error: package or namespace load failed for 'deseq2

R version 4.0.1 (2020-06-06) [13] ggplot23.3.0 car3.0-7 carData3.0-3 Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. May be the version has problem How can I do ? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Content type 'application/zip' length 233860 bytes (228 KB) there is no package called locfit. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Running under: macOS Catalina 10.15.3, Matrix products: default I'm having a similar error, but different package: library("DESeq2") [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Warning message: While a notebook is attached to a cluster, the R namespace cannot be refreshed. Surly Straggler vs. other types of steel frames. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Thank you @hharder. Thanks for contributing an answer to Bioinformatics Stack Exchange! [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 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. 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. and then updating the packages that command indicates. If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead of the one you've installed via conda. Whats the grammar of "For those whose stories they are"? library(DESeq2) I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Is a PhD visitor considered as a visiting scholar? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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 Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. or install using BiocManager that will also install CRAN packages BiocManager::install('locfit'), I couldn't intall locfit but somehow, i did so many different things and it worked. 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. Sounds like you might have an issue with which R Rstudio is running. install.packages ("zip") I also tried something I found on google: but the installation had errors too, I can write them here if needed. Surly Straggler vs. other types of steel frames. If it fails, required operating system facilities are missing. 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. package rlang was built under R version 3.5.1. Try installing zip, and then loading olsrr. 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. [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. What do I need to do to reproduce your problem? DESeq2: Error: package or namespace load failed for 'DESeq2': objects [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Join us at CRISPR workshops in Koper, Slovenia in 2023. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. guide. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Why is there a voltage on my HDMI and coaxial cables? Just to add on -- do you require an old version of Bioconductor for your current project? Policy. I would like to install DESeq2 for DE analysis. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? there is no package called GenomeInfoDbData Making statements based on opinion; back them up with references or personal experience. Retrying with flexible solve.Solving environment: Found conflicts! Installation instructions to use this Thanks for your suggestion. [R] Error: package or namespace load failed for 'ggplot2' in [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): To view documentation for the version of this package installed [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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. Find centralized, trusted content and collaborate around the technologies you use most. but when I go to load the libraries I get this error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 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. When you load the package, you can observe this error. Replacing broken pins/legs on a DIP IC package. Then I reinstalled R then Rstudio then RTools. You signed in with another tab or window. rev2023.3.3.43278. library(DESeq2) binary source needs_compilation [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 it would be good to hear any speculation you have of how this might have happened). Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. installation of package GenomeInfoDbData had non-zero exit status. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. I even tried BiocManager::install("XML") but all failed as shown below. Documentation Use of this site constitutes acceptance of our User Agreement and Privacy That plugin is has not been updated to work with later releases of QIIME 2. I highly recommend that any R/RStudio version not installed inside conda be removed. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Feedback C:\R\R-3.4.3\library). Running under: macOS Sierra 10.12.6. rstudio - Error: package or namespace load failed for 'tidyverse One solution is to find all available packages. to one of the following locations: https://code.bioconductor.org/browse/DESeq2/, https://bioconductor.org/packages/DESeq2/, git clone https://git.bioconductor.org/packages/DESeq2, git clone git@git.bioconductor.org:packages/DESeq2. In install.packages() : Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). DESeq2_2301_76497647-CSDN 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. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under 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. Please try reinstalling rlang on a fresh session. 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. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 4. March 1, 2023, 3:25pm It is working now. - the incident has nothing to do with me; can I use this this way? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. "After the incident", I started to be more careful not to trip over things. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Policy. Why is this sentence from The Great Gatsby grammatical? dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext So, supposedly the issue is with Hmisc. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Is there anyone the same as mine error while loading library(DESeq2)? Old packages: 'RcppArmadillo', 'survival' 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. How to notate a grace note at the start of a bar with lilypond? to allow custom library locations. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Glad everything is finally working now. 2. Looking for incompatible packages. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Press CTRL-C to abort. How can I fix error with loading package in R ? | ResearchGate Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Choose Yes. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Platform: x86_64-w64-mingw32/x64 (64-bit) Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Use this. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Use of this site constitutes acceptance of our User Agreement and Privacy Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Policy. Loading required package: GenomeInfoDb To learn more, see our tips on writing great answers. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Hello, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so library(caret) namespace load failed Object sigma not found caret , . Is the God of a monotheism necessarily omnipotent? 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). [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 I installed the package successfully with conda, but Rstudio is apparently does not know about it. Already on GitHub? Solving environment: Found conflicts! 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'. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. 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. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) How do I align things in the following tabular environment? Language(R, Python, SQL) Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? ERROR: dependency Hmisc is not available for package DESeq2 [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 [1] stats4 parallel stats graphics grDevices utils Not the answer you're looking for? /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Open Source Biology & Genetics Interest Group. Error when installing Aldex2 - Community Plugin Support - Open Source [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Disconnect between goals and daily tasksIs it me, or the industry? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Installing package(s) 'htmlTable', 'xfun' 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. 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. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Is a PhD visitor considered as a visiting scholar? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. library (olsrr) - Error - General - RStudio Community What is the output of. [16] phyloseq1.30.0, loaded via a namespace (and not attached): package in your R session. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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: To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 enter citation("DESeq2")): To install this package, start R (version Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 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]]): now when I tried installing the missing packages they did install. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Start R to confirm they are gone. Install DESeq2 through anaconda - Bioinformatics Stack Exchange

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