To learn more, see our tips on writing great answers. downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked Making statements based on opinion; back them up with references or personal experience. Please try reinstalling rlang on a fresh session. install.packages("BiocManager"), I get this error: .onLoad failed in loadNamespace() for 'rlang', details: Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. Well occasionally send you account related emails. Press CTRL-C to abort. Making statements based on opinion; back them up with references or personal experience. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so C:\R\R-3.4.3\library). package in your R session. You are doing something very wrong when installing your packages. 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. R version 3.6.3 (2020-02-29) How to use Slater Type Orbitals as a basis functions in matrix method correctly? While a notebook is attached to a cluster, the R namespace cannot be refreshed. Given this is a Bioinformatics package, are you by any chance using Ubuntu or another linux distribution @RedRabbit? I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. 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. package rlang was built under R version 3.5.1. 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. I guess that means we can finally close this issue. Styling contours by colour and by line thickness in QGIS. If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1 The other option is to download and older version of locfit from the package archive and install manually. Do I need a thermal expansion tank if I already have a pressure tank? [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 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 [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. binary source needs_compilation [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 In addition: Warning message: From the console install.packages ("rlang") should fix this. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. "After the incident", I started to be more careful not to trip over things. In install.packages() : Running under: macOS Sierra 10.12.3, locale: Did you do that? 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. running multiple versions of the same package, keeping separate libraries for some projects). I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) 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. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Warning message: Also note, however, that the error you got has been associated in the past with mirror outages. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? 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. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. + ), update = TRUE, ask = FALSE) March 1, 2023, 7:31pm [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 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. New replies are no longer allowed. So, supposedly the issue is with Hmisc. I would suggest to install data.table, lme4 and all of the packages denoted in the 2 statements that said Packages which are only available in source form, and may need compilation of C/C++/Fortran: with pacman then re-run the Bioconductor installation of your target package. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 I hope you can see something I can't see and help me solving this issue. Statistics ; Algorithm(ML, DL,.) Update all/some/none? guide. Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I am using R 3.6.1 and Rstudio 1.2. technocrat August 27, 2020, 10:15pm #2 RedRabbit: DESeq2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Documentation library ("DESeq2") 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 'Hmisc' Installing Hmisc as suggested above did not solve the issue. Bioconductor release. As such there are two solutions that may be more or less attainable given your own IT system. I tried to download the "locfit" package but I can't find it anywhere. 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. Why are physically impossible and logically impossible concepts considered separate in terms of probability? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 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. Can't Load R DESeq2 Library, Installed All Missing Packages and Still Warning message: /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages I even tried BiocManager::install("XML") but all failed as shown below. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Find centralized, trusted content and collaborate around the technologies you use most. I do know that it works well in qiime2-2020.6. Traffic: 307 users visited in the last hour, I am new to all this! Retrying with flexible solve.Solving environment: Found conflicts! What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. and then updating the packages that command indicates. Why is there a voltage on my HDMI and coaxial cables? [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 [a/s/n]: [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 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 . How do you ensure that a red herring doesn't violate Chekhov's gun? Have you tried install.packages("locfit") ? data . Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? A place where magic is studied and practiced? now when I tried installing the missing packages they did install. if (!require("BiocManager", quietly = TRUE)) [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 library(caret) namespace load failed Object sigma not found caret , . Assuming that your conda environment name is renv, try running this in the terminal: This should open up the Rstudio interface, like normal, but using everything defined in your renv environment. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Learn more about Stack Overflow the company, and our products. To view documentation for the version of this package installed + "htmlTable", "xfun" now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : I highly recommend that any R/RStudio version not installed inside conda be removed. vegan) just to try it, does this inconvenience the caterers and staff? 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") 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 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. 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. 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. Why do academics stay as adjuncts for years rather than move around? May I know is there any other approach I can try? Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Asking for help, clarification, or responding to other answers. /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages Old packages: 'RcppArmadillo', 'survival' 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. I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: If you have a query related to it or one of the replies, start a new topic and refer back with a link. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 in your system, start R and enter: Follow More info about Internet Explorer and Microsoft Edge. Any other suggestion? Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. To learn more, see our tips on writing great answers. So if you still get this error try changing your CRAN mirror. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages library(caret) namespace load failed Object sigma not [5] IRanges_2.8.1 S4Vectors_0.12.1 [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): . [13] ggplot23.3.0 car3.0-7 carData3.0-3 I installed the package successfully with conda, but Rstudio is apparently does not know about it. What is the output of. Thanks for contributing an answer to Bioinformatics Stack Exchange! 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!!! Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? 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: [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: 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. Installing packages directly into that location fixes the issue but is not desirable for all the reasons that people might want to use custom locations (e.g. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 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. Thanks! Use of this site constitutes acceptance of our User Agreement and Privacy 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. 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. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. 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. Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Installing Hmisc as suggested above did not solve the issue. DESeq2 installation in R - Bioconductor By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Use of this site constitutes acceptance of our User Agreement and Privacy Content type 'application/zip' length 233860 bytes (228 KB) Just updated my previous R to 4.01 and now I cant load DESeq2. Error: package or namespace load failed for 'DESeq2 - Bioconductor 9. [Note I have now updated to 3.5.1 and 1.1.453 and am still experiencing the issues below with the exception of the "built under R version 3.5.1" warning messages], I have installed the rlang package using install.packages("rlang") without encountering any issues but when I attempt to load the package I get the following error, Error: package or namespace load failed for rlang: @KonradRudolph It's pacman (not packman) and you are correct in that it's basically just a wrapper for, Thanks for your suggestion, I tried doing this step by step as you said but the biocLite command still did throw errors for missing packages. biocLite(), install.packages() (and the devtools equivalent?) When an R package depends on a newer package version, the required package is downloaded but not loaded. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Already on GitHub? 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. I need help installing a package "DESeq2" having - RStudio Community nnet, spatial, survival Thanks for contributing an answer to Stack Overflow! 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. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. 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). Should I update the Bioconductor to latest version instead? Whats the grammar of "For those whose stories they are"? After 3-4 manual installs everything worked. If I run install.packages(GenomeInfoDb) from R console, it is telling me that the package is not available for R version 3.5.1. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence?