The error states that the current version is 0.4.5 but 0.4.10 is required. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. March 1, 2023, 4:56pm [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Installing package(s) 'XML' That plugin is has not been updated to work with later releases of QIIME 2. Installation instructions to use this Just realize that I need to write the script "library("DESeq2")" before I proceed. [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 Feedback 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. [13] ggplot23.3.0 car3.0-7 carData3.0-3 @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. data . Making statements based on opinion; back them up with references or personal experience. Join us at CRISPR workshops in Koper, Slovenia in 2023. I also tried something I found on google: but the installation had errors too, I can write them here if needed. 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? [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 [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. Remember to always click on the red Show me the content on this page notice when navigating these older versions. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Just to add on -- do you require an old version of Bioconductor for your current project? 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. Connect and share knowledge within a single location that is structured and easy to search. Platform: x86_64-apple-darwin13.4.0 (64-bit) Well occasionally send you account related emails. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 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. so I would try to use BiocManager::install("XML"). I'm having a similar error, but different package: library("DESeq2") [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 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. Running under: Windows 10 x64 (build 18362), locale: I would recommend installing an older version of QIIME 2 for this plugin to work. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Use of this site constitutes acceptance of our User Agreement and Privacy [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: How do I align things in the following tabular environment? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Find centralized, trusted content and collaborate around the technologies you use most. Why are physically impossible and logically impossible concepts considered separate in terms of probability? 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: Thanks for contributing an answer to Stack Overflow! I guess that means we can finally close this issue. I installed the package successfully with conda, but Rstudio is apparently does not know about it. As such there are two solutions that may be more or less attainable given your own IT system. Learn more about Stack Overflow the company, and our products. "htmlTable", "xfun" [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Why is there a voltage on my HDMI and coaxial cables? sessionInfo() [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Press CTRL-C to abort. While a notebook is attached to a cluster, the R namespace cannot be refreshed. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Just updated my previous R to 4.01 and now I cant load DESeq2. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. there is no package called data.table Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? [7] edgeR_3.16.5 limma_3.30.12 Content type 'application/zip' length 233860 bytes (228 KB) So if you still get this error try changing your CRAN mirror. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 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. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Erasmus+ funds available! [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 In addition: Warning message: Policy. May be the version has problem How can I do ? 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. R version 3.6.1 (2019-07-05) Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Installing Hmisc as suggested above did not solve the issue. and then updating the packages that command indicates. I can download DESeq2 using, User Agreement and Privacy It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. install.packages ("zip") 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). [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 "After the incident", I started to be more careful not to trip over things. Try installing zip, and then loading olsrr. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. 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'. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Update all/some/none? 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. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? By clicking Sign up for GitHub, you agree to our terms of service and in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) 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. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 After 3-4 manual installs everything worked. Is a PhD visitor considered as a visiting scholar? Also make sure that you have RTools.exe installed and working. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) I highly recommend that any R/RStudio version not installed inside conda be removed. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. March 1, 2023, 7:31pm To learn more, see our tips on writing great answers. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. privacy statement. now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Does anyone know why I'm getting the following message when I load tidyverse in a new session. Post questions about Bioconductor Bad: conda install -c bioconda bioconductor-deseq2. it would be good to hear any speculation you have of how this might have happened). error: object 'rlang_dots_list' not found I am running a new install of R (3.5.0) and RStudio (1.1.414). Making statements based on opinion; back them up with references or personal experience. running multiple versions of the same package, keeping separate libraries for some projects). - the incident has nothing to do with me; can I use this this way? RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE 2. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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: 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. Surly Straggler vs. other types of steel frames. Is there a single-word adjective for "having exceptionally strong moral principles"? Is a PhD visitor considered as a visiting scholar? Installing package(s) 'htmlTable', 'xfun' library(DESeq2) If you have a query related to it or one of the replies, start a new topic and refer back with a link. I thought that working in a new environment would help, but it didnt. To resolve this error, install the required package as a cluster-installed library. there is no package called locfit. Content type 'application/zip' length 4255589 bytes (4.1 MB) 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. 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") @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. 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.