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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. This includes any installed libraries. in your system, start R and enter: Follow "After the incident", I started to be more careful not to trip over things. :), BiocManager::install("locift") Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. 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). How can we prove that the supernatural or paranormal doesn't exist? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Retrying with flexible solve.Solving environment: Found conflicts! How do I align things in the following tabular environment? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 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]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Bioconductor release. Use of this site constitutes acceptance of our User Agreement and Privacy 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. By clicking Sign up for GitHub, you agree to our terms of service and 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!!! Policy. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [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. @artembus Sounds like it was a ton of work! 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. Connect and share knowledge within a single location that is structured and easy to search. [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: And finally, install the problem packages, perhaps also DESeq2. Not the answer you're looking for? [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 "After the incident", I started to be more careful not to trip over things. 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. To add to this, I have also been using DESeq2 recently and ran into the same problem. Running. I tried again and again was met with missing packages BUT!!! Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: After 3-4 manual installs everything worked. When an R package depends on a newer package version, the required package is downloaded but not loaded. Disconnect between goals and daily tasksIs it me, or the industry? Open Source Biology & Genetics Interest Group. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 "4.2") and enter: For older versions of R, please refer to the appropriate Join us at CRISPR workshops in Koper, Slovenia in 2023. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 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. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. [5] IRanges_2.8.1 S4Vectors_0.12.1 Any suggestions would be greatly appreciated. How to use Slater Type Orbitals as a basis functions in matrix method correctly? To view documentation for the version of this package installed [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 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. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I am running a new install of R (3.5.0) and RStudio (1.1.414). Installation instructions to use this Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, 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 also tried something I found on google: but the installation had errors too, I can write them here if needed. ERROR: dependency Hmisc is not available for package DESeq2 rev2023.3.3.43278. 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. March 1, 2023, 8:52pm Making statements based on opinion; back them up with references or personal experience. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () library(caret) namespace load failed Object sigma not found caret , . [7] edgeR_3.16.5 limma_3.30.12 Whats the grammar of "For those whose stories they are"? install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Just to add on -- do you require an old version of Bioconductor for your current project? Then I reinstalled R then Rstudio then RTools. 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. a, There are binary versions available but the source versions are later: install.packages("BiocManager"), I get this error: 4. I would recommend installing an older version of QIIME 2 for this plugin to work. vegan) just to try it, does this inconvenience the caterers and staff? 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. Platform: x86_64-w64-mingw32/x64 (64-bit) Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. 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). [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: 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. Platform: x86_64-apple-darwin17.0 (64-bit) 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: Loading required package: GenomeInfoDb rev2023.3.3.43278. Installing Hmisc as suggested above did not solve the issue. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 data . [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 This topic was automatically closed 21 days after the last reply. 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. 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. 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. Old packages: 'RcppArmadillo', 'survival' Find centralized, trusted content and collaborate around the technologies you use most. Just realize that I need to write the script "library("DESeq2")" before I proceed. nnet, spatial, survival. March 1, 2023, 4:56pm Acidity of alcohols and basicity of amines. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 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. Why is this sentence from The Great Gatsby grammatical? Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR 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: 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). 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 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. Use MathJax to format equations. .onLoad failed in loadNamespace() for 'rlang', details: Warning: restored xfun, The downloaded binary packages are in Is there a proper earth ground point in this switch box? Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Not the answer you're looking for? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. 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. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 + "htmlTable", "xfun" As such there are two solutions that may be more or less attainable given your own IT system. 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. Please remember to confirm an answer once you've received one. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so and then updating the packages that command indicates. Use of this site constitutes acceptance of our User Agreement and Privacy 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. there is no package called GenomeInfoDbData there is no package called locfit. Is a PhD visitor considered as a visiting scholar? [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. install.packages ("zip") I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. 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. Please try the following steps: Quit all R/Rstudio sessions. 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. - the incident has nothing to do with me; can I use this this way? [a/s/n]: 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]]) : If you preorder a special airline meal (e.g. Making statements based on opinion; back them up with references or personal experience. Why are physically impossible and logically impossible concepts considered separate in terms of probability? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Try installing zip, and then loading olsrr. Policy. [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: 9. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Is there anyone the same as mine error while loading library(DESeq2)? . New replies are no longer allowed. 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. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Connect and share knowledge within a single location that is structured and easy to search. To learn more, see our tips on writing great answers. Why do many companies reject expired SSL certificates as bugs in bug bounties? Installing package(s) 'GenomeInfoDbData' The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Convince your IT department to relax the permissions for R packages To learn more, see our tips on writing great answers. 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. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Whats the grammar of "For those whose stories they are"? Thanks for contributing an answer to Stack Overflow! 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. Statistics ; Algorithm(ML, DL,.) nnet, spatial, survival 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. call: dots_list() ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: (I have the most recent version of tidyverse, RStudio, and R.) Error: package or namespace load failed for 'tidyverse': .onAttach failed in attachNamespace() for 'tidyverse', details: call: glue(str, .envir = .envir, .transformer = transformer . When you load the package, you can observe this error. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. 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. @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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. R version 3.6.1 (2019-07-05) biocLite(), install.packages() (and the devtools equivalent?) 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Should I update the Bioconductor to latest version instead? Language(R, Python, SQL) library ("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 'Hmisc' Installing Hmisc as suggested above did not solve the issue. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. May I know is there any other approach I can try? To resolve this error, install the required package as a cluster-installed library. MathJax reference. now when I tried installing the missing packages they did install. March 1, 2023, 7:31pm Is it suspicious or odd to stand by the gate of a GA airport watching the planes? How to use Slater Type Orbitals as a basis functions in matrix method correctly? there is no package called Hmisc. Sorry, I'm newbie. The best answers are voted up and rise to the top, Not the answer you're looking for? [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 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. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Warning: cannot remove prior installation of package xfun Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Sign in If not fixed, Try removing remove.packages (rlang) then. 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. Thank you @hharder. It is working now. R version 4.0.1 (2020-06-06) [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Do I need a thermal expansion tank if I already have a pressure tank? privacy statement. When you load the package, you can observe this error. What am I doing wrong here in the PlotLegends specification? [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Surly Straggler vs. other types of steel frames. Policy. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Thanks for your suggestion. Running under: macOS Catalina 10.15.3, Matrix products: default I can download DESeq2 using, User Agreement and Privacy By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. @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. Warning message: 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 Does anyone know why I'm getting the following message when I load tidyverse in a new session. In addition: Warning message: Documentation