error: package or namespace load failed for 'deseq2

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: Solution To resolve this error, install the required package as a cluster-installed library. Why is this sentence from The Great Gatsby grammatical? Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I am using R 3.6.1 and Rstudio 1.2. technocrat August 27, 2020, 10:15pm #2 RedRabbit: DESeq2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. "4.2") and enter: For older versions of R, please refer to the appropriate 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: I highly recommend that any R/RStudio version not installed inside conda be removed. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 now when I tried installing the missing packages they did install. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Why is there a voltage on my HDMI and coaxial cables? This can take several minutes. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Content type 'application/zip' length 233860 bytes (228 KB) 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. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. I guess that means we can finally close this issue. Policy. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Running. 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. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Glad everything is finally working now. 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. Is there anyone the same as mine error while loading library(DESeq2)? survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in @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. I am running a new install of R (3.5.0) and RStudio (1.1.414). 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'. package xfun successfully unpacked and MD5 sums checked 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. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 there is no package called GenomeInfoDbData ERROR: lazy loading failed for package Hmisc + "htmlTable", "xfun" [a/s/n]: (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 . Platform: x86_64-apple-darwin15.6.0 (64-bit) Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. This includes any installed libraries. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Platform: x86_64-apple-darwin17.0 (64-bit) there is no package called GenomeInfoDbData And finally, install the problem packages, perhaps also DESeq2. How can we prove that the supernatural or paranormal doesn't exist? I even tried BiocManager::install("XML") but all failed as shown below. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 I then launched the R application (from the finder, not RStudio) and installed BiocManager. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. By clicking Sign up for GitHub, you agree to our terms of service and So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? When you load the package, you can observe this error. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Is a PhD visitor considered as a visiting scholar? 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: downloaded 228 KB, package htmlTable 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]]): install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Remember to always click on the red Show me the content on this page notice when navigating these older versions. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. March 1, 2023, 7:31pm To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Is there a proper earth ground point in this switch box? "After the incident", I started to be more careful not to trip over things. Warning message: What is a word for the arcane equivalent of a monastery? enter citation("DESeq2")): To install this package, start R (version [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 You are doing something very wrong when installing your packages. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Well occasionally send you account related emails. As such there are two solutions that may be more or less attainable given your own IT system. Do I need a thermal expansion tank if I already have a pressure tank? there is no package called locfit. Join us at CRISPR workshops in Koper, Slovenia in 2023. Running under: macOS Sierra 10.12.3, locale: so I would try to use BiocManager::install("XML"). I also tried something I found on google: but the installation had errors too, I can write them here if needed. 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 package in your R session. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Is the God of a monotheism necessarily omnipotent? It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 package rlang was built under R version 3.5.1. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Please try reinstalling rlang on a fresh session. A place where magic is studied and practiced? Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib 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. It only takes a minute to sign up. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 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. Statistics ; Algorithm(ML, DL,.) 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. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Is there a single-word adjective for "having exceptionally strong moral principles"? Finally After 3-4 manual installations of missing packages everything worked. installation of package GenomeInfoDbData had non-zero exit status. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Choose Yes. Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace (i, c (lib.loc, .libPaths ()), versionCheck = vI [ [i]]): there is no package called 'GenomeInfoDbData' Error: package 'GenomeInfoDb' could not be loaded When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Is there a proper earth ground point in this switch box? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Sounds like you might have an issue with which R Rstudio is running. Are there tables of wastage rates for different fruit and veg? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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 MathJax reference. In file.copy(savedcopy, lib, recursive = TRUE) : If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Retrying with flexible solve.Solving environment: Found conflicts! To learn more, see our tips on writing great answers. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. One solution is to find all available packages. Thnaks anyway, Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems, How Intuit democratizes AI development across teams through reusability. How to notate a grace note at the start of a bar with lilypond? [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. + ), update = TRUE, ask = FALSE) [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): 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 . C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . What do I need to do to reproduce your problem? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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. Content type 'application/zip' length 386703 bytes (377 KB) Installing Hmisc as suggested above did not solve the issue. To learn more, see our tips on writing great answers. Did you do that? I do know that it works well in qiime2-2020.6. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 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]]): Feedback [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 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. "htmlTable", "xfun" downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' From the console install.packages ("rlang") should fix this. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Thanks! Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. - the incident has nothing to do with me; can I use this this way? and then updating the packages that command indicates. sessionInfo() @artembus Sounds like it was a ton of work! That plugin is has not been updated to work with later releases of QIIME 2. In addition: Warning message: library(DESeq2) Styling contours by colour and by line thickness in QGIS. 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. Policy. Surly Straggler vs. other types of steel frames. Sign in 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. Any suggestions would be greatly appreciated. R version 4.0.1 (2020-06-06) Press CTRL-C to abort. Does a summoned creature play immediately after being summoned by a ready action? [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Hello, - the incident has nothing to do with me; can I use this this way? Platform: x86_64-apple-darwin13.4.0 (64-bit) [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 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. 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. Looking for incompatible packages. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 How do I align things in the following tabular environment? Already on GitHub? I have tried your suggestion and also updating the packages that command indicates. Is a PhD visitor considered as a visiting scholar? BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib [7] datasets methods base, other attached 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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Warning message: 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. 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"). Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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. Installing package(s) 'XML' 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. You signed in with another tab or window. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. I tried to download the "locfit" package but I can't find it anywhere. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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[1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: I'm having a similar error, but different package: library("DESeq2") Content type 'application/zip' length 4255589 bytes (4.1 MB) If you try loading the DEseq2 library now, that might work. rev2023.3.3.43278. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 When you load the package, you can observe this error. Use of this site constitutes acceptance of our User Agreement and Privacy To resolve this error, install the required package as a cluster-installed library. 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!!! [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? To add to this, I have also been using DESeq2 recently and ran into the same problem. Just realize that I need to write the script "library("DESeq2")" before I proceed. In install.packages() : Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. We've tried this - and can replicate this issue on a completely new install with no existing package installs. 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? locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Open Source Biology & Genetics Interest Group. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. While a notebook is attached to a cluster, the R namespace cannot be refreshed. binary source needs_compilation 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. What is the output of. 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]]): How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Bioconductor release. Let me confer with the team. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Have you tried install.packages("locfit") ? in your system, start R and enter: Follow Asking for help, clarification, or responding to other answers. Replacing broken pins/legs on a DIP IC package. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. [5] IRanges_2.8.1 S4Vectors_0.12.1 Sounds like there might be an issue with conda setup? 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: nnet, spatial, survival. Not the answer you're looking for? More info about Internet Explorer and Microsoft Edge.
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