Surly Straggler vs. other types of steel frames. package in your R session. So, supposedly the issue is with Hmisc. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. data . Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Sounds like there might be an issue with conda setup? From the console install.packages ("rlang") should fix this. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Replacing broken pins/legs on a DIP IC package. I want to import DESeq2 in Rstudio though and it is giving me a different error when I try importing DESeq2: Error in library("DESeq2") : there is no package called DESeq2. This includes any installed libraries. Press CTRL-C to abort. When an R package depends on a newer package version, the required package is downloaded but not loaded. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 I hope you can see something I can't see and help me solving this issue. Does a summoned creature play immediately after being summoned by a ready action? I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. Installing package(s) 'XML' library(DESeq2) The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. So if you still get this error try changing your CRAN mirror. March 1, 2023, 8:52pm LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 Citation (from within R, . Content type 'application/zip' length 4255589 bytes (4.1 MB) 1. 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: macOS Sierra 10.12.6. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Platform: x86_64-apple-darwin13.4.0 (64-bit) After 3-4 manual installs everything worked. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Just realize that I need to write the script "library("DESeq2")" before I proceed. nnet, spatial, survival. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. The other option is to download and older version of locfit from the package archive and install manually. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). 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. [1] stats4 parallel stats graphics grDevices utils installation of package GenomeInfoDbData had non-zero exit status. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. or install using BiocManager that will also install CRAN packages BiocManager::install('locfit'), I couldn't intall locfit but somehow, i did so many different things and it worked. there is no package called Hmisc. One solution is to find all available packages. Feedback "After the incident", I started to be more careful not to trip over things. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 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. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Finally After 3-4 manual installations of missing packages everything worked. Any other suggestion? [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? Is a PhD visitor considered as a visiting scholar? March 1, 2023, 3:25pm Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. [5] IRanges_2.8.1 S4Vectors_0.12.1 to allow custom library locations. 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. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 9. Policy. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. What is the output of. 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. Please remember to confirm an answer once you've received one. 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 'XML' so I would try to use BiocManager::install ("XML"). Solution To resolve this error, install the required package as a cluster-installed library. I've copied the output below in case it helps with troubleshooting. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Follow Up: struct sockaddr storage initialization by network format-string. "4.2") and enter: For older versions of R, please refer to the appropriate 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. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Making statements based on opinion; back them up with references or personal experience. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. library(DESeq2) [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: 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. Why do many companies reject expired SSL certificates as bugs in bug bounties? Thanks for contributing an answer to Stack Overflow! nnet, spatial, survival 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. Is there anyone the same as mine error while loading library(DESeq2)? What is a word for the arcane equivalent of a monastery? [7] edgeR_3.16.5 limma_3.30.12 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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