Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. call: dots_list() Find centralized, trusted content and collaborate around the technologies you use most. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: Documentation [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib rev2023.3.3.43278. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Language(R, Python, SQL) 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. C:\R\R-3.4.3\library). Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. 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: Use this. sessionInfo() To add to this, I have also been using DESeq2 recently and ran into the same problem. library(DESeq2) there is no package called locfit. What do I need to do to reproduce your problem? Is there anyone the same as mine error while loading library(DESeq2)? Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Just to add on -- do you require an old version of Bioconductor for your current project? To view documentation for the version of this package installed 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. Use MathJax to format equations. 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 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: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Convince your IT department to relax the permissions for R packages The best answers are voted up and rise to the top, Not the answer you're looking for? Running under: macOS Sierra 10.12.6. + ), update = TRUE, ask = FALSE) Installing package(s) 'htmlTable', 'xfun' Sign up for a free GitHub account to open an issue and contact its maintainers and the community. How do I align things in the following tabular environment? I can download DESeq2 using, User Agreement and Privacy Is the God of a monotheism necessarily omnipotent? 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 [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. .onLoad failed in loadNamespace() for 'rlang', details: RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Bad: conda install -c bioconda bioconductor-deseq2. Policy. Let me confer with the team. Please try the following steps: Quit all R/Rstudio sessions. How to use Slater Type Orbitals as a basis functions in matrix method correctly? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' @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. I even tried BiocManager::install("XML") but all failed as shown below. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Sounds like you might have an issue with which R Rstudio is running. 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 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages there is no package called Hmisc. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 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. Policy. Remember to always click on the red Show me the content on this page notice when navigating these older versions. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR R version 4.0.1 (2020-06-06) Erasmus+ funds available! Use of this site constitutes acceptance of our User Agreement and Privacy The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. I tried again and again was met with missing packages BUT!!! package in your R session. ERROR: lazy loading failed for package Hmisc Did you do that? I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. I guess that means we can finally close this issue. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) 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. Thank you @hharder. I have tried your suggestion and also updating the packages that command indicates. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Why do academics stay as adjuncts for years rather than move around? [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 This article explains how to resolve the package or namespace loading error. Author: Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb], RADIANT EU FP7 [fnd], NIH NHGRI [fnd], CZI [fnd], Maintainer: Michael Love . Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Post questions about Bioconductor To resolve this error, install the required package as a cluster-installed library. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 In install.packages() : Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Then I reinstalled R then Rstudio then RTools. - the incident has nothing to do with me; can I use this this way? Sorry, I'm newbie. 9. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Loading required package: GenomicRanges I also tried something I found on google: but the installation had errors too, I can write them here if needed. R version 3.6.1 (2019-07-05) 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]]): [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Join us at CRISPR workshops in Koper, Slovenia in 2023. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? It is working now. Whats the grammar of "For those whose stories they are"? Platform: x86_64-apple-darwin15.6.0 (64-bit) It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. 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. Making statements based on opinion; back them up with references or personal experience. To learn more, see our tips on writing great answers. Making statements based on opinion; back them up with references or personal experience. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 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 . So if you still get this error try changing your CRAN mirror. 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. data . March 1, 2023, 7:31pm [a/s/n]: Citation (from within R, Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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 Thanks for contributing an answer to Stack Overflow! Following successful installation of backports BiocManager::install ("DESeq2") will succeed under [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Thanks for contributing an answer to Stack Overflow! Should I update the Bioconductor to latest version instead? to your account. Looking for incompatible packages.This can take several minutes. Installing package(s) 'XML' installation of package GenomeInfoDbData had non-zero exit status. Replacing broken pins/legs on a DIP IC package. Does a summoned creature play immediately after being summoned by a ready action? No error messages are returned. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. Asking for help, clarification, or responding to other answers. After 3-4 manual installs everything worked. In file.copy(savedcopy, lib, recursive = TRUE) : [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 [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: [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Not the answer you're looking for? 2. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: I would recommend installing an older version of QIIME 2 for this plugin to work. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Start R to confirm they are gone. 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? How to notate a grace note at the start of a bar with lilypond? Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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"). install.packages ("zip") [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. [7] datasets methods base, other attached packages: 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: Any suggestions would be greatly appreciated. Try again and choose No. May be the version has problem How can I do ? Are there tables of wastage rates for different fruit and veg? A place where magic is studied and practiced? biocLite(), install.packages() (and the devtools equivalent?) Error: package GenomeInfoDb could not be loaded. "After the incident", I started to be more careful not to trip over things. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. What is a word for the arcane equivalent of a monastery? Styling contours by colour and by line thickness in QGIS. Connect and share knowledge within a single location that is structured and easy to search. We've tried this - and can replicate this issue on a completely new install with no existing package installs. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Acidity of alcohols and basicity of amines. install.packages("BiocManager"), I get this error: 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. You signed in with another tab or window. Surly Straggler vs. other types of steel frames. it would be good to hear any speculation you have of how this might have happened). Is there a single-word adjective for "having exceptionally strong moral principles"? 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 Installation instructions to use this New replies are no longer allowed. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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). 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. 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. This topic was automatically closed 21 days after the last reply. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. "After the incident", I started to be more careful not to trip over things. I tried following the instructions for 2019.7 as well and I am getting the same error. March 1, 2023, 8:52pm I hope you can see something I can't see and help me solving this issue. Traffic: 307 users visited in the last hour, I am new to all this! a, There are binary versions available but the source versions are later: Not the answer you're looking for? (Factorization). [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 "4.2") and enter: For older versions of R, please refer to the appropriate [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 enter citation("DESeq2")): To install this package, start R (version Old packages: 'RcppArmadillo', 'survival' binary source needs_compilation now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. 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]]) : Update all/some/none? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin17.0 (64-bit) guide. 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. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Please read the posting Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Asking for help, clarification, or responding to other answers. Then I reinstalled R then Rstudio then RTools. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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? 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. 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. To learn more, see our tips on writing great answers. 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. Solution To resolve this error, install the required package as a cluster-installed library. Already on GitHub? 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. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 In addition: Warning message: + "htmlTable", "xfun" Warning: cannot remove prior installation of package xfun The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). More info about Internet Explorer and Microsoft Edge. Why do many companies reject expired SSL certificates as bugs in bug bounties? When an R package depends on a newer package version, the required package is downloaded but not loaded. ERROR: dependency Hmisc is not available for package DESeq2 The other option is to download and older version of locfit from the package archive and install manually. Try installing zip, and then loading olsrr. Content type 'application/zip' length 4255589 bytes (4.1 MB) Platform: x86_64-apple-darwin13.4.0 (64-bit) Thanks for contributing an answer to Bioinformatics Stack Exchange! I'm trying to reproduce your problem, so being as precise as possible is important. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Warning: restored xfun, The downloaded binary packages are in Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat

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