relax the permissions for R packages Please try reinstalling rlang on a fresh session. R version 4.0.1 (2020-06-06) No error messages are returned. install.packages ("zip") [R] Error: package or namespace load failed for 'ggplot2' in Error: package or namespace load failed, object not found Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Any other suggestion? 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: 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 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 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. 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"). As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. From the console install.packages ("rlang") should fix this. I tried again and again was met with missing packages BUT!!! The other option is to download and older version of locfit from the package archive and install manually. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 R version 3.6.1 (2019-07-05) Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Why is this sentence from The Great Gatsby grammatical? Warning: cannot remove prior installation of package xfun

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