I also tried something I found on google: but the installation had errors too, I can write them here if needed. + "htmlTable", "xfun" [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Looking for incompatible packages.This can take several minutes. 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. sessionInfo() Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? a, There are binary versions available but the source versions are later: 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. 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. Follow Up: struct sockaddr storage initialization by network format-string. 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'm having a similar error, but different package: library("DESeq2") If you try loading the DEseq2 library now, that might work. 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. 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. 9. Not the answer you're looking for? [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 After 3-4 manual installs everything worked. [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. 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. 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 [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( package rlang was built under R version 3.5.1. I guess that means we can finally close this issue. Warning: restored xfun, The downloaded binary packages are in LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Remember to always click on the red Show me the content on this page notice when navigating these older versions. Policy. As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Join us at CRISPR workshops in Koper, Slovenia in 2023. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 Does anyone know why I'm getting the following message when I load tidyverse in a new session. What is the output of. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages You signed in with another tab or window. This includes any installed libraries. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 installation of package GenomeInfoDbData had non-zero exit status. But I guess you have many problems with your installation, and I'd suggest. 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. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Asking for help, clarification, or responding to other answers. [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: [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 This topic was automatically closed 21 days after the last reply. Running under: Windows 10 x64 (build 18362), locale: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. I hope you can see something I can't see and help me solving this issue. if (!require("BiocManager", quietly = TRUE)) Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Platform: x86_64-apple-darwin15.6.0 (64-bit) I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Well occasionally send you account related emails. Old packages: 'RcppArmadillo', 'survival' library(caret) namespace load failed Object sigma not found caret , . Solution To resolve this error, install the required package as a cluster-installed library. Running under: macOS Sierra 10.12.6. Warning message: Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. 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'. How to use Slater Type Orbitals as a basis functions in matrix method correctly? Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Should I update the Bioconductor to latest version instead? If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. What do I need to do to reproduce your problem? Content type 'application/zip' length 386703 bytes (377 KB) Fortunately I was able to solve it by doing things from several suggested solutions. Asking for help, clarification, or responding to other answers. Installing package(s) 'XML' Is there anything I can do to speed it up? [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 How to notate a grace note at the start of a bar with lilypond? 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. Making statements based on opinion; back them up with references or personal experience. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? call: dots_list() Thanks for contributing an answer to Stack Overflow! To resolve this error, install the required package as a cluster-installed library. Acidity of alcohols and basicity of amines. 2. March 1, 2023, 4:56pm Please remember to confirm an answer once you've received one. I was assuming that to be the case. I can download DESeq2 using, User Agreement and Privacy RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Sounds like you might have an issue with which R Rstudio is running. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Why is there a voltage on my HDMI and coaxial cables? To learn more, see our tips on writing great answers. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R To view documentation for the version of this package installed Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Loading required package: GenomicRanges In install.packages() : 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? Please try reinstalling rlang on a fresh session. Use of this site constitutes acceptance of our User Agreement and Privacy Sorry, I'm newbie. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 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. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 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. CRAN: https://mirrors.sjtug.sjtu.edu.cn/cran/, Bioconductor version 3.12 (BiocManager 1.30.17), R 4.0.3 (2020-10-10), Old packages: 'cli', 'dplyr', 'igraph', 'MASS', 'ps', 'RSQLite', 'testthat', 'tibble', package locift is not available for Bioconductor version '3.12', A version of this package for your version of R might be available elsewhere,see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages. Bad: conda install -c bioconda bioconductor-deseq2. [7] datasets methods base, other attached packages: rev2023.3.3.43278. If you have a query related to it or one of the replies, start a new topic and refer back with a link. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Replacing broken pins/legs on a DIP IC package. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. I even tried BiocManager::install("XML") but all failed as shown below. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 March 1, 2023, 8:52pm install.packages ("zip") Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Policy. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Making statements based on opinion; back them up with references or personal experience. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib How do you ensure that a red herring doesn't violate Chekhov's gun? Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext So, supposedly the issue is with Hmisc. Does a summoned creature play immediately after being summoned by a ready action? 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. When you load the package, you can observe this error. Platform: x86_64-apple-darwin13.4.0 (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. R version 4.0.1 (2020-06-06) [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Platform: x86_64-w64-mingw32/x64 (64-bit) [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 - the incident has nothing to do with me; can I use this this way? The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Update all/some/none? 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: Learn more about Stack Overflow the company, and our products. Did you do that? By clicking Sign up for GitHub, you agree to our terms of service and 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). [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: 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"). Surly Straggler vs. other types of steel frames. Post questions about Bioconductor Use this. 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: But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () 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"). Choose Yes. 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
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