error: package or namespace load failed for 'deseq2

Follow Up: struct sockaddr storage initialization by network format-string. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. So if you still get this error try changing your CRAN mirror. Learn more about Stack Overflow the company, and our products. Why do academics stay as adjuncts for years rather than move around? 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 Why do many companies reject expired SSL certificates as bugs in bug bounties? Then I reinstalled R then Rstudio then RTools. 9. Just realize that I need to write the script "library("DESeq2")" before I proceed. @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. As such there are two solutions that may be more or less attainable given your own IT system. [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. Styling contours by colour and by line thickness in QGIS. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, R DESeq2 - [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Warning message: 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. Bioconductor release. Please remember to confirm an answer once you've received one. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Please try reinstalling rlang on a fresh session. 2. it would be good to hear any speculation you have of how this might have happened). 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 Sign up for a free GitHub account to open an issue and contact its maintainers and the community. To learn more, see our tips on writing great answers. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Finally After 3-4 manual installations of missing packages everything worked. 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. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Use MathJax to format equations. That plugin is has not been updated to work with later releases of QIIME 2. I would like to install DESeq2 for DE analysis. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Error: package or namespace load failed for 'DESeq2 - Bioconductor So, supposedly the issue is with Hmisc. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. When an R package depends on a newer package version, the required package is downloaded but not loaded. RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE library(caret) namespace load failed Object sigma not found caret , . ERROR: dependency Hmisc is not available for package DESeq2 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. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: [7] edgeR_3.16.5 limma_3.30.12 Error: package GenomeInfoDb could not be loaded. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. rev2023.3.3.43278. Then I reinstalled R then Rstudio then RTools. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Not the answer you're looking for? Installing package(s) 'GenomeInfoDbData' binary source needs_compilation Just updated my previous R to 4.01 and now I cant load DESeq2. Any other suggestion? [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 This can take several minutes. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? If it fails, required operating system facilities are missing. (Factorization). 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: package or namespace load failed, object not found Install DESeq2 through anaconda - Bioinformatics Stack Exchange to allow custom library locations. Policy. 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. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 package rlang was built under R version 3.5.1. This is the beauty of installing QIIME 2 via conda, you can have many different versions of QIIME 2 on your system at the same time and activate the version you want to use. "After the incident", I started to be more careful not to trip over things. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. sessionInfo() [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Making statements based on opinion; back them up with references or personal experience. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 [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: Use of this site constitutes acceptance of our User Agreement and Privacy [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Press CTRL-C to abort. library(DESeq2) [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Are there tables of wastage rates for different fruit and veg? Try installing zip, and then loading olsrr. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I need help installing a package "DESeq2" having - RStudio Community To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. 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. Remember to always click on the red Show me the content on this page notice when navigating these older versions. 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. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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. Why do academics stay as adjuncts for years rather than move around? Should I update the Bioconductor to latest version instead? 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. If you preorder a special airline meal (e.g. Citation (from within R, I then launched the R application (from the finder, not RStudio) and installed BiocManager. Running. install.packages("BiocManager"), I get this error: Also note, however, that the error you got has been associated in the past with mirror outages. Replacing broken pins/legs on a DIP IC package. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. 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: @artembus Sounds like it was a ton of work! downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked 0 packages out-of-date; 2 packages too new, BiocManager::install(c( R version 3.6.3 (2020-02-29) To learn more, see our tips on writing great answers. 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 not fixed, Try removing remove.packages (rlang) then. How can we prove that the supernatural or paranormal doesn't exist? Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Warning: cannot remove prior installation of package xfun * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc If you try loading the DEseq2 library now, that might work. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Update all/some/none? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Well occasionally send you account related emails. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Not the answer you're looking for? dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Making statements based on opinion; back them up with references or personal experience. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 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). Policy. This includes any installed libraries. Platform: x86_64-apple-darwin15.6.0 (64-bit) 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. to your account. Connect and share knowledge within a single location that is structured and easy to search. ERROR: lazy loading failed for package Hmisc 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. Platform: x86_64-w64-mingw32/x64 (64-bit) It only takes a minute to sign up. Policy. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Also make sure that you have RTools.exe installed and working. March 1, 2023, 3:25pm Platform: x86_64-apple-darwin13.4.0 (64-bit) March 1, 2023, 8:52pm 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"). locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. The package has place the R version constraint. - the incident has nothing to do with me; can I use this this way? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Warning message: Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Use of this site constitutes acceptance of our User Agreement and Privacy But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? I do know that it works well in qiime2-2020.6. 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.