In addition: Warning message: now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. 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. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) downloaded 228 KB, package htmlTable successfully unpacked and MD5 sums checked When you load the package, you can observe this error. 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. Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). Is there a proper earth ground point in this switch box? Policy. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. 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. And finally, install the problem packages, perhaps also DESeq2. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 As such there are two solutions that may be more or less attainable given your own IT system. So, supposedly the issue is with Hmisc. MathJax reference. [13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3 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. 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. nnet, spatial, survival 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. 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 . 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. May be the version has problem How can I do ? 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. library(DESeq2) How to use Slater Type Orbitals as a basis functions in matrix method correctly? 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. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 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. [57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5 vegan) just to try it, does this inconvenience the caterers and staff? 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 Surly Straggler vs. other types of steel frames. Sorry, I'm newbie. First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth but it was on Linux), Then trying to install the DESeq2 package with biocLite (looks like everything is good). [13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in I also tried something I found on google: but the installation had errors too, I can write them here if needed. Platform: x86_64-apple-darwin15.6.0 (64-bit) How do I align things in the following tabular environment? Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) DESeq2: Error: package or namespace load failed for 'DESeq2': objects Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. Thanks for contributing an answer to Stack Overflow! I'm trying to reproduce your problem, so being as precise as possible is important. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR "4.2") and enter: For older versions of R, please refer to the appropriate Policy. Learn more about Stack Overflow the company, and our products. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( I thought that working in a new environment would help, but it didnt. ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: and then updating the packages that command indicates. How to use Slater Type Orbitals as a basis functions in matrix method correctly? I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' + ), update = TRUE, ask = FALSE) If not, I recommend using the latest version of R and Bioconductor for bug fixes and improvements. library(DESeq2) Is there a single-word adjective for "having exceptionally strong moral principles"? Policy. 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. What am I doing wrong here in the PlotLegends specification? Why do academics stay as adjuncts for years rather than move around? Is the God of a monotheism necessarily omnipotent? Connect and share knowledge within a single location that is structured and easy to search. Policy. 1. I think the latest version of QIIME 2 that can run this plugin is qiime2-2021.2. Can't Load R DESeq2 Library, Installed All Missing Packages and Still Error: package or namespace load failed, object not found 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). Install DESeq2 through anaconda - Bioinformatics Stack Exchange Platform: x86_64-apple-darwin17.0 (64-bit) there is no package called GenomeInfoDbData 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. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 Policy. [5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3 Disconnect between goals and daily tasksIs it me, or the industry? To learn more, see our tips on writing great answers. running multiple versions of the same package, keeping separate libraries for some projects). R| - there is no package called Hmisc. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. One solution is to find all available packages. March 1, 2023, 7:31pm Any other suggestion? 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"). Try installing zip, and then loading olsrr. Sounds like you might have an issue with which R Rstudio is running. 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: Does a summoned creature play immediately after being summoned by a ready action? I'm having a similar error, but different package: library("DESeq2") In file.copy(savedcopy, lib, recursive = TRUE) : Connect and share knowledge within a single location that is structured and easy to search. Is there anyone the same as mine error while loading library(DESeq2)? Replacing broken pins/legs on a DIP IC package. It is working now. Is a PhD visitor considered as a visiting scholar? R DESeq2 - [9] Biobase_2.34.0 BiocGenerics_0.20.0, loaded via a namespace (and not attached): When an R package depends on a newer package version, the required package is downloaded but not loaded. Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Running. 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. Asking for help, clarification, or responding to other answers. 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") Have you tried install.packages("locfit") ? Solving environment: Found conflicts! I downloaded the R-4.0.1.pkg link from https://cran.r-project.org/bin/macosx/ and installed it as an administrator. Running under: macOS Sierra 10.12.3, locale: [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 [41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4 [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 After 3-4 manual installs everything worked. How can we prove that the supernatural or paranormal doesn't exist? Choose Yes. [R] Error: package or namespace load failed for 'ggplot2' in Acidity of alcohols and basicity of amines. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 Connect and share knowledge within a single location that is structured and easy to search. ERROR: lazy loading failed for package Hmisc [49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0 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]]) : [5] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1 IRanges2.20.2 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. Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: Error when installing Aldex2 - Community Plugin Support - Open Source package xfun successfully unpacked and MD5 sums checked Solution To resolve this error, install the required package as a cluster-installed library. C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages 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. Is there anything I can do to speed it up? Use this. The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). To learn more, see our tips on writing great answers. /var/folders/0t/8jm6lgqs0qj63rprpf9q_nfw0000gn/T//RtmpMNoZz3/downloaded_packages Well occasionally send you account related emails. [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: R version 3.6.3 (2020-02-29) "htmlTable", "xfun" If it fails, required operating system facilities are missing. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in [69] tidyselect_1.0.0. @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. Making statements based on opinion; back them up with references or personal experience. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 I then launched the R application (from the finder, not RStudio) and installed BiocManager. so I would try to use BiocManager::install("XML"). The best answers are voted up and rise to the top, Not the answer you're looking for? I tried again and again was met with missing packages BUT!!! Content type 'application/zip' length 233860 bytes (228 KB) What do I need to do to reproduce your problem? Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. 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. Platform: x86_64-w64-mingw32/x64 (64-bit) Thanks for your suggestion. Warning message: Why is there a voltage on my HDMI and coaxial cables? I installed the package successfully with conda, but Rstudio is apparently does not know about it. Bioconductor - DESeq2 Maybe it is not a kind of quick fix and it could have been solved easier, but I was not able to. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): [a/s/n]: [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 Installing package(s) 'XML' However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. 4. there is no package called locfit. .onLoad failed in loadNamespace() for 'rlang', details: Sounds like there might be an issue with conda setup? Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Just to add on -- do you require an old version of Bioconductor for your current project? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Traffic: 307 users visited in the last hour, I am new to all this! [3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3 C:\Users\ASUS\AppData\Local\Temp\RtmpCiM0wL\downloaded_packages It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. [51] rstudioapi0.11 R62.4.1 rpart4.1-15 nnet7.3-14 compiler_3.6.1, BiocManager::install(c( [34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 if (!require("BiocManager", quietly = TRUE)) I have been working on installing Aldex2 (@dgiguer) in my Qiime environment using Ubuntu. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? Installing package(s) 'GenomeInfoDbData' [1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0 Not the answer you're looking for? Find centralized, trusted content and collaborate around the technologies you use most. a, There are binary versions available but the source versions are later: Join us at CRISPR workshops in Koper, Slovenia in 2023. there is no package called GenomeInfoDbData 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: [5] IRanges_2.8.1 S4Vectors_0.12.1 To view documentation for the version of this package installed Did you do that? Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin?). By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3 library(caret) namespace load failed Object sigma not Installing package(s) 'htmlTable', 'xfun' 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. 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 Content type 'application/zip' length 386703 bytes (377 KB) 9. Looking for incompatible packages.This can take several minutes. What is the output of. 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!!! Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Can you provide a screen shot of the errors when you try to setup a new conda environment for QIIME 2? If you preorder a special airline meal (e.g. rev2023.3.3.43278. Warning: restored xfun, The downloaded binary packages are in (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 . Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? How can I fix error with loading package in R ? | ResearchGate What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Is there a proper earth ground point in this switch box? [17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0 When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Error: package or namespace load failed, object not found, How Intuit democratizes AI development across teams through reusability. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. This includes any installed libraries. 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. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in New replies are no longer allowed. [1] SummarizedExperiment1.16.1 DelayedArray0.12.3 BiocParallel1.20.1 matrixStats0.56.0 in /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Content type 'application/zip' length 4255589 bytes (4.1 MB)