It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Making statements based on opinion; back them up with references or personal experience. now when I tried installing the missing packages they did install. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Is the God of a monotheism necessarily omnipotent? In file.copy(savedcopy, lib, recursive = TRUE) : Error when installing Aldex2 - Community Plugin Support - Open Source Update all/some/none? [16] phyloseq1.30.0, loaded via a namespace (and not attached): Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. [5] IRanges_2.8.1 S4Vectors_0.12.1 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 . sessionInfo() Installing package(s) 'XML' Running under: macOS Catalina 10.15.3, Matrix products: default Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Policy. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 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. library(DESeq2) I tried following the instructions for 2019.7 as well and I am getting the same error. and then updating the packages that command indicates. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? By clicking Sign up for GitHub, you agree to our terms of service and rstudio - Error: package or namespace load failed for 'tidyverse [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 When you load the package, you can observe this error. [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 This article explains how to resolve the package or namespace loading error. LAMMPS KOKKOS for NVIDIA GPUs using CUDA - LAMMPS Installation - Open [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Why are physically impossible and logically impossible concepts considered separate in terms of probability? so I would try to use BiocManager::install("XML"). Disconnect between goals and daily tasksIs it me, or the industry? 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 Asking for help, clarification, or responding to other answers. Running under: Windows 10 x64 (build 18362), locale: If you try loading the DEseq2 library now, that might work. Have a question about this project? I'm having a similar error, but different package: library("DESeq2") DESeq2_2301_76497647-CSDN 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. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc We've tried this - and can replicate this issue on a completely new install with no existing package installs. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? [R] Error: package or namespace load failed for 'ggplot2' in 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. Whats the grammar of "For those whose stories they are"? Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Should I update the Bioconductor to latest version instead? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Content type 'application/zip' length 4255589 bytes (4.1 MB) Is a PhD visitor considered as a visiting scholar? [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. (Factorization). [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 If not fixed, Try removing remove.packages (rlang) then. @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. 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 Thanks for your suggestion. Thank you @hharder. library(caret) namespace load failed Object sigma not 9. Post questions about Bioconductor Platform: x86_64-apple-darwin15.6.0 (64-bit) But I guess you have many problems with your installation, and I'd suggest. Styling contours by colour and by line thickness in QGIS. library(caret) namespace load failed Object sigma not found caret , . Whats the grammar of "For those whose stories they are"? As such there are two solutions that may be more or less attainable given your own IT system. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( A place where magic is studied and practiced? Sorry, I'm newbie. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? It only takes a minute to sign up. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Why do many companies reject expired SSL certificates as bugs in bug bounties? 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: 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. 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!!! Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Running. R version 3.6.3 (2020-02-29) [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Let me confer with the team. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. This topic was automatically closed 21 days after the last reply. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Finally After 3-4 manual installations of missing packages everything worked. guide. Installation instructions to use this 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [1] stats4 parallel stats graphics grDevices utils 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 Solution To resolve this error, install the required package as a cluster-installed library. I just figured Id ask. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 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. Installing package(s) 'htmlTable', 'xfun' Bioconductor - DESeq2 binary source needs_compilation Resolving package or namespace loading error [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Learn more about Stack Overflow the company, and our products. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Running under: macOS Sierra 10.12.6. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Thanks for contributing an answer to Stack Overflow! [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 Documentation "After the incident", I started to be more careful not to trip over things. Making statements based on opinion; back them up with references or personal experience. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. 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. Installing package(s) 'GenomeInfoDbData' 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. 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. 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. What is a word for the arcane equivalent of a monastery? March 1, 2023, 3:25pm Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: privacy statement. Looking for incompatible packages. Error: package GenomeInfoDb could not be loaded. install.packages("BiocManager"), I get this error: [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 How to use Slater Type Orbitals as a basis functions in matrix method correctly? Any suggestions would be greatly appreciated. installation of package GenomeInfoDbData had non-zero exit status. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. I installed the package successfully with conda, but Rstudio is apparently does not know about it. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Thanks! . Use of this site constitutes acceptance of our User Agreement and Privacy New replies are no longer allowed. [7] edgeR_3.16.5 limma_3.30.12 package xfun successfully unpacked and MD5 sums checked The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. So, supposedly the issue is with Hmisc. 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. Start R to confirm they are gone. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Statistics ; Algorithm(ML, DL,.) Content type 'application/zip' length 233860 bytes (228 KB) Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Why is there a voltage on my HDMI and coaxial cables? Not the answer you're looking for? 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. it would be good to hear any speculation you have of how this might have happened). requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Connect and share knowledge within a single location that is structured and easy to search. What is the output of. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 In addition: Warning message: Just realize that I need to write the script "library("DESeq2")" before I proceed. Error: package or namespace load failed for 'DESeq2 - Bioconductor [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 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 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 . to your account. 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'. It is working now. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': 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. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled.

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