May be the version has problem How can I do ? I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. there is no package called Hmisc. Connect and share knowledge within a single location that is structured and easy to search. From the console install.packages ("rlang") should fix this. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under a, There are binary versions available but the source versions are later: 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 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Why do academics stay as adjuncts for years rather than move around? Then I reinstalled R then Rstudio then RTools. [69] tidyselect_1.0.0. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. 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. This article explains how to resolve the package or namespace loading error. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. In file.copy(savedcopy, lib, recursive = TRUE) : 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. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Policy. Warning: cannot remove prior installation of package xfun Replacing broken pins/legs on a DIP IC package. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 To learn more, see our tips on writing great answers. Start R to confirm they are gone. What is the output of. I've copied the output below in case it helps with troubleshooting. @artembus Sounds like it was a ton of work! 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. Well occasionally send you account related emails. Are you sure the R you're running from the command line is installed through Anaconda as well? Whats the grammar of "For those whose stories they are"? Is there anything I can do to speed it up? Is a PhD visitor considered as a visiting scholar? How to use Slater Type Orbitals as a basis functions in matrix method correctly? [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 I just figured Id ask. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Content type 'application/zip' length 4255589 bytes (4.1 MB) 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. Just to add on -- do you require an old version of Bioconductor for your current project? 1. I would like to install DESeq2 for DE analysis. Post questions about Bioconductor [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 Try installing zip, and then loading olsrr. Assuming that your conda environment name is renv, try running this in the terminal: This should open up the Rstudio interface, like normal, but using everything defined in your renv environment. C:\R\R-3.4.3\library). Making statements based on opinion; back them up with references or personal experience. After 3-4 manual installs everything worked. Convince your IT department to relax the permissions for R packages Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. .onLoad failed in loadNamespace() for 'rlang', details: Any other suggestion? Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. 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). downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Why is there a voltage on my HDMI and coaxial cables? [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 March 1, 2023, 8:52pm Citation (from within R, enter citation ("DESeq2") ): Installation To install this package, start R (version "4.2") and enter: if (!require ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") BiocManager::install ("DESeq2") For older versions of R, please refer to the appropriate Bioconductor release . Thanks for your suggestion. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. @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. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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 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 sessionInfo() Why do many companies reject expired SSL certificates as bugs in bug bounties? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Surly Straggler vs. other types of steel frames. there is no package called GenomeInfoDbData A place where magic is studied and practiced? I am running a new install of R (3.5.0) and RStudio (1.1.414). [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 there is no package called locfit. 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. 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. there is no package called Hmisc. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 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'. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Content type 'application/zip' length 386703 bytes (377 KB) Warning message: "htmlTable", "xfun" Traffic: 307 users visited in the last hour, I am new to all this! Installation instructions to use this Platform: x86_64-w64-mingw32/x64 (64-bit) data . BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Acidity of alcohols and basicity of amines. 9. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Give up and run everything from the "permitted" library location (e.g. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. I guess that means we can finally close this issue. Platform: x86_64-apple-darwin13.4.0 (64-bit) March 1, 2023, 7:31pm ERROR: dependency Hmisc is not available for package DESeq2 "4.2") and enter: For older versions of R, please refer to the appropriate R version 3.6.3 (2020-02-29) And finally, install the problem packages, perhaps also DESeq2. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Connect and share knowledge within a single location that is structured and easy to search. there is no package called data.table 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") So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Thanks for contributing an answer to Stack Overflow! New replies are no longer allowed. Please read the posting How can we prove that the supernatural or paranormal doesn't exist? Any suggestions would be greatly appreciated. In addition: Warning message: Sounds like you might have an issue with which R Rstudio is running. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Open Source Biology & Genetics Interest Group. How to use Slater Type Orbitals as a basis functions in matrix method correctly? sessionInfo() You signed in with another tab or window. Language(R, Python, SQL) Join us at CRISPR workshops in Koper, Slovenia in 2023. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, I tried following the instructions for 2019.7 as well and I am getting the same error. R version 4.0.1 (2020-06-06) Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) It only takes a minute to sign up. Thanks for contributing an answer to Bioinformatics Stack Exchange! I was assuming that to be the case. :), BiocManager::install("locift") Installing Hmisc as suggested above did not solve the issue. Just realize that I need to write the script "library("DESeq2")" before I proceed. 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 Content type 'application/zip' length 233860 bytes (228 KB) 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. Not the answer you're looking for? to your account. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. How to notate a grace note at the start of a bar with lilypond? Sounds like there might be an issue with conda setup? Bad: conda install -c bioconda bioconductor-deseq2. March 1, 2023, 4:56pm 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 The best answers are voted up and rise to the top, Not the answer you're looking for? Why is this sentence from The Great Gatsby grammatical? 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. Making statements based on opinion; back them up with references or personal experience. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. It is working now. You are doing something very wrong when installing your packages. 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: [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Find centralized, trusted content and collaborate around the technologies you use most. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? As such there are two solutions that may be more or less attainable given your own IT system. Not the answer you're looking for? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Is there a proper earth ground point in this switch box? [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 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'. running multiple versions of the same package, keeping separate libraries for some projects). I'm having a similar error, but different package: library("DESeq2") Retrying with flexible solve.Solving environment: Found conflicts! nnet, spatial, survival How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? 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. If you preorder a special airline meal (e.g. [1] stats4 parallel stats graphics grDevices utils [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 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. Making statements based on opinion; back them up with references or personal experience. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. 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. Choose Yes. Installing package(s) 'XML' Loading required package: GenomicRanges Running under: macOS Catalina 10.15.3, Matrix products: default Solution To resolve this error, install the required package as a cluster-installed library. package xfun successfully unpacked and MD5 sums checked The error states that the current version is 0.4.5 but 0.4.10 is required. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2

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