R version 3.6.3 (2020-02-29) Is there anything I can do to speed it up? Try again and choose No. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Remember to always click on the red Show me the content on this page notice when navigating these older versions. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Use of this site constitutes acceptance of our User Agreement and Privacy [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 When an R package depends on a newer package version, the required package is downloaded but not loaded. Any suggestions would be greatly appreciated. Citation (from within R, 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. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Please try the following steps: Quit all R/Rstudio sessions. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Surly Straggler vs. other types of steel frames. You signed in with another tab or window. To learn more, see our tips on writing great answers. Warning: cannot remove prior installation of package xfun Is a PhD visitor considered as a visiting scholar? 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. This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. Are you sure the R you're running from the command line is installed through Anaconda as well? DESeq2_2301_76497647-CSDN C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages I also tried something I found on google: but the installation had errors too, I can write them here if needed. ERROR: lazy loading failed for package Hmisc 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. Disconnect between goals and daily tasksIs it me, or the industry? 4. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 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: [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 library(caret) namespace load failed Object sigma not found caret , . [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 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 ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. 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. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. 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. Sounds like you might have an issue with which R Rstudio is running. No error messages are returned. 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. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. So, supposedly the issue is with Hmisc. 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. Follow Up: struct sockaddr storage initialization by network format-string. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Choose Yes. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 library(DESeq2) Acidity of alcohols and basicity of amines. .onLoad failed in loadNamespace() for 'rlang', details: Running. Policy. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Content type 'application/zip' length 4255589 bytes (4.1 MB) R| - install.packages("BiocManager"), I get this error: [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Installing package(s) 'GenomeInfoDbData' binary source needs_compilation Bioconductor - DESeq2 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: Press CTRL-C to abort. "htmlTable", "xfun" How do I align things in the following tabular environment? if (!require("BiocManager", quietly = TRUE)) 2. Error: package GenomeInfoDb could not be loaded. 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. [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: What do I need to do to reproduce your problem? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Solving environment: Found conflicts! I tried again and again was met with missing packages BUT!!! Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Platform: x86_64-apple-darwin17.0 (64-bit) Not the answer you're looking for? Also note, however, that the error you got has been associated in the past with mirror outages. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Just updated my previous R to 4.01 and now I cant load DESeq2. [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. rev2023.3.3.43278. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 biocLite(), install.packages() (and the devtools equivalent?) 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. R version 3.6.1 (2019-07-05) "After the incident", I started to be more careful not to trip over things. I would like to install DESeq2 for DE analysis. a, There are binary versions available but the source versions are later: As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Is there a single-word adjective for "having exceptionally strong moral principles"? guide. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Connect and share knowledge within a single location that is structured and easy to search. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 If you have a query related to it or one of the replies, start a new topic and refer back with a link. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Following successful installation of backports BiocManager::install ("DESeq2") will succeed under there is no package called Hmisc. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so nnet, spatial, survival I'm having a similar error, but different package: library("DESeq2") Bad: conda install -c bioconda bioconductor-deseq2. Resolving package or namespace loading error Is the God of a monotheism necessarily omnipotent? I tried following the instructions for 2019.7 as well and I am getting the same error. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. 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 'locfit' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: Thanks for your suggestion. What am I doing wrong here in the PlotLegends specification? If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. 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. If you try loading the DEseq2 library now, that might work. DESeq2 - I can't get the library to load - Bioconductor
error: package or namespace load failed for 'deseq2