error: package or namespace load failed for 'deseq2 error: package or namespace load failed for 'deseq2

[7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Give up and run everything from the "permitted" library location (e.g. In file.copy(savedcopy, lib, recursive = TRUE) : Whats the grammar of "For those whose stories they are"? The package has place the R version constraint. I guess that means we can finally close this issue. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 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. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 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]]) : 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"). 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"). If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Remember to always click on the red Show me the content on this page notice when navigating these older versions. C:\R\R-3.4.3\library). From the console install.packages ("rlang") should fix this. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 What is a word for the arcane equivalent of a monastery? Open Source Biology & Genetics Interest Group. there is no package called GenomeInfoDbData 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") - the incident has nothing to do with me; can I use this this way? [13] ggplot23.3.0 car3.0-7 carData3.0-3 Is there a proper earth ground point in this switch box? How do you ensure that a red herring doesn't violate Chekhov's gun? Bad: conda install -c bioconda bioconductor-deseq2. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. 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. [1] stats4 parallel stats graphics grDevices utils 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. @artembus Sounds like it was a ton of work! [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Why do academics stay as adjuncts for years rather than move around? I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. More info about Internet Explorer and Microsoft Edge. [7] datasets methods base, other attached packages: Why is this sentence from The Great Gatsby grammatical? Policy. guide. Is there anything I can do to speed it up? Are there tables of wastage rates for different fruit and veg? It is working now. I also tried something I found on google: but the installation had errors too, I can write them here if needed. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Why are physically impossible and logically impossible concepts considered separate in terms of probability? [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': No error messages are returned. binary source needs_compilation Then I reinstalled R then Rstudio then RTools. 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. Try again and choose No. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 package xfun successfully unpacked and MD5 sums checked 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 When you load the package, you can observe this error. I even tried BiocManager::install("XML") but all failed as shown below. Already on GitHub? 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. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 rev2023.3.3.43278. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Solving environment: Found conflicts! Following successful installation of backports BiocManager::install ("DESeq2") will succeed under [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Feedback By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 9. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") 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. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked .onLoad failed in loadNamespace() for 'rlang', details: Acidity of alcohols and basicity of amines. Not the answer you're looking for? Does a summoned creature play immediately after being summoned by a ready action? It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. R version 3.6.1 (2019-07-05) As such there are two solutions that may be more or less attainable given your own IT system. So if you still get this error try changing your CRAN mirror. This article explains how to resolve the package or namespace loading error. To add to this, I have also been using DESeq2 recently and ran into the same problem. Documentation ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Please try reinstalling rlang on a fresh session. And finally, install the problem packages, perhaps also DESeq2. now when I tried installing the missing packages they did install. Use this. 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, R version 3.3.2 (2016-10-31) Convince your IT department to relax the permissions for R packages May be the version has problem How can I do ? . Join us at CRISPR workshops in Koper, Slovenia in 2023. Policy. Erasmus+ funds available! Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. 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. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Sounds like you might have an issue with which R Rstudio is running. I tried to download the "locfit" package but I can't find it anywhere. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Then I reinstalled R then Rstudio then RTools. [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. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) "htmlTable", "xfun" Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) If you preorder a special airline meal (e.g. So, supposedly the issue is with Hmisc. 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. Hello, Platform: x86_64-apple-darwin13.4.0 (64-bit) Old packages: 'RcppArmadillo', 'survival' [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 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"). Press CTRL-C to abort. nnet, spatial, survival [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Thank you @hharder. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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 I just figured Id ask. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Did you do that? [69] tidyselect_1.0.0. Just realize that I need to write the script "library("DESeq2")" before I proceed. To view documentation for the version of this package installed Why is there a voltage on my HDMI and coaxial cables? I tried following the instructions for 2019.7 as well and I am getting the same error. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) When you load the package, you can observe this error. Warning: restored xfun, The downloaded binary packages are in [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 March 1, 2023, 4:56pm install.packages("BiocManager"), I get this error: [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Statistics ; Algorithm(ML, DL,.) [5] IRanges_2.8.1 S4Vectors_0.12.1 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. How to notate a grace note at the start of a bar with lilypond? Sorry, I'm newbie. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. I have tried your suggestion and also updating the packages that command indicates. Installing Hmisc as suggested above did not solve the issue. package in your R session. Any other suggestion? By clicking Sign up for GitHub, you agree to our terms of service and This includes any installed libraries. Use MathJax to format equations. 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: ERROR: lazy loading failed for package Hmisc :), BiocManager::install("locift") If not fixed, Try removing remove.packages (rlang) then. Styling contours by colour and by line thickness in QGIS. 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. I can download DESeq2 using, User Agreement and Privacy You are doing something very wrong when installing your packages. 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. Try installing zip, and then loading olsrr. Connect and share knowledge within a single location that is structured and easy to search. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Use of this site constitutes acceptance of our User Agreement and Privacy [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Is there a single-word adjective for "having exceptionally strong moral principles"? Is a PhD visitor considered as a visiting scholar? there is no package called Hmisc. + ), update = TRUE, ask = FALSE) Platform: x86_64-apple-darwin15.6.0 (64-bit) Should I update the Bioconductor to latest version instead? 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. The best answers are voted up and rise to the top, Not the answer you're looking for? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Replacing broken pins/legs on a DIP IC package. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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. enter citation("DESeq2")): To install this package, start R (version vegan) just to try it, does this inconvenience the caterers and staff? But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. 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. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? In install.packages() : [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 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 . sessionInfo() Solution To resolve this error, install the required package as a cluster-installed library. Glad everything is finally working now. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. 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. nnet, spatial, survival. installation of package GenomeInfoDbData had non-zero exit status. Connect and share knowledge within a single location that is structured and easy to search. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Have a question about this project? 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. 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: Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R.