I even tried BiocManager::install("XML") but all failed as shown below. What is the output of. You are doing something very wrong when installing your packages. [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. nnet, spatial, survival. Did you do that? Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Disconnect between goals and daily tasksIs it me, or the industry? Error: package or namespace load failed for 'DESeq2 - Bioconductor Warning message: Is there a proper earth ground point in this switch box? To learn more, see our tips on writing great answers. package xfun successfully unpacked and MD5 sums checked New replies are no longer allowed. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 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. In addition: Warning message: [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Platform: x86_64-apple-darwin15.6.0 (64-bit) 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Remember to always click on the red Show me the content on this page notice when navigating these older versions. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 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!!! When you load the package, you can observe this error. @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. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Running under: macOS Sierra 10.12.6. Policy. Press CTRL-C to abort. How can we prove that the supernatural or paranormal doesn't exist? Is a PhD visitor considered as a visiting scholar? Open Source Biology & Genetics Interest Group. 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. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. 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. 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: I guess that means we can finally close this issue. After 3-4 manual installs everything worked. 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. Platform: x86_64-apple-darwin13.4.0 (64-bit) Surly Straggler vs. other types of steel frames. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 By clicking Sign up for GitHub, you agree to our terms of service and To learn more, see our tips on writing great answers. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Thanks for your suggestion. Not the answer you're looking for? DESeq2_2301_76497647-CSDN [a/s/n]: You signed in with another tab or window. 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 . [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 rev2023.3.3.43278. 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 Just realize that I need to write the script "library("DESeq2")" before I proceed. Just updated my previous R to 4.01 and now I cant load DESeq2. Running under: Windows 10 x64 (build 18362), locale: Is a PhD visitor considered as a visiting scholar? there is no package called Hmisc. One solution is to find all available packages. I also tried something I found on google: but the installation had errors too, I can write them here if needed. The package has place the R version constraint. Any suggestions would be greatly appreciated. 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'. 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 DESeq2 - I can't get the library to load - Bioconductor Documentation 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. Connect and share knowledge within a single location that is structured and easy to search. When an R package depends on a newer package version, the required package is downloaded but not loaded. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Running. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): binary source needs_compilation Sorry, I'm newbie. I tried following the instructions for 2019.7 as well and I am getting the same error. Convince your IT department to relax the permissions for R packages By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. .onLoad failed in loadNamespace() for 'rlang', details: [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Thanks for contributing an answer to Stack Overflow! Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 call: dots_list() It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [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: Replacing broken pins/legs on a DIP IC package. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? 9. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Does a summoned creature play immediately after being summoned by a ready action? 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. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Use MathJax to format equations. Installation instructions to use this Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Feedback If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. 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. A place where magic is studied and practiced? March 1, 2023, 3:25pm So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. 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. This topic was automatically closed 21 days after the last reply. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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 library(caret) namespace load failed Object sigma not found caret , . - the incident has nothing to do with me; can I use this this way? [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 What am I doing wrong here in the PlotLegends specification? to your account. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Platform: x86_64-apple-darwin17.0 (64-bit) install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Have a question about this project? Bioconductor - 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. Asking for help, clarification, or responding to other answers. We've tried this - and can replicate this issue on a completely new install with no existing package installs. 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. Statistics ; Algorithm(ML, DL,.) I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. 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: install.packages("BiocManager"), I get this error: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. running multiple versions of the same package, keeping separate libraries for some projects). [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: rev2023.3.3.43278. Old packages: 'RcppArmadillo', 'survival' + "htmlTable", "xfun" @artembus Sounds like it was a ton of work! So, supposedly the issue is with Hmisc. Platform: x86_64-w64-mingw32/x64 (64-bit) Making statements based on opinion; back them up with references or personal experience. Retrying with flexible solve.Solving environment: Found conflicts! If it fails, required operating system facilities are missing. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. 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. and then updating the packages that command indicates. Connect and share knowledge within a single location that is structured and easy to search. Why do many companies reject expired SSL certificates as bugs in bug bounties? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Loading required package: GenomicRanges Use of this site constitutes acceptance of our User Agreement and Privacy there is no package called Hmisc. 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'. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. in your system, start R and enter: Follow I hope you can see something I can't see and help me solving this issue. Solution To resolve this error, install the required package as a cluster-installed library. No error messages are returned. I highly recommend that any R/RStudio version not installed inside conda be removed. 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. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached):