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. 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: Policy. Running under: Windows 10 x64 (build 18362), locale: What is a word for the arcane equivalent of a monastery? Traffic: 307 users visited in the last hour, I am new to all this! there is no package called data.table Policy. Content type 'application/zip' length 4255589 bytes (4.1 MB) downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in installation of package GenomeInfoDbData had non-zero exit status. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Whats the grammar of "For those whose stories they are"? Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Please read the posting [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 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' 0 cbravo11 0 @e0025e70 Last seen 10 months ago United States I installed DESeq2 using this code: 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). 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 I've copied the output below in case it helps with troubleshooting. Styling contours by colour and by line thickness in QGIS. a, There are binary versions available but the source versions are later: Old packages: 'RcppArmadillo', 'survival' ERROR: dependency Hmisc is not available for package DESeq2 [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. package xfun successfully unpacked and MD5 sums checked How do I align things in the following tabular environment? May be the version has problem How can I do ? Documentation Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
Error: package or namespace load failed for 'DESeq2 - Bioconductor Policy. We've tried this - and can replicate this issue on a completely new install with no existing package installs. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Thanks for contributing an answer to Stack Overflow! [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages:
Installing DESeq2 Error: no package called 'GenomeInfoDbData - GitHub Platform: x86_64-apple-darwin13.4.0 (64-bit) If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) :
Error when installing Aldex2 - Community Plugin Support - Open Source running multiple versions of the same package, keeping separate libraries for some projects). call: dots_list() Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Asking for help, clarification, or responding to other answers. I installed the package successfully with conda, but Rstudio is apparently does not know about it. 2. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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 - the incident has nothing to do with me; can I use this this way? in your system, start R and enter: Follow [7] edgeR_3.16.5 limma_3.30.12 rev2023.3.3.43278. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 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. Hello, How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Thanks for contributing an answer to Bioinformatics Stack Exchange!
there is no package called GenomeInfoDbData Is there a proper earth ground point in this switch box? [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 binary source needs_compilation I'm having a similar error, but different package: library("DESeq2") The other option is to download and older version of locfit from the package archive and install manually. I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. And finally, install the problem packages, perhaps also DESeq2. Did you do that? [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Convince your IT department to relax the permissions for R packages Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. March 1, 2023, 7:31pm In file.copy(savedcopy, lib, recursive = TRUE) : Use of this site constitutes acceptance of our User Agreement and Privacy By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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). [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. How can we prove that the supernatural or paranormal doesn't exist?
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 I am running a new install of R (3.5.0) and RStudio (1.1.414). Policy. Learn more about Stack Overflow the company, and our products. Running under: macOS Catalina 10.15.3, Matrix products: default + "htmlTable", "xfun" March 1, 2023, 4:56pm [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages:
DESeq2: Error: package or namespace load failed for 'DESeq2': objects C:\R\R-3.4.3\library). [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: To resolve this error, install the required package as a cluster-installed library. Any other suggestion? [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 Disconnect between goals and daily tasksIs it me, or the industry? [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Running under: macOS Sierra 10.12.6. I tried again and again was met with missing packages BUT!!! 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. [69] tidyselect_1.0.0. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib enter citation("DESeq2")): To install this package, start R (version if (!require("BiocManager", quietly = TRUE))
Resolving package or namespace loading error What is the output of. Update all/some/none? Is a PhD visitor considered as a visiting scholar? Looking for incompatible packages. I can download DESeq2 using, User Agreement and Privacy Content type 'application/zip' length 233860 bytes (228 KB) Warning message: Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . "After the incident", I started to be more careful not to trip over things. 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. Then I reinstalled R then Rstudio then RTools. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. When you load the package, you can observe this error. To learn more, see our tips on writing great answers.
DESeq2_2301_76497647-CSDN Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. As mentioned above, my institutional IT can replicate this on a laptop with a completely fresh R install and no prior package installations (meaning isn't to do with installing with another version of the package already running). Try installing zip, and then loading olsrr. library(DESeq2) Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Thank you @hharder. 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. Installation instructions to use this /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): Then I reinstalled R then Rstudio then RTools. I would recommend installing an older version of QIIME 2 for this plugin to work. Is there anything I can do to speed it up? Sign in When you load the package, you can observe this error. I guess that means we can finally close this issue.
[R] Error: package or namespace load failed for 'ggplot2' in If it fails, required operating system facilities are missing. @artembus Sounds like it was a ton of work! It is working now. Does anyone know why I'm getting the following message when I load tidyverse in a new session. This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer: What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt. Running under: macOS Sierra 10.12.3, locale:
Install DESeq2 through anaconda - Bioinformatics Stack Exchange Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Looking for incompatible packages.This can take several minutes. What am I doing wrong here in the PlotLegends specification? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? there is no package called Hmisc. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Well occasionally send you account related emails. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. 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
[email protected]:packages/DESeq2. Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. Not the answer you're looking for? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment.
No error messages are returned. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Do I need a thermal expansion tank if I already have a pressure tank? I highly recommend that any R/RStudio version not installed inside conda be removed. I noticed that you are trying to install qiime2-2019.4, this may not work as ALDEx2 was made for qiime2-2019.7 as outlined here, up to and including the versions I mentioned earlier. sessionInfo() library(caret) namespace load failed Object sigma not found caret , . error: object 'rlang_dots_list' not found Is it suspicious or odd to stand by the gate of a GA airport watching the planes? [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
How can I fix error with loading package in R ? | ResearchGate Is the God of a monotheism necessarily omnipotent? Join us at CRISPR workshops in Koper, Slovenia in 2023. I tried to download the "locfit" package but I can't find it anywhere. That plugin is has not been updated to work with later releases of QIIME 2. 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: 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!!! A place where magic is studied and practiced? Please try reinstalling rlang on a fresh session. Please try the following steps: Quit all R/Rstudio sessions. 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"). 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. 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"). So, I recommend following the install instructions for the respective versions of QIIME 2, and then install the plugin. Platform: x86_64-w64-mingw32/x64 (64-bit) Is there a proper earth ground point in this switch box?
library(caret) namespace load failed Object sigma not + ), update = TRUE, ask = FALSE) 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.