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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. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 vegan) just to try it, does this inconvenience the caterers and staff? I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Error: package or namespace load failed for 'olsrr' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'zip' mara May 25, 2021, 12:49pm #2 It looks like you need a package that it depends on. Any suggestions would be greatly appreciated. Please try reinstalling rlang on a fresh session. Also note, however, that the error you got has been associated in the past with mirror outages. package in your R session. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): I tried to download the "locfit" package but I can't find it anywhere. 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. Hello, Find centralized, trusted content and collaborate around the technologies you use most. 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 . * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: 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). Then I reinstalled R then Rstudio then RTools. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 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") Disconnect between goals and daily tasksIs it me, or the industry? If it fails, required operating system facilities are missing. More info about Internet Explorer and Microsoft Edge. 2. Platform: x86_64-apple-darwin15.6.0 (64-bit) How can we prove that the supernatural or paranormal doesn't exist? Please remember to confirm an answer once you've received one. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Running under: macOS Catalina 10.15.3, Matrix products: default Not the answer you're looking for? [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. [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. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? rev2023.3.3.43278. Please try the following steps: Quit all R/Rstudio sessions. "4.2") and enter: For older versions of R, please refer to the appropriate Content type 'application/zip' length 386703 bytes (377 KB) How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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. I'm trying to reproduce your problem, so being as precise as possible is important. installation of package GenomeInfoDbData had non-zero exit status. We've tried this - and can replicate this issue on a completely new install with no existing package installs. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. (Factorization). [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 In install.packages() : The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). From the console install.packages ("rlang") should fix this. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Whats the grammar of "For those whose stories they are"? This includes any installed libraries. I guess that means we can finally close this issue. 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. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [7] datasets methods base, other attached packages: By clicking Sign up for GitHub, you agree to our terms of service and :), BiocManager::install("locift") [7] edgeR_3.16.5 limma_3.30.12 I installed the package successfully with conda, but Rstudio is apparently does not know about it. Asking for help, clarification, or responding to other answers. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Following successful installation of backports BiocManager::install ("DESeq2") will succeed under enter citation("DESeq2")): To install this package, start R (version I'm having a similar error, but different package: library("DESeq2") I can download DESeq2 using, User Agreement and Privacy When you load the package, you can observe this error. "htmlTable", "xfun" This topic was automatically closed 21 days after the last reply. 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. Replacing broken pins/legs on a DIP IC package. Platform: x86_64-apple-darwin17.0 (64-bit) C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Does anyone know why I'm getting the following message when I load tidyverse in a new session. Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. The package has place the R version constraint. 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. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. Bad: conda install -c bioconda bioconductor-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: call: dots_list() 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 locfit, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy Well occasionally send you account related emails. Already on GitHub? Making statements based on opinion; back them up with references or personal experience. Does a summoned creature play immediately after being summoned by a ready action? To learn more, see our tips on writing great answers. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. 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]]) : 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 Join us at CRISPR workshops in Koper, Slovenia in 2023. there is no package called GenomeInfoDbData Installing package(s) 'XML' to allow custom library locations. it would be good to hear any speculation you have of how this might have happened). It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. 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. If not fixed, Try removing remove.packages (rlang) then. The error states that the current version is 0.4.5 but 0.4.10 is required. 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 Give up and run everything from the "permitted" library location (e.g. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Is a PhD visitor considered as a visiting scholar? R version 3.6.1 (2019-07-05) But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () I even tried BiocManager::install("XML") but all failed as shown below. To learn more, see our tips on writing great answers. Is there a proper earth ground point in this switch box? Language(R, Python, SQL) Retrying with flexible solve.Solving environment: Found conflicts! What do I need to do to reproduce your problem? 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. You signed in with another tab or window. Try again and choose No. This article explains how to resolve the package or namespace loading error. "After the incident", I started to be more careful not to trip over things. Documentation [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 Choose Yes. Please read the posting Looking for incompatible packages.This can take several minutes. Is there anyone the same as mine error while loading library(DESeq2)? I have tried your suggestion and also updating the packages that command indicates. Not the answer you're looking for? 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. Policy. Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. To learn more, see our tips on writing great answers. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 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. To add to this, I have also been using DESeq2 recently and ran into the same problem. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). I've copied the output below in case it helps with troubleshooting. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 Looking for incompatible packages. Use of this site constitutes acceptance of our User Agreement and Privacy Sorry, I'm newbie. R version 3.6.3 (2020-02-29) Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Have you tried install.packages("locfit") ? 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. Use of this site constitutes acceptance of our User Agreement and Privacy Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. Surly Straggler vs. other types of steel frames. What am I doing wrong here in the PlotLegends specification? there is no package called GenomeInfoDbData Policy. Bioconductor release. [16] phyloseq1.30.0, loaded via a namespace (and not attached): [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 So if you still get this error try changing your CRAN mirror. Policy. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. I hope you can see something I can't see and help me solving this issue. there is no package called data.table Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. One solution is to find all available packages. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. guide. 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. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Running under: macOS Sierra 10.12.6. Did you do that? No error messages are returned. sessionInfo() dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext