[28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Installing Hmisc as suggested above did not solve the issue. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Language(R, Python, SQL) Also make sure that you have RTools.exe installed and working. 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") As such there are two solutions that may be more or less attainable given your own IT system. Why do academics stay as adjuncts for years rather than move around? I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib I hope you can see something I can't see and help me solving this issue. That plugin is has not been updated to work with later releases of QIIME 2. Running under: Windows 10 x64 (build 18362), locale: New replies are no longer allowed. How do I align things in the following tabular environment? Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Sounds like you might have an issue with which R Rstudio is running. [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: 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). Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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. I tried again and again was met with missing packages BUT!!! If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Content type 'application/zip' length 386703 bytes (377 KB) As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Any other suggestion? [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Platform: x86_64-apple-darwin17.0 (64-bit) Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Error in R: (Package which is only available in source form, and may need compilation of C/C++/Fortran), Loading BioConductor library "GO.db" fails, Installing R packages from a local repo (all .tar.gz files have been downloaded there), Cannot remove prior installation of package, but package not found, I can't seem to install the 'ecospat' package on R studio for windows, I am unable to install ggplot, there occurs some error. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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 you preorder a special airline meal (e.g. Use of this site constitutes acceptance of our User Agreement and Privacy LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Platform: x86_64-apple-darwin15.6.0 (64-bit) Warning: restored xfun, The downloaded binary packages are in When you load the package, you can observe this error. 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. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. 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. Finally After 3-4 manual installations of missing packages everything worked. I'm having a similar error, but different package: library("DESeq2") Whats the grammar of "For those whose stories they are"? After 3-4 manual installs everything worked. Solution To resolve this error, install the required package as a cluster-installed library. Asking for help, clarification, or responding to other answers. Let me confer with the team. a, There are binary versions available but the source versions are later: package rlang was built under R version 3.5.1. How do you ensure that a red herring doesn't violate Chekhov's gun? 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. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) data . Content type 'application/zip' length 233860 bytes (228 KB) [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Why do many companies reject expired SSL certificates as bugs in bug bounties? privacy statement. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Have a question about this project? Whats the grammar of "For those whose stories they are"? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so By clicking Sign up for GitHub, you agree to our terms of service and I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 More info about Internet Explorer and Microsoft Edge. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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. 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]]): now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Is a PhD visitor considered as a visiting scholar? Installing package(s) 'htmlTable', 'xfun' R version 4.0.1 (2020-06-06) March 1, 2023, 8:52pm call: dots_list() [7] edgeR_3.16.5 limma_3.30.12 "After the incident", I started to be more careful not to trip over things. What is the output of. @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. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Statistics ; Algorithm(ML, DL,.) guide. 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]]): Try installing zip, and then loading olsrr. 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!!! install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. and then updating the packages that command indicates. [a/s/n]: downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Acidity of alcohols and basicity of amines. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). 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: By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Find centralized, trusted content and collaborate around the technologies you use most. 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. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Find centralized, trusted content and collaborate around the technologies you use most. it would be good to hear any speculation you have of how this might have happened). It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Please try reinstalling rlang on a fresh session. running multiple versions of the same package, keeping separate libraries for some projects). [5] IRanges_2.8.1 S4Vectors_0.12.1 there is no package called locfit. Surly Straggler vs. other types of steel frames. Should I update the Bioconductor to latest version instead? there is no package called Hmisc. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. 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. (Factorization). there is no package called data.table Is there a proper earth ground point in this switch box? "After the incident", I started to be more careful not to trip over things. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. [13] ggplot23.3.0 car3.0-7 carData3.0-3 + "htmlTable", "xfun" @artembus Sounds like it was a ton of work! Use this. Running under: macOS Sierra 10.12.6. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Remember to always click on the red Show me the content on this page notice when navigating these older versions. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Looking for incompatible packages. 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. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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 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. Are you sure the R you're running from the command line is installed through Anaconda as well? Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R You are doing something very wrong when installing your packages. 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. A place where magic is studied and practiced? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Disconnect between goals and daily tasksIs it me, or the industry? Loading required package: GenomicRanges If it fails, required operating system facilities are missing. Connect and share knowledge within a single location that is structured and easy to search. Please remember to confirm an answer once you've received one. 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? [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 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 rev2023.3.3.43278. 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. - the incident has nothing to do with me; can I use this this way? R version 3.6.3 (2020-02-29) How to use Slater Type Orbitals as a basis functions in matrix method correctly? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 :), BiocManager::install("locift") 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 sessionInfo() However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? . C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages To learn more, see our tips on writing great answers. 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. 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 Bad: conda install -c bioconda bioconductor-deseq2. The package has place the R version constraint. [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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 9. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Learn more about Stack Overflow the company, and our products. Why do academics stay as adjuncts for years rather than move around? 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. - the incident has nothing to do with me; can I use this this way? 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. Glad everything is finally working now. March 1, 2023, 4:56pm Loading required package: GenomeInfoDb And finally, install the problem packages, perhaps also DESeq2. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Start R to confirm they are gone. Warning message: I highly recommend that any R/RStudio version not installed inside conda be removed. 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
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