marshall high school bell schedule | error: package or namespace load failed for 'deseq2
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"). I was assuming that to be the case. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) CRAN: https://mirrors.sjtug.sjtu.edu.cn/cran/, Bioconductor version 3.12 (BiocManager 1.30.17), R 4.0.3 (2020-10-10), Old packages: 'cli', 'dplyr', 'igraph', 'MASS', 'ps', 'RSQLite', 'testthat', 'tibble', package locift is not available for Bioconductor version '3.12', A version of this package for your version of R might be available elsewhere,see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. May I know is there any other approach I can try? Not the answer you're looking for? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? "After the incident", I started to be more careful not to trip over things. 2. Old packages: 'RcppArmadillo', 'survival' Statistics ; Algorithm(ML, DL,.) 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. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? a, There are binary versions available but the source versions are later: 0 packages out-of-date; 2 packages too new, BiocManager::install(c( This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was -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. DESeq2_2301_76497647-CSDN Erasmus+ funds available! Content type 'application/zip' length 386703 bytes (377 KB) [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Is it suspicious or odd to stand by the gate of a GA airport watching the planes? [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: rev2023.3.3.43278. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): ERROR: dependency Hmisc is not available for package DESeq2 DESeq2 - I can't get the library to load - Bioconductor library (olsrr) - Error - General - RStudio Community Update all/some/none? [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Surly Straggler vs. other types of steel frames. When an R package depends on a newer package version, the required package is downloaded but not loaded. Sorry if I missed this, the question was quite long so I kind of skimmed, but I noticed that early on some of the packages were reported as requiring manual compilation from source. 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 [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. package in your R session. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Warning: restored xfun, The downloaded binary packages are in When an R package depends on a newer package version, the required package is downloaded but not loaded. Citation (from within R, Styling contours by colour and by line thickness in QGIS. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. privacy statement. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Bad: conda install -c bioconda bioconductor-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 'locfit' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: Learn more about Stack Overflow the company, and our products. I just figured Id ask. Installing package(s) 'GenomeInfoDbData' it would be good to hear any speculation you have of how this might have happened). DESeq2: Error: package or namespace load failed for 'DESeq2': objects 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). now when I tried installing the missing packages they did install. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Convince your IT department to relax the permissions for R packages By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. I can download DESeq2 using, User Agreement and Privacy Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R @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. When you load the package, you can observe this error. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Then I reinstalled R then Rstudio then RTools. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Error: package or namespace load failed for 'DESeq2 - Bioconductor [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 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. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). there is no package called data.table install.packages("BiocManager"), I get this error: Is a PhD visitor considered as a visiting scholar? [1] stats4 parallel stats graphics grDevices utils package xfun successfully unpacked and MD5 sums checked Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? No error messages are returned. New replies are no longer allowed. - the incident has nothing to do with me; can I use this this way? If you preorder a special airline meal (e.g. In file.copy(savedcopy, lib, recursive = TRUE) : You signed in with another tab or window. library(DESeq2) [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Are there tables of wastage rates for different fruit and veg? Is a PhD visitor considered as a visiting scholar? Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. 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. After 3-4 manual installs everything worked. 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. [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: If you have a query related to it or one of the replies, start a new topic and refer back with a link. Press CTRL-C to abort.failedUnsatisfiableError: The following specifications were foundto be incompatible with the existing python installation in your environment:Specifications: It also hung on the solving environment for over an hour. Is there a proper earth ground point in this switch box? 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. 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. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. It is working now. Is there a proper earth ground point in this switch box? R DESeq2 - 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). March 1, 2023, 4:56pm [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Already on GitHub? enter citation("DESeq2")): To install this package, start R (version To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. Content type 'application/zip' length 233860 bytes (228 KB) I tried again and again was met with missing packages BUT!!! 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'. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). vegan) just to try it, does this inconvenience the caterers and staff? Please read the posting 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 Did you do that? there is no package called Hmisc. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 I thought that working in a new environment would help, but it didnt. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Language(R, Python, SQL) How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? I even tried BiocManager::install("XML") but all failed as shown below. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. This is the beauty of installing QIIME 2 via conda, you can have many different versions of QIIME 2 on your system at the same time and activate the version you want to use. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Sign in Have a question about this project? How can we prove that the supernatural or paranormal doesn't exist? 4. To learn more, see our tips on writing great answers. Platform: x86_64-w64-mingw32/x64 (64-bit) call: dots_list() In addition: Warning message: there is no package called Hmisc. Installation instructions to use this The package has place the R version constraint. [5] IRanges_2.8.1 S4Vectors_0.12.1 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. Also make sure that you have RTools.exe installed and working. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in 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 'XML' so I would try to use BiocManager::install ("XML"). Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. 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. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. installation of package GenomeInfoDbData had non-zero exit status. 9. [16] phyloseq1.30.0, loaded via a namespace (and not attached): Post questions about Bioconductor March 1, 2023, 3:25pm I need help installing a package "DESeq2" having - RStudio Community You are doing something very wrong when installing your packages. Why is this sentence from The Great Gatsby grammatical? check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Platform: x86_64-apple-darwin13.4.0 (64-bit) The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. Thanks for your suggestion. Why do academics stay as adjuncts for years rather than move around? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, By clicking Sign up for GitHub, you agree to our terms of service and there is no package called locfit. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Retrying with flexible solve.Solving environment: Found conflicts! If not fixed, Try removing remove.packages (rlang) then. 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: [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 rev2023.3.3.43278. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages guide. 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"). [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 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. MathJax reference. This includes any installed libraries. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: As such there are two solutions that may be more or less attainable given your own IT system. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Can't Load R DESeq2 Library, Installed All Missing Packages and Still To learn more, see our tips on writing great answers. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Thanks for contributing an answer to Bioinformatics Stack Exchange! 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'. Error: package GenomeInfoDb could not be loaded. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Running under: macOS Sierra 10.12.3, locale: locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) 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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) install.packages ("zip") rev2023.3.3.43278. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit?
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