Are you sure the R you're running from the command line is installed through Anaconda as well? there is no package called Hmisc. In install.packages() : 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, object not found, How Intuit democratizes AI development across teams through reusability. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? I am running a new install of R (3.5.0) and RStudio (1.1.414). Hello, When an R package depends on a newer package version, the required package is downloaded but not loaded. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR Join us at CRISPR workshops in Koper, Slovenia in 2023. "htmlTable", "xfun" If not fixed, Try removing remove.packages (rlang) then. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? .onLoad failed in loadNamespace() for 'rlang', details: What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. You signed in with another tab or window. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( Content type 'application/zip' length 4255589 bytes (4.1 MB) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc Does anyone know why I'm getting the following message when I load tidyverse in a new session. 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") R version 4.0.1 (2020-06-06) By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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: Policy. package in your R session. Installing package(s) 'htmlTable', 'xfun' I highly recommend that any R/RStudio version not installed inside conda be removed. binary source needs_compilation [7] edgeR_3.16.5 limma_3.30.12 Platform: x86_64-apple-darwin13.4.0 (64-bit) [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: Error: package GenomeInfoDb could not be loaded. Is a PhD visitor considered as a visiting scholar? [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 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. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Use MathJax to format equations. I do not get why Rstudio does not see that I alrerady installed DESeq2 with conda. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. This can take several minutes. Thanks! rev2023.3.3.43278. Please read the posting Asking for help, clarification, or responding to other answers. But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) I even tried BiocManager::install("XML") but all failed as shown below. 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 to your account. If you try loading the DEseq2 library now, that might work. Sounds like there might be an issue with conda setup? Fortunately I was able to solve it by doing things from several suggested solutions. Is there anyone the same as mine error while loading library(DESeq2)? [5] IRanges_2.8.1 S4Vectors_0.12.1 Is there anything I can do to speed it up? C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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. Is there a single-word adjective for "having exceptionally strong moral principles"? Making statements based on opinion; back them up with references or personal experience. [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): - the incident has nothing to do with me; can I use this this way? Looking for incompatible packages. March 1, 2023, 3:25pm Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? I guess that means we can finally close this issue. 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 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already 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). Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? 9. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Erasmus+ funds available! The error states that the current version is 0.4.5 but 0.4.10 is required. No error messages are returned. I've copied the output below in case it helps with troubleshooting. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Sorry if I missed this, the question was quite long so I kind of skimmed, but I noticed that early on some of the packages were reported as requiring manual compilation from source. [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 Traffic: 307 users visited in the last hour, I am new to all this! [31] tools_3.3.2 bitops_1.0-6 magrittr_1.5 Content type 'application/zip' length 386703 bytes (377 KB) [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Already on GitHub? I thought that working in a new environment would help, but it didnt. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( How do I align things in the following tabular environment? 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. 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]]) : Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [7] datasets methods base, other attached packages: [69] tidyselect_1.0.0. Also make sure that you have RTools.exe installed and working. I was assuming that to be the case. The package has place the R version constraint. Why do academics stay as adjuncts for years rather than move around? 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 . Styling contours by colour and by line thickness in QGIS. Please try reinstalling rlang on a fresh session. Warning message: Should I update the Bioconductor to latest version instead? - the incident has nothing to do with me; can I use this this way? 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. 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. [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 How to use Slater Type Orbitals as a basis functions in matrix method correctly? running multiple versions of the same package, keeping separate libraries for some projects). install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? How to notate a grace note at the start of a bar with lilypond? 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. 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 all/some/none? 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. If you have a query related to it or one of the replies, start a new topic and refer back with a link. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? To learn more, see our tips on writing great answers. The issue here was likely that you used two different package managers (conda and R), each setting and managing their own paths. "After the incident", I started to be more careful not to trip over things. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 So, supposedly the issue is with Hmisc. Retrying with flexible solve.Solving environment: Found conflicts! Old packages: 'RcppArmadillo', 'survival' [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Acidity of alcohols and basicity of amines. @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. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, "4.2") and enter: For older versions of R, please refer to the appropriate installation of package GenomeInfoDbData had non-zero exit status. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. When you load the package, you can observe this error. Does a summoned creature play immediately after being summoned by a ready action? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 sessionInfo() [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 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. Whats the grammar of "For those whose stories they are"? From the console install.packages ("rlang") should fix this. 4. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Thanks for contributing an answer to Stack Overflow! Is it suspicious or odd to stand by the gate of a GA airport watching the planes? If you preorder a special airline meal (e.g. Why is this sentence from The Great Gatsby grammatical? It only takes a minute to sign up. Your best bet would be to download the package source code and change the R version and install manually if you wanted the most recent version of locfit to install on your computer. What am I doing wrong here in the PlotLegends specification? I'm having a similar error, but different package: library("DESeq2") I tried following the instructions for 2019.7 as well and I am getting the same error. Policy. A place where magic is studied and practiced? Try again and choose No. Policy. [13] ggplot23.3.0 car3.0-7 carData3.0-3 So if you still get this error try changing your CRAN mirror. 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. 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. [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Connect and share knowledge within a single location that is structured and easy to search. 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. . Policy. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Documentation R version 3.6.3 (2020-02-29) im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Well occasionally send you account related emails. Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. I tried again and again was met with missing packages BUT!!! [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 vegan) just to try it, does this inconvenience the caterers and staff? data . LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: To resolve this error, install the required package as a cluster-installed library. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. if (!require("BiocManager", quietly = TRUE)) Sounds like you might have an issue with which R Rstudio is running. binary R install.packages("XML",type="binary") install.packages("RCurl",type="binary") R"had non-zero exit status" - (zhihu.com) 1 R APP "" wx 1 1.1W 4 0 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Any suggestions would be greatly appreciated. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? Thanks for contributing an answer to Bioinformatics Stack Exchange! Thnaks anyway, Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems, How Intuit democratizes AI development across teams through reusability. If I try running biocLite("DESeq2") from Rstudio I get the following error: Error in dyn.load(file, DLLpath = DLLpath, ) : [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 I would recommend installing an older version of QIIME 2 for this plugin to work.