Making statements based on opinion; back them up with references or personal experience. And finally, install the problem packages, perhaps also DESeq2. Running. Post questions about Bioconductor I tried following the instructions for 2019.7 as well and I am getting the same error. MathJax reference. 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 Already on GitHub? 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. Is a PhD visitor considered as a visiting scholar? [69] tidyselect_1.0.0. [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. [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 to your account. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. R version 3.6.3 (2020-02-29) [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. 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. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie 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. rev2023.3.3.43278. Retrying with flexible solve.Solving environment: Found conflicts! Thanks for contributing an answer to Bioinformatics Stack Exchange! Warning: restored xfun, The downloaded binary packages are in 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 Traffic: 307 users visited in the last hour, I am new to all this! Why do academics stay as adjuncts for years rather than move around? package in your R session. 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. 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 tried running few commands and I hope the information from them will help finding the cause of all the errors: (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 . 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. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. To learn more, see our tips on writing great answers. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Looking for incompatible packages. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. A place where magic is studied and practiced? This can take several minutes. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. Is a PhD visitor considered as a visiting scholar? Also note, however, that the error you got has been associated in the past with mirror outages. If you preorder a special airline meal (e.g. To learn more, see our tips on writing great answers. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Find centralized, trusted content and collaborate around the technologies you use most. Glad everything is finally working now. 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. 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. 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 library(DESeq2) Solving environment: Found conflicts! Use of this site constitutes acceptance of our User Agreement and Privacy install.packages ("zip") [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Also make sure that you have RTools.exe installed and working. Policy. nnet, spatial, survival. Thank you @hharder. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Why do many companies reject expired SSL certificates as bugs in bug bounties? [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 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. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages 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. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Bioconductor release. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): When an R package depends on a newer package version, the required package is downloaded but not loaded. No error messages are returned. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in if (!require("BiocManager", quietly = TRUE)) installation of package GenomeInfoDbData had non-zero exit status. Loading required package: GenomeInfoDb As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. Feedback [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Please read the posting Installation instructions to use this This topic was automatically closed 21 days after the last reply. :), BiocManager::install("locift") Whats the grammar of "For those whose stories they are"? Platform: x86_64-apple-darwin17.0 (64-bit) If not fixed, Try removing remove.packages (rlang) then. + ), update = TRUE, ask = FALSE) 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. 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 Why are physically impossible and logically impossible concepts considered separate in terms of probability? If you have a query related to it or one of the replies, start a new topic and refer back with a link. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 If you try loading the DEseq2 library now, that might work. I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and try to import DESeq2 I am getting the error message: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [a/s/n]: [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 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]]) : there is no package called Hmisc. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? May I know is there any other approach I can try? 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"). Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) [13] ggplot23.3.0 car3.0-7 carData3.0-3 [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( I was assuming that to be the case. Any suggestions would be greatly appreciated. When an R package depends on a newer package version, the required package is downloaded but not loaded. 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. 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. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Error in R: (Package which is only available in source form, and may need compilation of C/C++/Fortran), Loading BioConductor library "GO.db" fails, Installing R packages from a local repo (all .tar.gz files have been downloaded there), Cannot remove prior installation of package, but package not found, I can't seem to install the 'ecospat' package on R studio for windows, I am unable to install ggplot, there occurs some error. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 I tried again and again was met with missing packages BUT!!! But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () I even tried BiocManager::install("XML") but all failed as shown below. 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. "After the incident", I started to be more careful not to trip over things. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: 4. 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. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 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 Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Remember to always click on the red Show me the content on this page notice when navigating these older versions. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Is there a proper earth ground point in this switch box? call: dots_list() The error states that the current version is 0.4.5 but 0.4.10 is required. Platform: x86_64-w64-mingw32/x64 (64-bit) [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 @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. The other option is to download and older version of locfit from the package archive and install manually. ERROR: lazy loading failed for package Hmisc 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. Policy. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Follow Up: struct sockaddr storage initialization by network format-string. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) What am I doing wrong here in the PlotLegends specification? I've copied the output below in case it helps with troubleshooting. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' As such there are two solutions that may be more or less attainable given your own IT system. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 I also tried something I found on google: but the installation had errors too, I can write them here if needed. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). This includes any installed libraries. Warning message: now when I tried installing the missing packages they did install. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 March 1, 2023, 4:56pm Press CTRL-C to abort. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 package xfun successfully unpacked and MD5 sums checked Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. You signed in with another tab or window. Surly Straggler vs. other types of steel frames. running multiple versions of the same package, keeping separate libraries for some projects). Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Does a summoned creature play immediately after being summoned by a ready action? One solution is to find all available packages. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 I would recommend installing an older version of QIIME 2 for this plugin to work. 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. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Are you sure the R you're running from the command line is installed through Anaconda as well? Whats the grammar of "For those whose stories they are"? a, There are binary versions available but the source versions are later: enter citation("DESeq2")): To install this package, start R (version Just updated my previous R to 4.01 and now I cant load DESeq2. biocLite(), install.packages() (and the devtools equivalent?) Platform: x86_64-apple-darwin15.6.0 (64-bit) I installed the package successfully with conda, but Rstudio is apparently does not know about it. May be the version has problem How can I do ? So, supposedly the issue is with Hmisc. As mentioned above, my institutional IT can replicate this on a laptop with a completely fresh R install and no prior package installations (meaning isn't to do with installing with another version of the package already running). ERROR: dependency Hmisc is not available for package DESeq2 [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 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). [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). C:\R\R-3.4.3\library). 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. I'm having a similar error, but different package: library("DESeq2") Please try the following steps: Quit all R/Rstudio sessions. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Installing package(s) 'GenomeInfoDbData' Documentation [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 I tried to download the "locfit" package but I can't find it anywhere. Thanks for contributing an answer to Stack Overflow! Installing Hmisc as suggested above did not solve the issue. Making statements based on opinion; back them up with references or personal experience. 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. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. I thought that working in a new environment would help, but it didnt. data . [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 I want to import DESeq2 in Rstudio though and it is giving me a different error when I try importing DESeq2: Error in library("DESeq2") : there is no package called DESeq2. 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. Asking for help, clarification, or responding to other answers. Sounds like there might be an issue with conda setup? now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Running under: Windows 10 x64 (build 18362), locale: it would be good to hear any speculation you have of how this might have happened). Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Platform: x86_64-apple-darwin13.4.0 (64-bit) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Making statements based on opinion; back them up with references or personal experience. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Installing package(s) 'XML' R version 4.0.1 (2020-06-06) [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 there is no package called locfit. 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. howard university graduation 2022,
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