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. to allow custom library locations. 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. Should I update the Bioconductor to latest version instead? If it fails, required operating system facilities are missing. When you load the package, you can observe this error. Why is this sentence from The Great Gatsby grammatical? Finally After 3-4 manual installations of missing packages everything worked. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' installation of package GenomeInfoDbData had non-zero exit status. error: object 'rlang_dots_list' not found survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Post questions about Bioconductor C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Please try the following steps: Quit all R/Rstudio sessions. In addition: Warning message: By clicking Sign up for GitHub, you agree to our terms of service and 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 Thanks! Not the answer you're looking for? installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 When an R package depends on a newer package version, the required package is downloaded but not loaded. And finally, install the problem packages, perhaps also DESeq2. How to use Slater Type Orbitals as a basis functions in matrix method correctly? in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Give up and run everything from the "permitted" library location (e.g. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. In file.copy(savedcopy, lib, recursive = TRUE) : By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Running. Why do academics stay as adjuncts for years rather than move around? As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. 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 Try installing zip, and then loading olsrr. 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") Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Is there anyone the same as mine error while loading library(DESeq2)? Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 How do I align things in the following tabular environment? I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 To learn more, see our tips on writing great answers. Policy. + "htmlTable", "xfun" However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. 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. Bioconductor release. Policy. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): After 3-4 manual installs everything worked. Are you sure the R you're running from the command line is installed through Anaconda as well? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext How can we prove that the supernatural or paranormal doesn't exist? Start R to confirm they are gone. That plugin is has not been updated to work with later releases of QIIME 2. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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 could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Running under: macOS Sierra 10.12.6. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Installing Hmisc as suggested above did not solve the issue. 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. Just to add on -- do you require an old version of Bioconductor for your current project? Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. 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 This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. I would recommend installing an older version of QIIME 2 for this plugin to work. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Then I reinstalled R then Rstudio then RTools. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: 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. Is a PhD visitor considered as a visiting scholar? library(DESeq2) call: dots_list() I also tried something I found on google: but the installation had errors too, I can write them here if needed. Thanks for contributing an answer to Stack Overflow! Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. 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. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. How to use Slater Type Orbitals as a basis functions in matrix method correctly? LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: 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"). Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Is there a proper earth ground point in this switch box? [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [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: Running under: Windows 10 x64 (build 18362), locale: Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Also note, however, that the error you got has been associated in the past with mirror outages. 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. "After the incident", I started to be more careful not to trip over things. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Platform: x86_64-apple-darwin13.4.0 (64-bit) and then updating the packages that command indicates. Are there tables of wastage rates for different fruit and veg? Sorry, I'm newbie. I'm trying to reproduce your problem, so being as precise as possible is important. 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: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. I can download DESeq2 using, User Agreement and Privacy Content type 'application/zip' length 4255589 bytes (4.1 MB) Any other suggestion? @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. [69] tidyselect_1.0.0. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) I was assuming that to be the case. Policy. This includes any installed libraries. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) I just figured Id ask. @artembus Sounds like it was a ton of work! ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: 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 there is no package called data.table I tried to download the "locfit" package but I can't find it anywhere. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. there is no package called GenomeInfoDbData [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 - the incident has nothing to do with me; can I use this this way? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). (Factorization). [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Platform: x86_64-apple-darwin17.0 (64-bit) [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Loading required package: GenomeInfoDb I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. ERROR: dependency Hmisc is not available for package DESeq2 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. there is no package called Hmisc. Traffic: 307 users visited in the last hour, I am new to all this! package in your R session. Use MathJax to format equations. Bad: conda install -c bioconda bioconductor-deseq2. 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. If you have a query related to it or one of the replies, start a new topic and refer back with a link. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. 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 Use of this site constitutes acceptance of our User Agreement and Privacy March 1, 2023, 8:52pm Try again and choose No. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Does anyone know why I'm getting the following message when I load tidyverse in a new session. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Have you tried install.packages("locfit") ? As such there are two solutions that may be more or less attainable given your own IT system. Have a question about this project? To learn more, see our tips on writing great answers. "After the incident", I started to be more careful not to trip over things. Thanks for your suggestion. 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. Is there a proper earth ground point in this switch box? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Error in R: (Package which is only available in source form, and may need compilation of C/C++/Fortran), Loading BioConductor library "GO.db" fails, Installing R packages from a local repo (all .tar.gz files have been downloaded there), Cannot remove prior installation of package, but package not found, I can't seem to install the 'ecospat' package on R studio for windows, I am unable to install ggplot, there occurs some error. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Citation (from within R, R version 3.6.1 (2019-07-05) Connect and share knowledge within a single location that is structured and easy to search. 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. 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. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 In install.packages() : enter citation("DESeq2")): To install this package, start R (version sessionInfo() if (!require("BiocManager", quietly = TRUE)) Update all/some/none? Sounds like there might be an issue with conda setup? To learn more, see our tips on writing great answers. Please read the posting Find centralized, trusted content and collaborate around the technologies you use most. I hope you can see something I can't see and help me solving this issue. [5] IRanges_2.8.1 S4Vectors_0.12.1 privacy statement. So if you still get this error try changing your CRAN mirror. rev2023.3.3.43278. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Not the answer you're looking for? Installing package(s) 'GenomeInfoDbData' So, supposedly the issue is with Hmisc. Thank you @hharder. Replacing broken pins/legs on a DIP IC package. This can take several minutes. Content type 'application/zip' length 386703 bytes (377 KB) Please try reinstalling rlang on a fresh session. Already on GitHub? [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 This article explains how to resolve the package or namespace loading error. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. nnet, spatial, survival Convince your IT department to relax the permissions for R packages 1. To add to this, I have also been using DESeq2 recently and ran into the same problem. March 1, 2023, 7:31pm 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. running multiple versions of the same package, keeping separate libraries for some projects). Just updated my previous R to 4.01 and now I cant load DESeq2. Warning: restored xfun, The downloaded binary packages are in binary source needs_compilation 2. 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 . biocLite(), install.packages() (and the devtools equivalent?) Why are physically impossible and logically impossible concepts considered separate in terms of probability? I thought that working in a new environment would help, but it didnt. Whats the grammar of "For those whose stories they are"? * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. 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. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. The best answers are voted up and rise to the top, Not the answer you're looking for? Content type 'application/zip' length 233860 bytes (228 KB) 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 [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': I'm having a similar error, but different package: library("DESeq2") Use this. 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'. Asking for help, clarification, or responding to other answers.

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