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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. Then I reinstalled R then Rstudio then RTools. vegan) just to try it, does this inconvenience the caterers and staff? Any suggestions would be greatly appreciated. I hope you can see something I can't see and help me solving this issue. I would like to install DESeq2 for DE analysis. Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Surly Straggler vs. other types of steel frames. 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. @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. Platform: x86_64-apple-darwin17.0 (64-bit) Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) What is the output of. Also make sure that you have RTools.exe installed and working. 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. To learn more, see our tips on writing great answers. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_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 - the incident has nothing to do with me; can I use this this way? Running under: macOS Catalina 10.15.3, Matrix products: default Policy. 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. Error: package GenomeInfoDb could not be loaded. I just figured Id ask. More info about Internet Explorer and Microsoft Edge. Bioconductor release. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR library(caret) namespace load failed Object sigma not [7] edgeR_3.16.5 limma_3.30.12 sessionInfo() I tried to download the "locfit" package but I can't find it anywhere. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_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 'XML' so I would try to use BiocManager::install ("XML"). As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' When an R package depends on a newer package version, the required package is downloaded but not loaded. Any other suggestion? Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. March 1, 2023, 4:56pm Content type 'application/zip' length 386703 bytes (377 KB) Bioconductor - DESeq2 Making statements based on opinion; back them up with references or personal experience. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Loading required package: GenomicRanges Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Join us at CRISPR workshops in Koper, Slovenia in 2023. By clicking Sign up for GitHub, you agree to our terms of service and 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. Try again and choose No. Update all/some/none? [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Installation instructions to use this Surly Straggler vs. other types of steel frames. Acidity of alcohols and basicity of amines. now when I tried installing the missing packages they did install. nnet, spatial, survival Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, 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. Please remember to confirm an answer once you've received one. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Is there a proper earth ground point in this switch box? Should I update the Bioconductor to latest version instead? To add to this, I have also been using DESeq2 recently and ran into the same problem. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 so I would try to use BiocManager::install("XML"). Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Also note, however, that the error you got has been associated in the past with mirror outages. Traffic: 307 users visited in the last hour, I am new to all this! This topic was automatically closed 21 days after the last reply. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. That plugin is has not been updated to work with later releases of QIIME 2. there is no package called GenomeInfoDbData [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 install.packages("BiocManager"), I get this error: [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 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. Thanks for contributing an answer to Bioinformatics Stack Exchange! 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]]) : Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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 to allow custom library locations. Why is this sentence from The Great Gatsby grammatical? Retrying with flexible solve.Solving environment: Found conflicts! 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"). 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 I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. binary source needs_compilation [a/s/n]: Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. Statistics ; Algorithm(ML, DL,.) I am running a new install of R (3.5.0) and RStudio (1.1.414). Error when installing Aldex2 - Community Plugin Support - Open Source Platform: x86_64-apple-darwin15.6.0 (64-bit) [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 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. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Why do academics stay as adjuncts for years rather than move around? The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Warning: cannot remove prior installation of package xfun Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. I highly recommend that any R/RStudio version not installed inside conda be removed. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 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). [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Not the answer you're looking for? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. To resolve this error, install the required package as a cluster-installed library. 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: I also tried something I found on google: but the installation had errors too, I can write them here if needed. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Glad everything is finally working now. 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 Disconnect between goals and daily tasksIs it me, or the industry? The other option is to download and older version of locfit from the package archive and install manually. How do I align things in the following tabular environment? 1. 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 So, supposedly the issue is with Hmisc. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 This can take several minutes. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 So if you still get this error try changing your CRAN mirror. [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: I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. [R] Error: package or namespace load failed for 'ggplot2' in 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' 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. 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. 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. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Solution To resolve this error, install the required package as a cluster-installed library. Let me confer with the team. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Content type 'application/zip' length 233860 bytes (228 KB) March 1, 2023, 3:25pm Finally After 3-4 manual installations of missing packages everything worked. March 1, 2023, 8:52pm 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. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Thanks for your suggestion. nnet, spatial, survival. to your account. Whats the grammar of "For those whose stories they are"? survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Give up and run everything from the "permitted" library location (e.g. [7] datasets methods base, other attached packages: 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. Policy. 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. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Policy. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Post questions about Bioconductor Use this. Does a summoned creature play immediately after being summoned by a ready action?