1. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Thank you @hharder. install.packages("BiocManager"), I get this error: [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Old packages: 'RcppArmadillo', 'survival' [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: Sounds like you might have an issue with which R Rstudio is running. so I would try to use BiocManager::install("XML"). biocLite(), install.packages() (and the devtools equivalent?) [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Why is this sentence from The Great Gatsby grammatical? Please try the following steps: Quit all R/Rstudio sessions. and then updating the packages that command indicates. Finally After 3-4 manual installations of missing packages everything worked. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 [13] ggplot23.3.0 car3.0-7 carData3.0-3 Use MathJax to format equations. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Are you sure the R you're running from the command line is installed through Anaconda as well? 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. 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: Platform: x86_64-apple-darwin13.4.0 (64-bit) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Is a PhD visitor considered as a visiting scholar? a, There are binary versions available but the source versions are later: [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Looking for incompatible packages. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Is the God of a monotheism necessarily omnipotent? Language(R, Python, SQL) Installing package(s) 'XML' Please try reinstalling rlang on a fresh session. It is working now. Any other suggestion? To add to this, I have also been using DESeq2 recently and ran into the same problem. Find centralized, trusted content and collaborate around the technologies you use most. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Find centralized, trusted content and collaborate around the technologies you use most. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Why do academics stay as adjuncts for years rather than move around? Surly Straggler vs. other types of steel frames. 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 [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat March 1, 2023, 3:25pm 2. This includes any installed libraries. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 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. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Policy. 4. You signed in with another tab or window. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. there is no package called Hmisc. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) there is no package called locfit. The error states that the current version is 0.4.5 but 0.4.10 is required. Are there tables of wastage rates for different fruit and veg? If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. 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 . Follow Up: struct sockaddr storage initialization by network format-string. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Installing Hmisc as suggested above did not solve the issue. Making statements based on opinion; back them up with references or personal experience. Open Source Biology & Genetics Interest Group. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I was assuming that to be the case. By clicking Sign up for GitHub, you agree to our terms of service and [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 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. Then I reinstalled R then Rstudio then RTools. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Also make sure that you have RTools.exe installed and working. + "htmlTable", "xfun" Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' 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). May be the version has problem How can I do ? Is a PhD visitor considered as a visiting scholar? When you load the package, you can observe this error. Thanks for contributing an answer to Bioinformatics Stack Exchange! 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. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Policy. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 In file.copy(savedcopy, lib, recursive = TRUE) : To learn more, see our tips on writing great answers. @artembus Sounds like it was a ton of work! 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. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: nnet, spatial, survival. One solution is to find all available packages. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Is there anything I can do to speed it up? Use of this site constitutes acceptance of our User Agreement and Privacy 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. Warning: cannot remove prior installation of package xfun To subscribe to this RSS feed, copy and paste this URL into your RSS reader. rev2023.3.3.43278. "htmlTable", "xfun" it would be good to hear any speculation you have of how this might have happened). Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I tried again and again was met with missing packages BUT!!! Error: package GenomeInfoDb could not be loaded. 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). I highly recommend that any R/RStudio version not installed inside conda be removed. Glad everything is finally working now. binary source needs_compilation 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") downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Running under: macOS Sierra 10.12.3, locale: Have a question about this project? [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Just to add on -- do you require an old version of Bioconductor for your current project? Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? 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. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). That plugin is has not been updated to work with later releases of QIIME 2. 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. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 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!!! It only takes a minute to sign up. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Acidity of alcohols and basicity of amines. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) "After the incident", I started to be more careful not to trip over things. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages How to use Slater Type Orbitals as a basis functions in matrix method correctly? there is no package called GenomeInfoDbData 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 What is the output of. Asking for help, clarification, or responding to other answers. there is no package called GenomeInfoDbData Just realize that I need to write the script "library("DESeq2")" before I proceed. Is there a proper earth ground point in this switch box? Why do many companies reject expired SSL certificates as bugs in bug bounties? I hope you can see something I can't see and help me solving this issue. library(caret) namespace load failed Object sigma not found caret , . Making statements based on opinion; back them up with references or personal experience. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Press CTRL-C to abort. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Post questions about Bioconductor Running under: Windows 10 x64 (build 18362), locale: Running. 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, If it fails, required operating system facilities are missing. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 9. So, supposedly the issue is with Hmisc. Surly Straggler vs. other types of steel frames. 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. R version 3.6.3 (2020-02-29) Well occasionally send you account related emails. Use this. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Replacing broken pins/legs on a DIP IC package. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Asking for help, clarification, or responding to other answers. Why are physically impossible and logically impossible concepts considered separate in terms of probability? How do I align things in the following tabular environment? Citation (from within R, Connect and share knowledge within a single location that is structured and easy to search. Why do academics stay as adjuncts for years rather than move around? 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 Thanks for contributing an answer to Stack Overflow! downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 What do I need to do to reproduce your problem? What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? We've tried this - and can replicate this issue on a completely new install with no existing package installs. 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. data . What is a word for the arcane equivalent of a monastery? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 (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 . 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'.