Are you sure the R you're running from the command line is installed through Anaconda as well? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 "After the incident", I started to be more careful not to trip over things. I would like to install DESeq2 for DE analysis. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). ERROR: lazy loading failed for package Hmisc So if you still get this error try changing your CRAN mirror. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. Why are physically impossible and logically impossible concepts considered separate in terms of probability? You are doing something very wrong when installing your packages. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Then I reinstalled R then Rstudio then RTools. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. 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 package xfun successfully unpacked and MD5 sums checked [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 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. Sign in To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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"). dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext 2. 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. Statistics ; Algorithm(ML, DL,.) [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: DESeq2 - I can't get the library to load - Bioconductor [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Have you tried install.packages("locfit") ? there is no package called data.table library(caret) namespace load failed Object sigma not . [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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. I thought that working in a new environment would help, but it didnt. Error: package or namespace load failed for 'DESeq2 - Bioconductor there is no package called GenomeInfoDbData 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. Running under: Windows 10 x64 (build 18362), locale: biocLite(), install.packages() (and the devtools equivalent?) "htmlTable", "xfun" Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Retrying with flexible solve.Solving environment: Found conflicts! privacy statement. Is there a proper earth ground point in this switch box? error: object 'rlang_dots_list' not found Bioconductor - DESeq2 1. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Give up and run everything from the "permitted" library location (e.g. Please remember to confirm an answer once you've received one. Installing package(s) 'htmlTable', 'xfun' I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. A place where magic is studied and practiced? downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked 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. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Installing package(s) 'XML' Start R to confirm they are gone. Why is there a voltage on my HDMI and coaxial cables? I've copied the output below in case it helps with troubleshooting. Sounds like you might have an issue with which R Rstudio is running. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 I guess that means we can finally close this issue. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. [69] tidyselect_1.0.0. a, There are binary versions available but the source versions are later: Finally After 3-4 manual installations of missing packages everything worked. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. This includes any installed libraries. How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 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 . Use MathJax to format equations. 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. I tried to download the "locfit" package but I can't find it anywhere. In install.packages() : C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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. Platform: x86_64-apple-darwin17.0 (64-bit) I tried again and again was met with missing packages BUT!!! rev2023.3.3.43278. Disconnect between goals and daily tasksIs it me, or the industry? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. 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. Use of this site constitutes acceptance of our User Agreement and Privacy Remember to always click on the red Show me the content on this page notice when navigating these older versions. 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 Convince your IT department to relax the permissions for R packages to your account. I was assuming that to be the case. Do I need a thermal expansion tank if I already have a pressure tank? [1] stats4 parallel stats graphics grDevices utils Asking for help, clarification, or responding to other answers. In addition: Warning message: To view documentation for the version of this package installed Warning message: By clicking Sign up for GitHub, you agree to our terms of service and I'm trying to reproduce your problem, so being as precise as possible is important. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. @artembus Sounds like it was a ton of work! [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Please try the following steps: Quit all R/Rstudio sessions. 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). [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: [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 binary source needs_compilation Let me confer with the team. 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: