[25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Whats the grammar of "For those whose stories they are"? [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Surly Straggler vs. other types of steel frames. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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 I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! By clicking Sign up for GitHub, you agree to our terms of service and [69] tidyselect_1.0.0. - the incident has nothing to do with me; can I use this this way? Learn more about Stack Overflow the company, and our products. I've previously written a blog post about this topic, and I can say from experience that installing R packages through conda can cause lots of headaches. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Bioconductor - 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 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 [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 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. "htmlTable", "xfun" 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. To view documentation for the version of this package installed [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. 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 ()library(DESeq2):Error in loadNamespace: no package called ""s library (olsrr) - Error - General - RStudio Community nnet, spatial, survival [7] datasets methods base, other attached packages: Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. .onLoad failed in loadNamespace() for 'rlang', details: If it fails, required operating system facilities are missing. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 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'. Follow Up: struct sockaddr storage initialization by network format-string. Platform: x86_64-apple-darwin17.0 (64-bit) What am I doing wrong here in the PlotLegends specification? Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") 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. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. to allow custom library locations. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Asking for help, clarification, or responding to other answers. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Why is this sentence from The Great Gatsby grammatical? R DESeq2 - trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Error: package GenomeInfoDb could not be loaded. 1. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Try installing zip, and then loading olsrr. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). Resolving package or namespace loading error Try again and choose No. library(DESeq2) 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") trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. there is no package called Hmisc. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc 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. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Running under: macOS Sierra 10.12.3, locale: [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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]]): there is no package called 'XML' so I would try to use BiocManager::install ("XML"). Just realize that I need to write the script "library("DESeq2")" before I proceed. it would be good to hear any speculation you have of how this might have happened). Looking for incompatible packages. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? After 3-4 manual installs everything worked. 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. If not fixed, Try removing remove.packages (rlang) then. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Then I reinstalled R then Rstudio then RTools. Find centralized, trusted content and collaborate around the technologies you use most. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) May I know is there any other approach I can try? I have tried your suggestion and also updating the packages that command indicates. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or? I'm trying to reproduce your problem, so being as precise as possible is important. guide. there is no package called data.table Connect and share knowledge within a single location that is structured and easy to search. To add to this, I have also been using DESeq2 recently and ran into the same problem. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. If you preorder a special airline meal (e.g. Why is there a voltage on my HDMI and coaxial cables? Running under: macOS Sierra 10.12.6. Citation (from within R, enter citation ("DESeq2") ): Installation To install this package, start R (version "4.2") and enter: if (!require ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") BiocManager::install ("DESeq2") For older versions of R, please refer to the appropriate Bioconductor release . in your system, start R and enter: Follow 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. [R] Error: package or namespace load failed for 'ggplot2' in 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: If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. R version 4.0.1 (2020-06-06) library(caret) namespace load failed Object sigma not (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 . + "htmlTable", "xfun" 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 error states that the current version is 0.4.5 but 0.4.10 is required. In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use, and would ask more Bioconductor-related questions on the Bioconductor support site. To learn more, see our tips on writing great answers. Any other suggestion? "After the incident", I started to be more careful not to trip over things. As such there are two solutions that may be more or less attainable given your own IT system. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 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. Start R to confirm they are gone. Documentation It is working now. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Hello, Policy. 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. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Thank you @hharder. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Use of this site constitutes acceptance of our User Agreement and Privacy "4.2") and enter: For older versions of R, please refer to the appropriate [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 I highly recommend that any R/RStudio version not installed inside conda be removed. Please try reinstalling rlang on a fresh session. Does a summoned creature play immediately after being summoned by a ready action? Policy. That plugin is has not been updated to work with later releases of QIIME 2. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? running multiple versions of the same package, keeping separate libraries for some projects). * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, "After the incident", I started to be more careful not to trip over things. C:\R\R-3.4.3\library). [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Update all/some/none? Asking for help, clarification, or responding to other answers. Traffic: 307 users visited in the last hour, I am new to all this! Powered by Discourse, best viewed with JavaScript enabled, DESeq2: Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. If you try loading the DEseq2 library now, that might work. Language(R, Python, SQL) Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Why do academics stay as adjuncts for years rather than move around? Running under: Windows 10 x64 (build 18362), locale: ERROR: lazy loading failed for package Hmisc [13] ggplot23.3.0 car3.0-7 carData3.0-3 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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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. What is the output of. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Making statements based on opinion; back them up with references or personal experience. library(caret) namespace load failed Object sigma not found caret , . 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. DESeq2_2301_76497647-CSDN Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. biocLite(), install.packages() (and the devtools equivalent?) Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 R| - Use MathJax to format equations. Installing DESeq2 Error: no package called GenomeInfoDbData, https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz, https://cran.rstudio.com/bin/macosx/contrib/4.0/RcppArmadillo_0.9.880.1.0.tgz, https://cran.rstudio.com/bin/macosx/contrib/4.0/survival_3.1-12.tgz. @KonradRudolph It's pacman (not packman) and you are correct in that it's basically just a wrapper for, Thanks for your suggestion, I tried doing this step by step as you said but the biocLite command still did throw errors for missing packages. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Warning: cannot remove prior installation of package xfun It only takes a minute to sign up. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( This includes any installed libraries. You are doing something very wrong when installing your packages. if (!require("BiocManager", quietly = TRUE)) 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. Looking for incompatible packages.This can take several minutes. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 binary source needs_compilation March 1, 2023, 7:31pm [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 installation of package GenomeInfoDbData had non-zero exit status. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): So if you still get this error try changing your CRAN mirror. error: object 'rlang_dots_list' not found 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. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: now when I tried installing the missing packages they did install. Is there a proper earth ground point in this switch box? Did you do that? The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). If you have a query related to it or one of the replies, start a new topic and refer back with a link. Installing package(s) 'GenomeInfoDbData' How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. Content type 'application/zip' length 386703 bytes (377 KB) I installed the package successfully with conda, but Rstudio is apparently does not know about it. Sounds like there might be an issue with conda setup? 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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). More info about Internet Explorer and Microsoft Edge. 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. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Erasmus+ funds available! Finally After 3-4 manual installations of missing packages everything worked. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? rev2023.3.3.43278. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. 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: Installing packages directly into that location fixes the issue but is not desirable for all the reasons that people might want to use custom locations (e.g. Sounds like you might have an issue with which R Rstudio is running. [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8, attached base packages: Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat A place where magic is studied and practiced? locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) sessionInfo() [16] phyloseq1.30.0, loaded via a namespace (and not attached): Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R 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. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. vegan) just to try it, does this inconvenience the caterers and staff? [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Why are physically impossible and logically impossible concepts considered separate in terms of probability? One solution is to find all available packages. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 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 Are you sure the R you're running from the command line is installed through Anaconda as well? Is there a proper earth ground point in this switch box? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Please try the following steps: Quit all R/Rstudio sessions. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Connect and share knowledge within a single location that is structured and easy to search. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Policy. sessionInfo() I then launched the R application (from the finder, not RStudio) and installed BiocManager. Have you tried install.packages("locfit") ? package in your R session. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Use this. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. The best answers are voted up and rise to the top, Not the answer you're looking for? And finally, install the problem packages, perhaps also DESeq2. Thanks for your suggestion. ERROR: dependency Hmisc is not available for package DESeq2 We've tried this - and can replicate this issue on a completely new install with no existing package installs. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. I also tried something I found on google: but the installation had errors too, I can write them here if needed. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 What do I need to do to reproduce your problem? 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. Install DESeq2 through anaconda - Bioinformatics Stack Exchange :), BiocManager::install("locift") Is there anyone the same as mine error while loading library(DESeq2)? a, There are binary versions available but the source versions are later: [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [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.