error: package or namespace load failed for 'deseq2

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. 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. 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. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Loading required package: GenomicRanges Traffic: 307 users visited in the last hour, https://cran.rstudio.com/src/contrib/htmlTable_2.1.0.tar.gz', https://wbc.upm.edu.my/cran/src/contrib/PACKAGES'. Update all/some/none? [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. nnet, spatial, survival. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. The error states that the current version is 0.4.5 but 0.4.10 is required. Is there anyone the same as mine error while loading library(DESeq2)? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Press CTRL-C to abort. It is working now. 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"). Use of this site constitutes acceptance of our User Agreement and Privacy [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Learn more about Stack Overflow the company, and our products. rev2023.3.3.43278. Well occasionally send you account related emails. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. The package has place the R version constraint. But I guess you have many problems with your installation, and I'd suggest. Whats the grammar of "For those whose stories they are"? I was assuming that to be the case. In file.copy(savedcopy, lib, recursive = TRUE) : How to use Slater Type Orbitals as a basis functions in matrix method correctly? Documentation [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Policy. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Just to add on -- do you require an old version of Bioconductor for your current project? I would recommend installing an older version of QIIME 2 for this plugin to work. Replacing broken pins/legs on a DIP IC package. Installing Hmisc as suggested above did not solve the issue. Policy. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR I tried to download the "locfit" package but I can't find it anywhere. You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Content type 'application/zip' length 4255589 bytes (4.1 MB) If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. 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. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. This includes any installed libraries. Remember to always click on the red Show me the content on this page notice when navigating these older versions. . Warning: restored xfun, The downloaded binary packages are in Disconnect between goals and daily tasksIs it me, or the industry? [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: Not the answer you're looking for? "htmlTable", "xfun" Let me confer with the team. I am using the latest stable LAMMPS version (updated 17th Feb 2023) Also I am having troubles with the CMAKE unit testing, in particular for the force styles. 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]]) : Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. package in your R session. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. I tried again and again was met with missing packages BUT!!! Is a PhD visitor considered as a visiting scholar? I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. To learn more, see our tips on writing great answers. 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 would be good to hear any speculation you have of how this might have happened). running multiple versions of the same package, keeping separate libraries for some projects). Bad: conda install -c bioconda bioconductor-deseq2. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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. (Factorization). Is there anything I can do to speed it up? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? And finally, install the problem packages, perhaps also DESeq2. Loading required package: GenomeInfoDb I can download DESeq2 using, User Agreement and Privacy [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. 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 [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. [1] stats4 parallel stats graphics grDevices utils By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. MathJax reference. Do I need a thermal expansion tank if I already have a pressure tank? Connect and share knowledge within a single location that is structured and easy to search. 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 Citation (from within R, I highly recommend that any R/RStudio version not installed inside conda be removed. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' This can take several minutes. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 biocLite(), install.packages() (and the devtools equivalent?) I tried following the instructions for 2019.7 as well and I am getting the same error. Sounds like there might be an issue with conda setup? What is a word for the arcane equivalent of a monastery? If you have a query related to it or one of the replies, start a new topic and refer back with a link. and then updating the packages that command indicates. Your best bet would be to download the package source code and change the R version and install manually if you wanted the most recent version of locfit to install on your computer. so I would try to use BiocManager::install("XML"). In addition: Warning message: How do I align things in the following tabular environment? One solution is to find all available packages. to your account. "After the incident", I started to be more careful not to trip over things. I am running a new install of R (3.5.0) and RStudio (1.1.414). [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. I also tried something I found on google: but the installation had errors too, I can write them here if needed. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Choose Yes. I noticed that you are trying to install qiime2-2019.4, this may not work as ALDEx2 was made for qiime2-2019.7 as outlined here, up to and including the versions I mentioned earlier. If you try loading the DEseq2 library now, that might work. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Is there a proper earth ground point in this switch box? Are you sure the R you're running from the command line is installed through Anaconda as well? If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : sessionInfo() The best answers are voted up and rise to the top, Not the answer you're looking for? library(caret) namespace load failed Object sigma not found caret , . [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 I then launched the R application (from the finder, not RStudio) and installed BiocManager. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Language(R, Python, SQL) [7] datasets methods base, other attached packages: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. I thought that working in a new environment would help, but it didnt. By clicking Sign up for GitHub, you agree to our terms of service and March 1, 2023, 3:25pm Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. :), BiocManager::install("locift") problem copying C:\Users\ASUS\Documents\R\win-library\3.6\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\ASUS\Documents\R\win-library\3.6\xfun\libs\x64\xfun.dll: Permission denied, BiocManager::install("XML") 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. Running under: macOS Sierra 10.12.3, locale: I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. When you load the package, you can observe this error. Platform: x86_64-apple-darwin15.6.0 (64-bit) [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Please read the posting From the console install.packages ("rlang") should fix this. (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 . 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 When an R package depends on a newer package version, the required package is downloaded but not loaded. 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: - the incident has nothing to do with me; can I use this this way? Find centralized, trusted content and collaborate around the technologies you use most. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: 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.