Thanks for your suggestion. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Making statements based on opinion; back them up with references or personal experience. Connect and share knowledge within a single location that is structured and easy to search. Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I am using R 3.6.1 and Rstudio 1.2. technocrat August 27, 2020, 10:15pm #2 RedRabbit: DESeq2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. 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. Language(R, Python, SQL) Connect and share knowledge within a single location that is structured and easy to search. 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'. Hello, Any other suggestion? there is no package called locfit. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. 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 package has place the R version constraint. I was assuming that to be the case. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) a, There are binary versions available but the source versions are later: Warning: cannot remove prior installation of package xfun You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. I even tried BiocManager::install("XML") but all failed as shown below. Fortunately I was able to solve it by doing things from several suggested solutions. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Policy. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE I guess that means we can finally close this issue. 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Statistics ; Algorithm(ML, DL,.) data . [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): As such there are two solutions that may be more or less attainable given your own IT system. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Should I update the Bioconductor to latest version instead? No error messages are returned. Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. Installing package(s) 'GenomeInfoDbData' I have tried your suggestion and also updating the packages that command indicates. Join us at CRISPR workshops in Koper, Slovenia in 2023. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Let me confer with the team. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 so I would try to use BiocManager::install("XML"). Use MathJax to format equations. Is there a proper earth ground point in this switch box? Find centralized, trusted content and collaborate around the technologies you use most. [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. "htmlTable", "xfun" ERROR: lazy loading failed for package Hmisc 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!!! If you have a query related to it or one of the replies, start a new topic and refer back with a link. vegan) just to try it, does this inconvenience the caterers and staff? Connect and share knowledge within a single location that is structured and easy to search. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Is a PhD visitor considered as a visiting scholar? Policy. .onLoad failed in loadNamespace() for 'rlang', details: 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. I tried to download the "locfit" package but I can't find it anywhere. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 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. 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 Installing Hmisc as suggested above did not solve the issue. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. rev2023.3.3.43278. Citation (from within R, ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 there is no package called Hmisc. Making statements based on opinion; back them up with references or personal experience. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): March 1, 2023, 7:31pm and then updating the packages that command indicates. 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 . The other option is to download and older version of locfit from the package archive and install manually. 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"). @artembus Sounds like it was a ton of work! I hope you can see something I can't see and help me solving this issue. in your system, start R and enter: Follow [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 We've tried this - and can replicate this issue on a completely new install with no existing package installs. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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). Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Sign in Erasmus+ funds available! R version 3.6.1 (2019-07-05) 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. call: dots_list() 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. Just to add on -- do you require an old version of Bioconductor for your current project? I just figured Id ask. Retrying with flexible solve.Solving environment: Found conflicts! Whats the grammar of "For those whose stories they are"? What is a word for the arcane equivalent of a monastery? I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Running under: Windows 10 x64 (build 18362), locale: One solution is to find all available packages. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? I highly recommend that any R/RStudio version not installed inside conda be removed. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. MathJax reference. Install DESeq2 through anaconda - Bioinformatics Stack Exchange ERROR: dependency Hmisc is not available for package DESeq2 I am running a new install of R (3.5.0) and RStudio (1.1.414). @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. Asking for help, clarification, or responding to other answers. DESeq2 installation in R - Bioconductor [16] phyloseq1.30.0, loaded via a namespace (and not attached): Is there a proper earth ground point in this switch box? I would like to install DESeq2 for DE analysis. Please try the following steps: Quit all R/Rstudio sessions. 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. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Solving environment: Found conflicts! Just updated my previous R to 4.01 and now I cant load DESeq2. 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. Have you tried install.packages("locfit") ? Start R to confirm they are gone. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Is there anyone the same as mine error while loading library(DESeq2)? Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [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: Update all/some/none? Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : If you try loading the DEseq2 library now, that might work. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Rload failed - By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Bioconductor - DESeq2 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. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Installation instructions to use this I also tried something I found on google: but the installation had errors too, I can write them here if needed. Error: package or namespace load failed, object not found [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Running under: macOS Sierra 10.12.6. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 there is no package called data.table R DESeq2 - But I guess you have many problems with your installation, and I'd suggest. It is working now. Why is this sentence from The Great Gatsby grammatical? biocLite(), install.packages() (and the devtools equivalent?) DESeq2_2301_76497647-CSDN Making statements based on opinion; back them up with references or personal experience. March 1, 2023, 3:25pm - the incident has nothing to do with me; can I use this this way? 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: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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. To resolve this error, install the required package as a cluster-installed library. 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. Platform: x86_64-apple-darwin15.6.0 (64-bit) 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. guide. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 rev2023.3.3.43278. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Looking for incompatible packages.This can take several minutes. Choose Yes. Find centralized, trusted content and collaborate around the technologies you use most. To learn more, see our tips on writing great answers. I need help installing a package "DESeq2" having - RStudio Community The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? package rlang was built under R version 3.5.1. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Why do academics stay as adjuncts for years rather than move around? [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in [5] IRanges_2.8.1 S4Vectors_0.12.1 It only takes a minute to sign up. 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. 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 9. Error when installing Aldex2 - Community Plugin Support - Open Source The best answers are voted up and rise to the top, Not the answer you're looking for? I tried following the instructions for 2019.7 as well and I am getting the same error. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Content type 'application/zip' length 233860 bytes (228 KB) What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 nnet, spatial, survival. How can we prove that the supernatural or paranormal doesn't exist? If not fixed, Try removing remove.packages (rlang) then. "4.2") and enter: For older versions of R, please refer to the appropriate there is no package called GenomeInfoDbData By clicking Sign up for GitHub, you agree to our terms of service and downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. 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. 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). May be the version has problem How can I do ? 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 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. Asking for help, clarification, or responding to other answers. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () I've previously written a blog post about this topic, and I can say from experience that installing R packages through conda can cause lots of headaches. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Why are physically impossible and logically impossible concepts considered separate in terms of probability? You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. there is no package called GenomeInfoDbData To subscribe to this RSS feed, copy and paste this URL into your RSS reader. sessionInfo() I can download DESeq2 using, User Agreement and Privacy March 1, 2023, 8:52pm Can't Load R DESeq2 Library, Installed All Missing Packages and Still Is there a single-word adjective for "having exceptionally strong moral principles"? Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. [7] datasets methods base, other attached packages: R| - Try installing zip, and then loading olsrr. Installing package(s) 'htmlTable', 'xfun' LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Please try reinstalling rlang on a fresh session. Already on GitHub? I then launched the R application (from the finder, not RStudio) and installed BiocManager. Why is there a voltage on my HDMI and coaxial cables? Press CTRL-C to abort. + "htmlTable", "xfun" to allow custom library locations. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. . library(DESeq2) [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 1. Follow Up: struct sockaddr storage initialization by network format-string. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 2. 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. Glad everything is finally working now. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. This includes any installed libraries. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 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]]): Replacing broken pins/legs on a DIP IC package. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 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'. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Well occasionally send you account related emails. + ), update = TRUE, ask = FALSE) [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( DESeq2: Error: package or namespace load failed for 'DESeq2': objects [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. there is no package called Hmisc. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 library(caret) namespace load failed Object sigma not found caret , . Solution To resolve this error, install the required package as a cluster-installed library. Then I reinstalled R then Rstudio then RTools. to your account. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Error: package or namespace load failed for 'DESeq2 - Bioconductor My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? error: object 'rlang_dots_list' not found When you load the package, you can observe this error. 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). nnet, spatial, survival Remember to always click on the red Show me the content on this page notice when navigating these older versions. Warning message: Post questions about Bioconductor Please read the posting 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. I've copied the output below in case it helps with troubleshooting. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Bioconductor release. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Looking for incompatible packages. Policy. Not the answer you're looking for? I thought that working in a new environment would help, but it didnt. I do know that it works well in qiime2-2020.6. privacy statement. To learn more, see our tips on writing great answers. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3
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