error: package or namespace load failed for 'deseq2
But I guess you have many problems with your installation, and I'd suggest. Why is this happening? R error message when calling libraries and installing packages I am facing the same problem. Platform: x86_64-apple-darwin17.0 (64-bit) Error: package or namespace load failed for 'ggplot2' in loadNamespace (i, c (lib.loc, .libPaths ()), versionCheck = vI [ [i]]): namespace 'rlang' 0.4.6 is already loaded, but >= 0.4.7 is required How do I solve this error?I have even tried uninstalling and installing r. 4 Likes technocrat September 8, 2020, 6:24am #2 一、问题. Powered by Discourse, best viewed with JavaScript enabled, I need help installing a package "DESeq2" having BiocManager issues. I also uploaded R from 3.6.2 to 3.6.3 but it didn't change anything. not found. Thanks! To subscribe to this RSS feed, copy and paste this URL into your RSS reader. The issue for me was that Ubuntu's repositories are out of date for R, and I needed to add a new repository. R 3.5 package 'lattice' was installed by an R version with different internals. I thought it would be a breeze given the blank slate but the first package I'm trying to install and load, DESeq2, continuously fails. Can a non-pilot realistically land a commercial airliner? To fix this error, there is need to increase the maximum number of DLLs which can be done by editing the ".Renviron" in the home directory the system, one may consider creating one if it does not exist. How do I solve a dependency error that prevents me from installing R 4.0 on Ubuntu 18.04? downloaded 4.1 MB, package ‘XML’ successfully unpacked and MD5 sums checked, The downloaded binary packages are in Many of my colleagues had these packages automatically downloaded with the same version of RStudio and R. XML installation seems to be failing and not load on R, https://cran.r-project.org/src/contrib/Archive/XML/, What developers with ADHD want you to know, MosaicML: Deep learning models for sale, all shapes and sizes (Ep. Hmm, I guess I can't help much until you have an installation that passes valid() as it will likely lead to mis-matching code across versions of Bioc. Thank you for bringing it to our attention Installing Hmisc as suggested above did not solve the issue. Can I drink black tea that’s 13 years past its best by date? [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 May I know is there any other approach I can try? nnet, spatial, survival I'm having a similar error, but different package: library("DESeq2") [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 @artembus Sounds like it was a ton of work! 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 'XML' Then I manually installed the XML package: install.packages ("XML") it printed this: This topic was automatically closed 21 days after the last reply. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. it worked. Connect and share knowledge within a single location that is structured and easy to search. [25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5 hz abbreviation in "7,5 t hz Gesamtmasse", Dereference a pointer to volatile structure in C++. By clicking “Accept all cookies”, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8, attached base packages: But avoid …. When trying to load DelayedArray using Warning messages: 1: In install.packages(.) It is usually not necessary to be at the latest point release, but problems begin accumuating as one or more installed versions begin lagging by a major release. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 $ cat counts.txt | deseq2.r 3x3 > results2.csv. Policy. This topic was automatically closed 21 days after the last reply. To add to this, I have also been using DESeq2 recently and ran into the same problem. Warning messages: Problems with loading any package - General - Posit Community Does a knockout punch always carry the risk of killing the receiver? Ultimately my colleague helped me to solve the issue by following the steps: Created environment: conda create --name myenv. [10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3 install.packages - R - Installing package with remotes::install_github ... sessionInfo() My advice is: when asked "Do you want to install from sources the package which needs compilation?" I get this error: 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' I tried to download the "locfit" package but I can't find it anywhere. 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've been reading some of the posts here and from my understanding I should be able to install from a source that does not need compilation to get access to an older version of the package but it still reports a non-zero exit status. Content type 'application/zip' length 233860 bytes (228 KB) DESeq2 • 6.8k views Platform: x86_64-w64-mingw32/x64 (64-bit) Do Christian proponents of Intelligent Design hold it to be a scientific position, and if not, do they see this lack of scientific rigor as an issue? Connect and share knowledge within a single location that is structured and easy to search. Is there a reason why these packages aren't automatically downloaded? stop (gettextf ("package %s could not be loaded", sQuote (pkg)), call. In Europe, do trains/buses get transported by ferries with the passengers inside? What is the first science fiction work to use the determination of sapience as a plot point? Share Improve this answer I have my packages (e.g.,tidyverse) stored in a separate directory to that provided by R so that I don't have to reinstall when upgrading R versions. Are all conservation of momentum scenarios simply particles bouncing on walls? rev 2023.6.6.43481. A zip file is a pre-built binary package for use on Windows, not a source package. DESeq2: Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' - General - Posit Community Posit Community library (olsrr) 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'. I tried removing the packges and re-install but i got the same error. Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I tried deleting manually and reinstalling the package ma nothing changed. rspatial/terra#408 Closed frabau1 mentioned this issue on Jun 3, 2022 Adding Packages in Docker Compose within Portainer Stack rocker-org/rocker-versioned2#476 Closed Sign up for free to join this conversation on GitHub . Policy. Policy. + ), update = TRUE, ask = FALSE) If you have a query related to it or one of the replies, start a new topic and refer back with a link. Not the answer you're looking for? Thanks for contributing an answer to Stack Overflow! 安装DESeq2时遇到的错误 - CSDN博客 Loading required package: GenomeInfoDb Powered by Discourse, best viewed with JavaScript enabled, DESeq2: Error: package or namespace load failed for ‘DESeq2’: objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:S4Vectors'. biocLite(), install.packages() (and the devtools equivalent?) Site design / logo © 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. [4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3 Why might a civilisation of robots invent organic organisms like humans or cows? Error: package 'GenomeInfoDb' could not be loaded Modeling a continuous variable which can't take values between a and b. I'm having a similar error, but different package: 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'. Error: package or namespace load failed for ' DESeq2 ' 因為使用下載其他package時也一直遇到類似問題，所以想可能主要原因不是錯誤訊息裡提到的找不到package或package無法載入這些原因，大家是否知道可以如何處理這樣的問題。 Running under: macOS Sierra 10.12.6, there is no package called ‘GenomeInfoDbData’, indicates another missing dependency to be installed, probably by. Dereference a pointer to volatile structure in C++. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Thanks for contributing an answer to Stack Overflow! I have managed to solve this issue - repeatedly installing and uninstalling all the packages involving vectors in R --vanilla mode helped to get DESeq2 functionalities back! r - Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck ... Installation failure - package 'stringi.so' is not available (for R ... Did you remove the old library files (pre R 4.x.x)? Do Christian proponents of Intelligent Design hold it to be a scientific position, and if not, do they see this lack of scientific rigor as an issue? Once the old, broken package is removed, use install.packages("factoextra") and it should work. : installation of package 'GenomeInfoDbData' had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l . Running under: Windows 10 x64 (build 18362), locale: [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: Hopefully BiocManager::valid() is then happy? 5. Error in rbind(info, getNamespaceInfo(env, "S3methods")) when ...