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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. Connect and share knowledge within a single location that is structured and easy to search. 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 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. "After the incident", I started to be more careful not to trip over things. Do I need a thermal expansion tank if I already have a pressure tank? In install.packages() : Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? 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. Did you do that? vegan) just to try it, does this inconvenience the caterers and staff? Find centralized, trusted content and collaborate around the technologies you use most. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, I would recommend installing an older version of QIIME 2 for this plugin to work. Making statements based on opinion; back them up with references or personal experience. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. 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. (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 . Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. 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. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. I installed the package successfully with conda, but Rstudio is apparently does not know about it. Solution To resolve this error, install the required package as a cluster-installed library. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 Why do many companies reject expired SSL certificates as bugs in bug bounties? Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [28] digest_0.6.12 stringi_1.1.2 grid_3.3.2 Is the God of a monotheism necessarily omnipotent? Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Post questions about Bioconductor I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Is there anything I can do to speed it up? package rlang was built under R version 3.5.1. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. Why are physically impossible and logically impossible concepts considered separate in terms of probability? [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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. if (!require("BiocManager", quietly = TRUE)) [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 Installing DESeq2 Error: no package called GenomeInfoDbData, https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz, https://cran.rstudio.com/bin/macosx/contrib/4.0/RcppArmadillo_0.9.880.1.0.tgz, https://cran.rstudio.com/bin/macosx/contrib/4.0/survival_3.1-12.tgz. Glad everything is finally working now. I'm trying to reproduce your problem, so being as precise as possible is important. This is the beauty of installing QIIME 2 via conda, you can have many different versions of QIIME 2 on your system at the same time and activate the version you want to use. (Factorization). trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' ERROR: dependency Hmisc is not available for package DESeq2 Follow Up: struct sockaddr storage initialization by network format-string. [19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1 That plugin is has not been updated to work with later releases of QIIME 2. unable to load shared object '/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so': 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: Thanks for contributing an answer to Bioinformatics Stack Exchange! Policy. Open Source Biology & Genetics Interest Group. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 How do you ensure that a red herring doesn't violate Chekhov's gun? data . Use MathJax to format equations. I thought that working in a new environment would help, but it didnt. Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Content type 'application/zip' length 4255589 bytes (4.1 MB) 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. May be the version has problem How can I do ? 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: . I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run R console and try to import DESeq2 I am getting the error message: Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): How can we prove that the supernatural or paranormal doesn't exist? Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. 4. Bad: conda install -c bioconda bioconductor-deseq2. What is the output of. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. [5] IRanges_2.8.1 S4Vectors_0.12.1 [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 To add to this, I have also been using DESeq2 recently and ran into the same problem. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Disconnect between goals and daily tasksIs it me, or the industry? Use this. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). When an R package depends on a newer package version, the required package is downloaded but not loaded. Policy. I even tried BiocManager::install("XML") but all failed as shown below. biocLite(), install.packages() (and the devtools equivalent?) Thank you @hharder. Is there a proper earth ground point in this switch box? [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: This can take several minutes. MathJax reference. How to notate a grace note at the start of a bar with lilypond? The other option is to download and older version of locfit from the package archive and install manually. 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. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc call: dots_list() Is there a single-word adjective for "having exceptionally strong moral principles"? Sign in Content type 'application/zip' length 233860 bytes (228 KB) Does a summoned creature play immediately after being summoned by a ready action? Policy. 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. When you load the package, you can observe this error. So, supposedly the issue is with Hmisc. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. I'm having a similar error, but different package: library("DESeq2") BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib Just realize that I need to write the script "library("DESeq2")" before I proceed. Installing Hmisc as suggested above did not solve the issue. Why is this sentence from The Great Gatsby grammatical? Try installing zip, and then loading olsrr. [16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1 Well occasionally send you account related emails. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages install.packages ("zip") there is no package called Hmisc. Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): 'KEGGREST' 2301_76497647 17 1 109+ 20+ 30 10 1 0 2 0 Looking for incompatible packages. 2. [1] stats4 parallel stats graphics grDevices utils and then updating the packages that command indicates. library(DESeq2) 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'. New replies are no longer allowed. rev2023.3.3.43278. Policy. 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). Is there a proper earth ground point in this switch box? 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!!! Warning: cannot remove prior installation of package xfun From the console install.packages ("rlang") should fix this. binary source needs_compilation Policy. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 Already on GitHub? Warning message: Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Warning message: Thanks for contributing an answer to Stack Overflow! Is there anyone the same as mine error while loading library(DESeq2)? Sorry, I'm newbie. 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. 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. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( 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. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: - the incident has nothing to do with me; can I use this this way? [a/s/n]: When an R package depends on a newer package version, the required package is downloaded but not loaded. Why is there a voltage on my HDMI and coaxial cables? If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. ERROR: lazy loading failed for package Hmisc C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) 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. 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. Asking for help, clarification, or responding to other answers. Documentation 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. As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. [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. I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages We've tried this - and can replicate this issue on a completely new install with no existing package installs. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. dlopen(/Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so, 6): Symbol not found: _libintl_dgettext Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 In file.copy(savedcopy, lib, recursive = TRUE) : You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. 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. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Then I reinstalled R then Rstudio then RTools. Platform: x86_64-apple-darwin17.0 (64-bit) Bioconductor release. Whats the grammar of "For those whose stories they are"? @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. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. While a notebook is attached to a cluster, the R namespace cannot be refreshed. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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: A place where magic is studied and practiced? sessionInfo() Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR How do I align things in the following tabular environment? Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. I guess that means we can finally close this issue. This topic was automatically closed 21 days after the last reply. Surly Straggler vs. other types of steel frames. Replacing broken pins/legs on a DIP IC package. Thanks for your suggestion. Platform: x86_64-apple-darwin13.4.0 (64-bit) 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. Update all/some/none? The best answers are voted up and rise to the top, Not the answer you're looking for? [69] tidyselect_1.0.0. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. 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").