error: package or namespace load failed for 'deseq2

[22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 March 1, 2023, 4:56pm When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. 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. and then updating the packages that command indicates. I've uninstalled and reinstalled rlang (closing restarting RStudio in between each command) and am still encountering this error. Do I need a thermal expansion tank if I already have a pressure tank? binary source needs_compilation [4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0 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. a, There are binary versions available but the source versions are later: [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 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. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? [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: [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. Use this. Thanks for contributing an answer to Stack Overflow! If you try loading the DEseq2 library now, that might work. 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. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' install.packages ("zip") Thanks for your suggestion. 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. Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [1] stats4 parallel stats graphics grDevices utils Making statements based on opinion; back them up with references or personal experience. install.packages('', repo='http://nbcgib.uesc.br/mirrors/cran/'). One solution is to find all available packages. What is the output of. As such there are two solutions that may be more or less attainable given your own IT system. I thought that working in a new environment would help, but it didnt. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 Just realize that I need to write the script "library("DESeq2")" before I proceed. [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 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. [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 If not fixed, Try removing remove.packages (rlang) then. Use of this site constitutes acceptance of our User Agreement and Privacy [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 biocLite(), install.packages() (and the devtools equivalent?) nnet, spatial, survival Choose Yes. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). library(DESeq2) [a/s/n]: Warning message: [5] IRanges_2.8.1 S4Vectors_0.12.1 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 . Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? there is no package called GenomeInfoDbData vegan) just to try it, does this inconvenience the caterers and staff? I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Sorry, I'm newbie. How to notate a grace note at the start of a bar with lilypond? Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? there is no package called data.table Press CTRL-C to abort. R version 3.6.3 (2020-02-29) 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. error: object 'rlang_dots_list' not found Platform: x86_64-w64-mingw32/x64 (64-bit) In install.packages() : I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. rev2023.3.3.43278. I tried to download the "locfit" package but I can't find it anywhere. 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. But I guess you have many problems with your installation, and I'd suggest. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Convince your IT department to relax the permissions for R packages Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . If it fails, required operating system facilities are missing. Is there a proper earth ground point in this switch box? To resolve this error, install the required package as a cluster-installed library. Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 Thanks for contributing an answer to Bioinformatics Stack Exchange! It is working now. If you preorder a special airline meal (e.g. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. What is a word for the arcane equivalent of a monastery? install.packages ("backport") You will be offered a choice to install v 1.1,10 from source. 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. So if you still get this error try changing your CRAN mirror. I have tried your suggestion and also updating the packages that command indicates. Find centralized, trusted content and collaborate around the technologies you use most. package in your R session. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( "htmlTable", "xfun" And finally, install the problem packages, perhaps also DESeq2. Installing package(s) 'htmlTable', 'xfun' Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. ERROR: lazy loading failed for package Hmisc /private/var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T/RtmpMNoZz3/downloaded_packages The error states that the current version is 0.4.5 but 0.4.10 is required. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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. Then I reinstalled R then Rstudio then RTools. [16] lifecycle0.2.0 stringr1.4.0 zlibbioc1.32.0 munsell0.5.0 gtable0.3.0 9. [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6: https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/PACKAGES', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip', https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip', User Agreement and Privacy [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Let me confer with the team. Start R to confirm they are gone. 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 now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Use MathJax to format equations. - the incident has nothing to do with me; can I use this this way? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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. Error: package GenomeInfoDb could not be loaded. Old packages: 'RcppArmadillo', 'survival' I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Looking for incompatible packages. 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 Running under: macOS Catalina 10.15.3, Matrix products: default im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. 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. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 Why are physically impossible and logically impossible concepts considered separate in terms of probability? How do you ensure that a red herring doesn't violate Chekhov's gun? Whats the grammar of "For those whose stories they are"? there is no package called locfit. [65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4 [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 Policy. Sign in + ), update = TRUE, ask = FALSE) Solution To resolve this error, install the required package as a cluster-installed library. Try installing zip, and then loading olsrr. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages I installed the package successfully with conda, but Rstudio is apparently does not know about it. Is a PhD visitor considered as a visiting scholar? 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. Join us at CRISPR workshops in Koper, Slovenia in 2023. Also note, however, that the error you got has been associated in the past with mirror outages. From the console install.packages ("rlang") should fix this. March 1, 2023, 7:31pm call: dots_list() Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): Im trying to use this code: install.packages("locfit"), but this warning appeared: package locfit is not available for this version of R Surly Straggler vs. other types of steel frames. Citation (from within R, sessionInfo() Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. The package has place the R version constraint. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 library(caret) namespace load failed Object sigma not found caret , . How to use Slater Type Orbitals as a basis functions in matrix method correctly? [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 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 am running a new install of R (3.5.0) and RStudio (1.1.414). [16] phyloseq1.30.0, loaded via a namespace (and not attached): However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Browse other questions tagged, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site. This includes any installed libraries. Well occasionally send you account related emails. When you load the package, you can observe this error. Fortunately I was able to solve it by doing things from several suggested solutions. How do I align things in the following tabular environment? Try again and choose No. Copyright 2021 IRZU Intitut za raziskovanje zvonih umetnosti. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Hello, Why do academics stay as adjuncts for years rather than move around? [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Why is this sentence from The Great Gatsby grammatical? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. privacy statement. Loading required package: GenomicRanges Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. 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. [36] digest0.6.25 stringi1.4.6 grid3.6.1 tools3.6.1 bitops1.0-6 Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. . We've tried this - and can replicate this issue on a completely new install with no existing package installs. 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]]): (Factorization). Please remember to confirm an answer once you've received one. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 Is there a proper earth ground point in this switch box? [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: Installation instructions to use this Is it suspicious or odd to stand by the gate of a GA airport watching the planes? [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 Connect and share knowledge within a single location that is structured and easy to search. 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. 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]]): 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 Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' Give up and run everything from the "permitted" library location (e.g. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. When you load the package, you can observe this error. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 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. running multiple versions of the same package, keeping separate libraries for some projects). Sounds like there might be an issue with conda setup? Content type 'application/zip' length 233860 bytes (228 KB) if (!require("BiocManager", quietly = TRUE)) downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Is the God of a monotheism necessarily omnipotent? package rlang was built under R version 3.5.1. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 R version 4.0.1 (2020-06-06) 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. Traffic: 307 users visited in the last hour, I am new to all this! Asking for help, clarification, or responding to other answers. New replies are no longer allowed. A place where magic is studied and practiced? 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. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Glad everything is finally working now. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Already on GitHub? This topic was automatically closed 21 days after the last reply. Running under: macOS Sierra 10.12.6. Please read the posting I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 The other option is to download and older version of locfit from the package archive and install manually. [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2 Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Using indicator constraint with two variables, Does there exist a square root of Euler-Lagrange equations of a field? Does a summoned creature play immediately after being summoned by a ready action? Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so I again tried installing with biocLite but was met with errors so I changed the CRAN mirror. May I know is there any other approach I can try? Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. @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. requires R 4 and running more than a couple of releases behind in R risks multiplying problems. I do know that it works well in qiime2-2020.6. Documentation So, supposedly the issue is with Hmisc. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Update all/some/none? I'm having a similar error, but different package: library("DESeq2") [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( By clicking Sign up for GitHub, you agree to our terms of service and rev2023.3.3.43278. Is there a single-word adjective for "having exceptionally strong moral principles"? Running. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Is there anything I can do to speed it up? [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Policy. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. March 1, 2023, 3:25pm Solving environment: Found conflicts! To learn more, see our tips on writing great answers. 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. "4.2") and enter: For older versions of R, please refer to the appropriate Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? 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). Warning: cannot remove prior installation of package xfun Follow Up: struct sockaddr storage initialization by network format-string, Styling contours by colour and by line thickness in QGIS. Should I update the Bioconductor to latest version instead? 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. Please try reinstalling rlang on a fresh session. - the incident has nothing to do with me; can I use this this way? You signed in with another tab or window. It only takes a minute to sign up. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. 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. Connect and share knowledge within a single location that is structured and easy to search. Are there tables of wastage rates for different fruit and veg? Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. Any suggestions would be greatly appreciated. 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. As far as I can tell, I have successfully installed the R package, but when I switch back to my Qiime environment to install Aldex2, I get an error. Installing package(s) 'XML' Making statements based on opinion; back them up with references or personal experience. :), BiocManager::install("locift") I just figured Id ask. install.packages("BiocManager"), I get this error: Platform: x86_64-apple-darwin17.0 (64-bit) sessionInfo() 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. When an R package depends on a newer package version, the required package is downloaded but not loaded. I highly recommend that any R/RStudio version not installed inside conda be removed.

error: package or namespace load failed for 'deseq2 2023