One solution is to find all available packages. And finally, install the problem packages, perhaps also DESeq2. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' 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. Not the answer you're looking for? Statistics ; Algorithm(ML, DL,.) Is there anything I can do to speed it up? Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). How to notate a grace note at the start of a bar with lilypond? In addition: Warning message: I am running a new install of R (3.5.0) and RStudio (1.1.414). To subscribe to this RSS feed, copy and paste this URL into your RSS reader. 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 Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 [7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2 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. Thanks! What do I need to do to reproduce your problem? [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 I highly recommend that any R/RStudio version not installed inside conda be removed. @artembus Sounds like it was a ton of work! 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. After 3-4 manual installs everything worked. I guess that means we can finally close this issue. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. and then updating the packages that command indicates. My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? 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 . How do I align things in the following tabular environment? [69] tidyselect_1.0.0. Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Warning message: MathJax reference. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 [5] IRanges_2.8.1 S4Vectors_0.12.1 To learn more, see our tips on writing great answers. Replacing broken pins/legs on a DIP IC package. "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? 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. locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Bad: conda install -c bioconda bioconductor-deseq2. It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Traffic: 307 users visited in the last hour, I am new to all this! im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. I tried following the instructions for 2019.7 as well and I am getting the same error. Sounds like you might have an issue with which R Rstudio is running. I would argue that the conclusion to, Yeah, just need to select one way of doing it and never use the other. .onLoad failed in loadNamespace() for 'rlang', details: Please remember to confirm an answer once you've received one. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: [1] LCCOLLATE=EnglishMalaysia.1252 LCCTYPE=EnglishMalaysia.1252 LCMONETARY=EnglishMalaysia.1252 Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . You are doing something very wrong when installing your packages. Is there a proper earth ground point in this switch box? Raise a support ticket every time you need to install a package into a custom location and hope that IT eventually gives in. If you preorder a special airline meal (e.g. Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 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 sessionInfo() Policy. 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 This is default text for notification bar, Removing Unwanted Variation Using Pseudoreplicates and Pseudosamples, Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver, Extension of scPipe Bioconductor Package for scATAC-seq Data, Matilda for Single-cell Multi-omics Data Integration, cellXY for Exploring Gender-specific Genes in Single Cell RNA-seq Data, Stereopy as an Advanced Tool for Interpreting Spatial Transcriptomics Data, Spectre Toolkit for Rapid Analysis of Cytometry Data, A Bioconductor Framework for High-dimensional in situ Cytometry Analysis, Error when installing Aldex2 Community Plugin Support, How the Gut Microbiota Affects COVID-19 Vaccine Immunogenicity , Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration. Have you tried install.packages("locfit") ? [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Error: package GenomeInfoDb could not be loaded, if (!requireNamespace("BiocManager", quietly = TRUE)), BiocManager::install("GenomeInfoDbData") [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: [21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31 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. Erasmus+ funds available! March 1, 2023, 4:56pm Use MathJax to format equations. It only takes a minute to sign up. Try installing zip, and then loading olsrr. Convince your IT department to relax the permissions for R packages Policy. rev2023.3.3.43278. [37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0 Update all/some/none? Join us at CRISPR workshops in Koper, Slovenia in 2023. Expected in: /usr/lib/libSystem.B.dylib, dyld: Symbol not found: _utimensat to allow custom library locations. install.packages("BiocManager"), I get this error: Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in Documentation I tried to download the "locfit" package but I can't find it anywhere. (Factorization). 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details, replacement repositories: Connect and share knowledge within a single location that is structured and easy to search. Sometimes packages get loaded automatically at startup from .RProfile and you can check this by calling sessionInfo() after starting up. It is working now. What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR To learn more, see our tips on writing great answers. Language(R, Python, SQL) 2. Well occasionally send you account related emails. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Is there anyone the same as mine error while loading library(DESeq2)? 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. 4. Asking for help, clarification, or responding to other answers. 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. 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. The package has place the R version constraint. 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 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: