[1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: How to notate a grace note at the start of a bar with lilypond? If not fixed, Try removing remove.packages (rlang) then. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? 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. 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). Feedback I just figured Id ask. 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. Thanks for contributing an answer to Stack Overflow! [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 March 1, 2023, 8:52pm 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]]) : Is there a proper earth ground point in this switch box? now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Did you do that? Platform: x86_64-apple-darwin13.4.0 (64-bit) Surly Straggler vs. other types of steel frames. Have a question about this project? Find centralized, trusted content and collaborate around the technologies you use most. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). When you load the package, you can observe this error. I'm trying to reproduce your problem, so being as precise as possible is important. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Is there a proper earth ground point in this switch box? If you preorder a special airline meal (e.g. Thanks for contributing an answer to Bioinformatics Stack Exchange! Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. 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. Use of this site constitutes acceptance of our User Agreement and Privacy Let me confer with the team. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 MathJax reference. Bad: conda install -c bioconda bioconductor-deseq2. 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. 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 [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Policy. How do you ensure that a red herring doesn't violate Chekhov's gun? [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? "After the incident", I started to be more careful not to trip over things. Installing package(s) 'XML' I highly recommend that any R/RStudio version not installed inside conda be removed. Press CTRL-C to abort.failedUnsatisfiableError: The following specifications were foundto be incompatible with the existing python installation in your environment:Specifications: It also hung on the solving environment for over an hour. Just updated my previous R to 4.01 and now I cant load DESeq2. It is working now. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. 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. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Should I update the Bioconductor to latest version instead? (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 . 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 physically impossible and logically impossible concepts considered separate in terms of probability? Why do academics stay as adjuncts for years rather than move around? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) How can we prove that the supernatural or paranormal doesn't exist? Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. rev2023.3.3.43278. Please remember to confirm an answer once you've received one. Id also remove and re-install the version of QIIME 2 you tried to force install an older version of python, as you can tell, many things just broke. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Choose Yes. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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. Give up and run everything from the "permitted" library location (e.g. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Old packages: 'RcppArmadillo', 'survival' Then I reinstalled R then Rstudio then RTools. Disconnect between goals and daily tasksIs it me, or the industry? installation of package GenomeInfoDbData had non-zero exit status. I am using the latest stable LAMMPS version (updated 17th Feb 2023) Also I am having troubles with the CMAKE unit testing, in particular for the force styles. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): R version 3.6.3 (2020-02-29) [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: [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. One solution is to find all available packages. Sounds like there might be an issue with conda setup? How do I align things in the following tabular environment? How to use Slater Type Orbitals as a basis functions in matrix method correctly? "4.2") and enter: For older versions of R, please refer to the appropriate Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Warning message: By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Press CTRL-C to abort. Finally After 3-4 manual installations of missing packages everything worked. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 So if you still get this error try changing your CRAN mirror. Sorry, I'm newbie. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. It only takes a minute to sign up. Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Please try reinstalling rlang on a fresh session. 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. Is there a single-word adjective for "having exceptionally strong moral principles"? Are there tables of wastage rates for different fruit and veg? requires R 4 and running more than a couple of releases behind in R risks multiplying problems. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Why is there a voltage on my HDMI and coaxial cables? "After the incident", I started to be more careful not to trip over things. 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
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