[9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): While a notebook is attached to a cluster, the R namespace cannot be refreshed. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 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. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. R version 3.6.3 (2020-02-29) BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (Factorization). + ), update = TRUE, ask = FALSE) 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. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked error: object 'rlang_dots_list' not found ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Old packages: 'RcppArmadillo', 'survival' How can we prove that the supernatural or paranormal doesn't exist? I installed the package successfully with conda, but Rstudio is apparently does not know about it. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: When an R package depends on a newer package version, the required package is downloaded but not loaded. 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). The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. Policy. I would suggest to install data.table, lme4 and all of the packages denoted in the 2 statements that said Packages which are only available in source form, and may need compilation of C/C++/Fortran: with pacman then re-run the Bioconductor installation of your target package. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in 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. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Use of this site constitutes acceptance of our User Agreement and Privacy @artembus Sounds like it was a ton of work! Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Bioconductor release. Join us at CRISPR workshops in Koper, Slovenia in 2023. [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: 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") [1] stats4 parallel stats graphics grDevices utils Content type 'application/zip' length 233860 bytes (228 KB) "After the incident", I started to be more careful not to trip over things. 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. "After the incident", I started to be more careful not to trip over things. Looking for incompatible packages.This can take several minutes. in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. Convince your IT department to relax the permissions for R packages I was assuming that to be the case. library(DESeq2) Documentation I then launched the R application (from the finder, not RStudio) and installed BiocManager. Sign in Does a summoned creature play immediately after being summoned by a ready action? 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'. Is a PhD visitor considered as a visiting scholar? sessionInfo() This includes any installed libraries. Learn more about Stack Overflow the company, and our products. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Running under: macOS Catalina 10.15.3, Matrix products: default :), BiocManager::install("locift") 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). To add to this, I have also been using DESeq2 recently and ran into the same problem. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. I'm having a similar error, but different package: library("DESeq2") Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so March 1, 2023, 4:56pm Acidity of alcohols and basicity of amines. Content type 'application/zip' length 4255589 bytes (4.1 MB) [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 From the console install.packages ("rlang") should fix this. March 1, 2023, 7:31pm Retrying with flexible solve.Solving environment: Found conflicts! 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 This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' there is no package called data.table It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Find centralized, trusted content and collaborate around the technologies you use most. Warning message: [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? 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. Just updated my previous R to 4.01 and now I cant load DESeq2. Use this. Policy. However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. Loading required package: GenomicRanges I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. install.packages("BiocManager"), I get this error: [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 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 To learn more, see our tips on writing great answers. Is there a single-word adjective for "having exceptionally strong moral principles"? Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") Traffic: 307 users visited in the last hour, I am new to all this! Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? Asking for help, clarification, or responding to other answers. Is there anyone the same as mine error while loading library(DESeq2)? [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( How do I align things in the following tabular environment? package xfun successfully unpacked and MD5 sums checked So if you still get this error try changing your CRAN mirror. Use of this site constitutes acceptance of our User Agreement and Privacy [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Asking for help, clarification, or responding to other answers. Warning message: [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 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. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Installing Hmisc as suggested above did not solve the issue. there is no package called GenomeInfoDbData Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. package in your R session. Policy. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) In addition: Warning message: New replies are no longer allowed. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Why do many companies reject expired SSL certificates as bugs in bug bounties? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? I've copied the output below in case it helps with troubleshooting. now when I tried installing the missing packages they did install. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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 . 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 Glad everything is finally working now. Please try reinstalling rlang on a fresh session. Running under: Windows 10 x64 (build 18362), locale: Whats the grammar of "For those whose stories they are"? [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 When an R package depends on a newer package version, the required package is downloaded but not loaded. Looking for incompatible packages. there is no package called locfit. How do you ensure that a red herring doesn't violate Chekhov's gun? Also note, however, that the error you got has been associated in the past with mirror outages. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Why do academics stay as adjuncts for years rather than move around? /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): The error states that the current version is 0.4.5 but 0.4.10 is required. Language(R, Python, SQL) 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. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 A place where magic is studied and practiced? Fortunately I was able to solve it by doing things from several suggested solutions. [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Sorry, I'm newbie. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. I would like to install DESeq2 for DE analysis. I tried to download the "locfit" package but I can't find it anywhere. 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: RcppArmadillo 0.9.880.1.0 0.9.900.1.0 TRUE Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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. Installing package(s) 'GenomeInfoDbData' Sounds like there might be an issue with conda setup? [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 library(caret) namespace load failed Object sigma not found caret , . Finally After 3-4 manual installations of missing packages everything worked. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' I can download DESeq2 using, User Agreement and Privacy 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: Follow Up: struct sockaddr storage initialization by network format-string. 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. The other option is to download and older version of locfit from the package archive and install manually. I just figured Id ask. Are you sure the R you're running from the command line is installed through Anaconda as well? it would be good to hear any speculation you have of how this might have happened). Just realize that I need to write the script "library("DESeq2")" before I proceed. So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. I even tried BiocManager::install("XML") but all failed as shown below. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 This article explains how to resolve the package or namespace loading error. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? 0 packages out-of-date; 2 packages too new, BiocManager::install(c( unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': 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. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Is there a proper earth ground point in this switch box? This can take several minutes. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? if (!require("BiocManager", quietly = TRUE)) [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 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 Find centralized, trusted content and collaborate around the technologies you use most. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Choose Yes. 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"). I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. 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 I hope you can see something I can't see and help me solving this issue. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Warning: cannot remove prior installation of package xfun What is the output of. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 .onLoad failed in loadNamespace() for 'rlang', details: After 3-4 manual installs everything worked. I guess that means we can finally close this issue. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. How to notate a grace note at the start of a bar with lilypond? rev2023.3.3.43278. 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.