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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 was assuming that to be the case. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. I hope you can see something I can't see and help me solving this issue. it would be good to hear any speculation you have of how this might have happened). 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. 1. I'm trying to reproduce your problem, so being as precise as possible is important. Surly Straggler vs. other types of steel frames. "After the incident", I started to be more careful not to trip over things. rev2023.3.3.43278. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 there is no package called Hmisc. If you preorder a special airline meal (e.g. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 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. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: While a notebook is attached to a cluster, the R namespace cannot be refreshed. 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]]): It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Find centralized, trusted content and collaborate around the technologies you use most. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: ERROR: lazy loading failed for package Hmisc enter citation("DESeq2")): To install this package, start R (version and then updating the packages that command indicates. (Factorization). nnet, spatial, survival. 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. I'm running into some bad problems installing and using the DESeq2 package for R. I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7. installation of package GenomeInfoDbData had non-zero exit status. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 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. 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. Policy. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. How do I align things in the following tabular environment? Let me confer with the team. Citation (from within R, [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 This includes any installed libraries. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. March 1, 2023, 7:31pm [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: R version 4.0.1 (2020-06-06) 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. Learn more about Stack Overflow the company, and our products. Choose Yes. I just figured Id ask. Making statements based on opinion; back them up with references or personal experience. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. I'm having a similar error, but different package: library("DESeq2") [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Making statements based on opinion; back them up with references or personal experience. Use of this site constitutes acceptance of our User Agreement and Privacy Is there anything I can do to speed it up? [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: Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Solving environment: Found conflicts! I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Loading required package: GenomicRanges Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Retrying with flexible solve.Solving environment: Found conflicts! To learn more, see our tips on writing great answers. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 From the console install.packages ("rlang") should fix this. nnet, spatial, survival C:\R\R-3.4.3\library). Is the God of a monotheism necessarily omnipotent? 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. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Sorry, I'm newbie. To view documentation for the version of this package installed [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): I've copied the output below in case it helps with troubleshooting. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Thank you @hharder. I then launched the R application (from the finder, not RStudio) and installed BiocManager. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. 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. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 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. To add to this, I have also been using DESeq2 recently and ran into the same problem. Old packages: 'RcppArmadillo', 'survival' [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 I can download DESeq2 using, User Agreement and Privacy package rlang was built under R version 3.5.1. Installing Hmisc as suggested above did not solve the issue. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. sessionInfo() Platform: x86_64-w64-mingw32/x64 (64-bit) there is no package called GenomeInfoDbData [16] phyloseq1.30.0, loaded via a namespace (and not attached): 2. Loading required package: GenomeInfoDb data . Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. 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 /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages [7] edgeR_3.16.5 limma_3.30.12 [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 After 3-4 manual installs everything worked. vegan) just to try it, does this inconvenience the caterers and staff? I even tried BiocManager::install("XML") but all failed as shown below. "After the incident", I started to be more careful not to trip over things. 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. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . I do know that it works well in qiime2-2020.6. But I guess you have many problems with your installation, and I'd suggest. Warning: cannot remove prior installation of package xfun How to use Slater Type Orbitals as a basis functions in matrix method correctly? .onLoad failed in loadNamespace() for 'rlang', details: Update all/some/none? Warning message: Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Policy. @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. Language(R, Python, SQL) Sign up for a free GitHub account to open an issue and contact its maintainers and the community. [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( call: dots_list() Have a question about this project? To resolve this error, install the required package as a cluster-installed library. Policy. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 4. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence?