Please try the following steps: Quit all R/Rstudio sessions. biocLite(), install.packages() (and the devtools equivalent?) If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Content type 'application/zip' length 386703 bytes (377 KB) Do I need a thermal expansion tank if I already have a pressure tank? Use of this site constitutes acceptance of our User Agreement and Privacy [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Post questions about Bioconductor package in your R session. .onLoad failed in loadNamespace() for 'rlang', details: 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. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Installing Hmisc as suggested above did not solve the issue. library(DESeq2) 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. [7] datasets methods base, other attached packages: To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 I tried following the instructions for 2019.7 as well and I am getting the same error. Are you sure the R you're running from the command line is installed through Anaconda as well? unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': What is a word for the arcane equivalent of a monastery? requires R 4 and running more than a couple of releases behind in R risks multiplying problems. From the console install.packages ("rlang") should fix this. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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 [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: Bad: conda install -c bioconda bioconductor-deseq2. 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. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Installing package(s) 'GenomeInfoDbData' Sounds like there might be an issue with conda setup? [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 [a/s/n]: Have you tried install.packages("locfit") ? Is there anything I can do to speed it up? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: I thought that working in a new environment would help, but it didnt. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 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'. Acidity of alcohols and basicity of amines. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. rev2023.3.3.43278. library(DESeq2) Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. [16] phyloseq1.30.0, loaded via a namespace (and not attached): New replies are no longer allowed. Installing package(s) 'htmlTable', 'xfun' dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Loading required package: GenomicRanges Warning message: Glad everything is finally working now. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. there is no package called locfit. Already on GitHub? Is the God of a monotheism necessarily omnipotent? there is no package called Hmisc. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 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). Whats the grammar of "For those whose stories they are"? Just updated my previous R to 4.01 and now I cant load DESeq2. Content type 'application/zip' length 4255589 bytes (4.1 MB) Is there a proper earth ground point in this switch box? Policy. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. March 1, 2023, 3:25pm [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 I have tried your suggestion and also updating the packages that command indicates. 9. 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. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 "After the incident", I started to be more careful not to trip over things. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 In file.copy(savedcopy, lib, recursive = TRUE) : How to use Slater Type Orbitals as a basis functions in matrix method correctly? Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): install.packages("BiocManager"), I get this error: [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Open Source Biology & Genetics Interest Group. I tried again and again was met with missing packages BUT!!! Why do academics stay as adjuncts for years rather than move around? I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and try to import DESeq2 I am getting the error message: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. and then updating the packages that command indicates. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? I was assuming that to be the case. Asking for help, clarification, or responding to other answers. Surly Straggler vs. other types of steel frames. (Factorization). Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Warning: restored xfun, The downloaded binary packages are in 0 packages out-of-date; 2 packages too new, BiocManager::install(c( 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. Have a question about this project? Running under: macOS Sierra 10.12.3, locale: Warning: cannot remove prior installation of package xfun Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Why are physically impossible and logically impossible concepts considered separate in terms of probability? Traffic: 307 users visited in the last hour, I am new to all this! Please try reinstalling rlang on a fresh session. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Just realize that I need to write the script "library("DESeq2")" before I proceed. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. More info about Internet Explorer and Microsoft Edge. So, supposedly the issue is with Hmisc. [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: /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Not the answer you're looking for? I tried to download the "locfit" package but I can't find it anywhere. Should I update the Bioconductor to latest version instead? Thanks for your suggestion. I would recommend installing an older version of QIIME 2 for this plugin to work. Are there tables of wastage rates for different fruit and veg? - the incident has nothing to do with me; can I use this this way? Is there anyone the same as mine error while loading library(DESeq2)? As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. @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. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 When an R package depends on a newer package version, the required package is downloaded but not loaded. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' 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 DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Any suggestions would be greatly appreciated. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 [5] IRanges_2.8.1 S4Vectors_0.12.1 Policy. Bioconductor release. Policy. The best answers are voted up and rise to the top, Not the answer you're looking for? If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages The package has place the R version constraint. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Also note, however, that the error you got has been associated in the past with mirror outages. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Start R to confirm they are gone. If it fails, required operating system facilities are missing. What am I doing wrong here in the PlotLegends specification? [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Replacing broken pins/legs on a DIP IC package. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 @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. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Find centralized, trusted content and collaborate around the technologies you use most. 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 . Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. I hope you can see something I can't see and help me solving this issue. 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. 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: [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 I also tried something I found on google: but the installation had errors too, I can write them here if needed. Why do many companies reject expired SSL certificates as bugs in bug bounties? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 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. Policy. 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. Follow Up: struct sockaddr storage initialization by network format-string. Learn more about Stack Overflow the company, and our products. rev2023.3.3.43278. What is the output of. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. While a notebook is attached to a cluster, the R namespace cannot be refreshed. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Feedback 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. As such there are two solutions that may be more or less attainable given your own IT system. C:\R\R-3.4.3\library). I've copied the output below in case it helps with troubleshooting. How do you ensure that a red herring doesn't violate Chekhov's gun? When you load the package, you can observe this error. [1] stats4 parallel stats graphics grDevices utils MathJax reference. 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. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. 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, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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. Loading required package: GenomeInfoDb 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. May be the version has problem How can I do ? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. call: dots_list() Is a PhD visitor considered as a visiting scholar? downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in nnet, spatial, survival. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? So if you still get this error try changing your CRAN mirror. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. If you preorder a special airline meal (e.g. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 To learn more, see our tips on writing great answers. rev2023.3.3.43278. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Running. Thanks! Citation (from within R, sessionInfo() 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 [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Surly Straggler vs. other types of steel frames. Then I reinstalled R then Rstudio then RTools. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. [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 . [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 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: Any other suggestion? Find centralized, trusted content and collaborate around the technologies you use most. Thanks for contributing an answer to Stack Overflow! This topic was automatically closed 21 days after the last reply. Please remember to confirm an answer once you've received one. [7] edgeR_3.16.5 limma_3.30.12 ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: so I would try to use BiocManager::install("XML"). R version 3.6.3 (2020-02-29) 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. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( 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. I can download DESeq2 using, User Agreement and Privacy Erasmus+ funds available! 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. It is working now. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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'm having a similar error, but different package: library("DESeq2") To view documentation for the version of this package installed Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 binary source needs_compilation Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Also make sure that you have RTools.exe installed and working. Let me confer with the team. I installed the package successfully with conda, but Rstudio is apparently does not know about it. 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.