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. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Error in R: (Package which is only available in source form, and may need compilation of C/C++/Fortran), Loading BioConductor library "GO.db" fails, Installing R packages from a local repo (all .tar.gz files have been downloaded there), Cannot remove prior installation of package, but package not found, I can't seem to install the 'ecospat' package on R studio for windows, I am unable to install ggplot, there occurs some error. This includes any installed libraries. package xfun successfully unpacked and MD5 sums checked Use MathJax to format equations. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 Also note, however, that the error you got has been associated in the past with mirror outages. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? How do I align things in the following tabular environment? I do know that it works well in qiime2-2020.6. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [1] stats4 parallel stats graphics grDevices utils A place where magic is studied and practiced? library(caret) namespace load failed Object sigma not found caret , . 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). You'll have an easier time if you install R/RStudio via conda and then install R packages the traditional way, inside R/RStudio. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): The error states that the current version is 0.4.5 but 0.4.10 is required. biocLite(), install.packages() (and the devtools equivalent?) By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Platform: x86_64-apple-darwin15.6.0 (64-bit) Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Is there a proper earth ground point in this switch box? I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. I tried to download the "locfit" package but I can't find it anywhere. Statistics ; Algorithm(ML, DL,.) [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Any other suggestion? and then updating the packages that command indicates. installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? Platform: x86_64-apple-darwin13.4.0 (64-bit) (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 . How to notate a grace note at the start of a bar with lilypond? check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. I hope you can see something I can't see and help me solving this issue. 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. That plugin is has not been updated to work with later releases of QIIME 2. May be the version has problem How can I do ? Thanks for your suggestion. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Have you tried install.packages("locfit") ? Not the answer you're looking for? to your account. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Convince your IT department to relax the permissions for R packages Use of this site constitutes acceptance of our User Agreement and Privacy "htmlTable", "xfun" Please try reinstalling rlang on a fresh session. In addition: Warning message: ERROR: dependency Hmisc is not available for package DESeq2 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. Is a PhD visitor considered as a visiting scholar? Start R to confirm they are gone. Thanks! [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Policy. in your system, start R and enter: Follow Did you do that? Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. I tried again and again was met with missing packages BUT!!! if (!require("BiocManager", quietly = TRUE)) Choose Yes. rev2023.3.3.43278. Then I reinstalled R then Rstudio then RTools. I then launched the R application (from the finder, not RStudio) and installed BiocManager. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Whats the grammar of "For those whose stories they are"? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). Documentation 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. [1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34 Does anyone know why I'm getting the following message when I load tidyverse in a new session. Installing package(s) 'GenomeInfoDbData' 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. install.packages ("zip") Any suggestions would be greatly appreciated. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 Solving environment: Found conflicts! there is no package called Hmisc. Old packages: 'RcppArmadillo', 'survival' Is there a single-word adjective for "having exceptionally strong moral principles"? I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I can download DESeq2 using, User Agreement and Privacy I tried following the instructions for 2019.7 as well and I am getting the same error. nnet, spatial, survival. And finally, install the problem packages, perhaps also DESeq2. package in your R session. I'm having a similar error, but different package: library("DESeq2") guide. [13] ggplot23.3.0 car3.0-7 carData3.0-3 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Styling contours by colour and by line thickness in QGIS. [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Use of this site constitutes acceptance of our User Agreement and Privacy But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Please try the following steps: Quit all R/Rstudio sessions. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc To learn more, see our tips on writing great answers. Why is this sentence from The Great Gatsby grammatical? Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Thanks for contributing an answer to Stack Overflow! Policy. im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Policy. 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. Update all/some/none? 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. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Just realize that I need to write the script "library("DESeq2")" before I proceed. Warning: restored xfun, The downloaded binary packages are in [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Loading required package: GenomicRanges 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'. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 install.packages("BiocManager"), I get this error: [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Surly Straggler vs. other types of steel frames. 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. Running under: macOS Sierra 10.12.6. Is there anything I can do to speed it up? As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. 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"). 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. Is there anyone the same as mine error while loading library(DESeq2)? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Sorry, I'm newbie. Policy. 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. "4.2") and enter: For older versions of R, please refer to the appropriate Why do many companies reject expired SSL certificates as bugs in bug bounties? Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? We've tried this - and can replicate this issue on a completely new install with no existing package installs. Running under: macOS Sierra 10.12.3, locale: Looking for incompatible packages.This can take several minutes. The package has place the R version constraint. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Finally After 3-4 manual installations of missing packages everything worked. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Connect and share knowledge within a single location that is structured and easy to search. Thanks for contributing an answer to Bioinformatics Stack Exchange! The best answers are voted up and rise to the top, Not the answer you're looking for? Do I need a thermal expansion tank if I already have a pressure tank? call: dots_list() Connect and share knowledge within a single location that is structured and easy to search. 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") Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. Sounds like you might have an issue with which R Rstudio is running. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 So if you still get this error try changing your CRAN mirror. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Follow Up: struct sockaddr storage initialization by network format-string. [7] edgeR_3.16.5 limma_3.30.12 Warning: cannot remove prior installation of package xfun locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Content type 'application/zip' length 233860 bytes (228 KB) 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. I even tried BiocManager::install("XML") but all failed as shown below. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 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. Try installing zip, and then loading olsrr. sessionInfo() 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: Have a question about this project? @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. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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 Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( Post questions about Bioconductor When you install and load some libraries in a notebook cell, like: While a notebook is attached to a cluster, the R namespace cannot be refreshed. Use of this site constitutes acceptance of our User Agreement and Privacy - the incident has nothing to do with me; can I use this this way? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie 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. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 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. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") How do you ensure that a red herring doesn't violate Chekhov's gun? Whats the grammar of "For those whose stories they are"? What do I need to do to reproduce your problem? 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"). (Factorization). Why are physically impossible and logically impossible concepts considered separate in terms of probability? Policy. Making statements based on opinion; back them up with references or personal experience. Just updated my previous R to 4.01 and now I cant load DESeq2. 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: Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. But I guess you have many problems with your installation, and I'd suggest. 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 . 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). Press CTRL-C to abort. Traffic: 307 users visited in the last hour, I am new to all this! [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 Is a PhD visitor considered as a visiting scholar? To resolve this error, install the required package as a cluster-installed library. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 I am running a new install of R (3.5.0) and RStudio (1.1.414). 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 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'GenomeInfoDbData' Error: package 'GenomeInfoDb' could not be loaded I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in.
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