[1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: I would recommend installing an older version of QIIME 2 for this plugin to work. Is there anyone the same as mine error while loading library(DESeq2)? Just to add on -- do you require an old version of Bioconductor for your current project? Fortunately I was able to solve it by doing things from several suggested solutions. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Have you tried install.packages("locfit") ? Also make sure that you have RTools.exe installed and working. If you preorder a special airline meal (e.g. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): 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 Why is there a voltage on my HDMI and coaxial cables? [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Press CTRL-C to abort. To learn more, see our tips on writing great answers. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Is it suspicious or odd to stand by the gate of a GA airport watching the planes? ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [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. Installing Hmisc as suggested above did not solve the issue. Running under: Windows 10 x64 (build 18362), locale: [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 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. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Already on GitHub? I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. 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: I tried to download the "locfit" package but I can't find it anywhere. Any suggestions would be greatly appreciated. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Is there a proper earth ground point in this switch box? installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Acidity of alcohols and basicity of amines. (Factorization). there is no package called GenomeInfoDbData If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Surly Straggler vs. other types of steel frames. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. (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 . I highly recommend that any R/RStudio version not installed inside conda be removed. Please remember to confirm an answer once you've received one. Policy. Just updated my previous R to 4.01 and now I cant load DESeq2. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Finally After 3-4 manual installations of missing packages everything worked. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Platform: x86_64-apple-darwin17.0 (64-bit) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Whats the grammar of "For those whose stories they are"? Disconnect between goals and daily tasksIs it me, or the industry? Not the answer you're looking for? 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). - the incident has nothing to do with me; can I use this this way? 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 Thanks for contributing an answer to Stack Overflow! What is the output of. . 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. Also note, however, that the error you got has been associated in the past with mirror outages. "After the incident", I started to be more careful not to trip over things. Give up and run everything from the "permitted" library location (e.g. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. + ), update = TRUE, ask = FALSE) 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. [69] tidyselect_1.0.0. [a/s/n]: Update all/some/none? I was assuming that to be the case. Post questions about Bioconductor 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. By clicking Sign up for GitHub, you agree to our terms of service and requires R 4 and running more than a couple of releases behind in R risks multiplying problems. 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. install.packages ("zip") [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 The best answers are voted up and rise to the top, Not the answer you're looking for? I can download DESeq2 using, User Agreement and Privacy Thanks for contributing an answer to Bioinformatics Stack Exchange! 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 Use of this site constitutes acceptance of our User Agreement and Privacy installation of package GenomeInfoDbData had non-zero exit status. Does a summoned creature play immediately after being summoned by a ready action? sessionInfo() 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). @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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages it would be good to hear any speculation you have of how this might have happened). 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. 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. Let me confer with the team. I tried following the instructions for 2019.7 as well and I am getting the same error. Language(R, Python, SQL) install.packages("BiocManager"), I get this error: I installed the package successfully with conda, but Rstudio is apparently does not know about it. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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]]) : Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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"). But I guess you have many problems with your installation, and I'd suggest. 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!). How to use Slater Type Orbitals as a basis functions in matrix method correctly? Retrying with flexible solve.Solving environment: Found conflicts! Thanks for your suggestion. Making statements based on opinion; back them up with references or personal experience. library(DESeq2) trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Traffic: 307 users visited in the last hour, I am new to all this! + "htmlTable", "xfun" Making statements based on opinion; back them up with references or personal experience. 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. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( This includes any installed libraries. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. rev2023.3.3.43278. Asking for help, clarification, or responding to other answers. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. 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. now when I tried installing the missing packages they did install. So, supposedly the issue is with Hmisc. there is no package called Hmisc. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 in your system, start R and enter: Follow [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 When you load the package, you can observe this error. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. 4. I've copied the output below in case it helps with troubleshooting. 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. package in your R session. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Use of this site constitutes acceptance of our User Agreement and Privacy running multiple versions of the same package, keeping separate libraries for some projects). Making statements based on opinion; back them up with references or personal experience. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Are there tables of wastage rates for different fruit and veg? and then updating the packages that command indicates. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, 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: im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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 . Is there anything I can do to speed it up? 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. While a notebook is attached to a cluster, the R namespace cannot be refreshed. 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"). [16] phyloseq1.30.0, loaded via a namespace (and not attached): How can we prove that the supernatural or paranormal doesn't exist? Follow Up: struct sockaddr storage initialization by network format-string. Is there a proper earth ground point in this switch box? 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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) When you load the package, you can observe this error. Thanks! 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. [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: 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. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 In install.packages() : I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. One solution is to find all available packages. so I would try to use BiocManager::install("XML"). 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. Try installing zip, and then loading olsrr. Is a PhD visitor considered as a visiting scholar? But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Sign in Platform: x86_64-apple-darwin15.6.0 (64-bit) By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? How to use Slater Type Orbitals as a basis functions in matrix method correctly? I am running a new install of R (3.5.0) and RStudio (1.1.414). More info about Internet Explorer and Microsoft Edge. Content type 'application/zip' length 233860 bytes (228 KB) I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Policy. Why do academics stay as adjuncts for years rather than move around? [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: Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. there is no package called data.table From the console install.packages ("rlang") should fix this. Are you sure the R you're running from the command line is installed through Anaconda as well? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. to allow custom library locations. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. :), BiocManager::install("locift") How to notate a grace note at the start of a bar with lilypond? RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 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. Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or? Not the answer you're looking for? [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 1. Use this. Documentation to your account. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) It is working now. This can take several minutes. Surly Straggler vs. other types of steel frames. Choose Yes. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. "4.2") and enter: For older versions of R, please refer to the appropriate Warning message: Feedback Installing package(s) 'htmlTable', 'xfun' R version 3.6.3 (2020-02-29) 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"). rev2023.3.3.43278. I also tried something I found on google: but the installation had errors too, I can write them here if needed. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Well occasionally send you account related emails. error: object 'rlang_dots_list' not found 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. Use MathJax to format equations. Erasmus+ funds available! Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) guide. 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. To learn more, see our tips on writing great answers. I just figured Id ask. 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. ERROR: dependency Hmisc is not available for package DESeq2 Warning: cannot remove prior installation of package xfun there is no package called GenomeInfoDbData [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: vegan) just to try it, does this inconvenience the caterers and staff? Start R to confirm they are gone. Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Warning: restored xfun, The downloaded binary packages are in check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Glad everything is finally working now. @artembus Sounds like it was a ton of work! Is the God of a monotheism necessarily omnipotent? Installing package(s) 'GenomeInfoDbData' call: dots_list() now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly.