error: package or namespace load failed for 'deseq2
New replies are no longer allowed. Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. To learn more, see our tips on writing great answers. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in guide. Making statements based on opinion; back them up with references or personal experience. 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. Why is this sentence from The Great Gatsby grammatical? Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Sign in [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Start R to confirm they are gone. Content type 'application/zip' length 386703 bytes (377 KB) From the console install.packages ("rlang") should fix this. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. 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. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Try again and choose No. 2. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 That plugin is has not been updated to work with later releases of QIIME 2. :), BiocManager::install("locift") Have you tried install.packages("locfit") ? I've copied the output below in case it helps with troubleshooting. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 enter citation("DESeq2")): To install this package, start R (version Citation (from within R, Whats the grammar of "For those whose stories they are"? [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: Press CTRL-C to abort. I even tried BiocManager::install("XML") but all failed as shown below. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR a, There are binary versions available but the source versions are later: Not the answer you're looking for? I have tried your suggestion and also updating the packages that command indicates. Rload failed - biocLite(), install.packages() (and the devtools equivalent?) However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Policy. @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. Sounds like you might have an issue with which R Rstudio is running. Running under: macOS Sierra 10.12.6. 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'. Just to add on -- do you require an old version of Bioconductor for your current project? 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. This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. If you have a query related to it or one of the replies, start a new topic and refer back with a link. Running under: Windows 10 x64 (build 18362), locale: [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. call: dots_list() sessionInfo() Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Use of this site constitutes acceptance of our User Agreement and Privacy 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"). This can take several minutes. Platform: x86_64-apple-darwin15.6.0 (64-bit) Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. I tried again and again was met with missing packages BUT!!! 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. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Update all/some/none? [R] Error: package or namespace load failed for 'ggplot2' in 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 Installing package(s) 'XML' package xfun successfully unpacked and MD5 sums checked March 1, 2023, 8:52pm By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. (Factorization). Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Bad: conda install -c bioconda bioconductor-deseq2. - the incident has nothing to do with me; can I use this this way? 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. Error: package GenomeInfoDb could not be loaded. When an R package depends on a newer package version, the required package is downloaded but not loaded. Replacing broken pins/legs on a DIP IC package. In install.packages() : library (olsrr) - Error - General - RStudio Community The best answers are voted up and rise to the top, Not the answer you're looking for? Policy. This topic was automatically closed 21 days after the last reply. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 there is no package called data.table 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. 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. to your account. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Hello, [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Any suggestions would be greatly appreciated. So, supposedly the issue is with Hmisc. Making statements based on opinion; back them up with references or personal experience. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Surly Straggler vs. other types of steel frames. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): If not fixed, Try removing remove.packages (rlang) then. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 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. package in your R session. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Should I update the Bioconductor to latest version instead? [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) 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 If it fails, required operating system facilities are missing. Surly Straggler vs. other types of steel frames. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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 I can download DESeq2 using, User Agreement and Privacy March 1, 2023, 7:31pm LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. install.packages ("zip") To learn more, see our tips on writing great answers. Just realize that I need to write the script "library("DESeq2")" before I proceed. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 to allow custom library locations. now when I tried installing the missing packages they did install. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. ERROR: lazy loading failed for package Hmisc Connect and share knowledge within a single location that is structured and easy to search. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) binary source needs_compilation Learn more about Stack Overflow the company, and our products. Thank you @hharder. Thanks for your suggestion. Is there anyone the same as mine error while loading library(DESeq2)? I'm having a similar error, but different package: library("DESeq2") Thanks for contributing an answer to Bioinformatics Stack Exchange! Warning: cannot remove prior installation of package xfun 9. Use MathJax to format equations. Just updated my previous R to 4.01 and now I cant load DESeq2. privacy statement. Are there tables of wastage rates for different fruit and veg? 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. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Warning message: Already on GitHub? [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: Installing package(s) 'htmlTable', 'xfun' March 1, 2023, 3:25pm Policy. I installed the package successfully with conda, but Rstudio is apparently does not know about it. I would recommend installing an older version of QIIME 2 for this plugin to work. there is no package called locfit. Is a PhD visitor considered as a visiting scholar? [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Then I reinstalled R then Rstudio then RTools. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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 [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: You signed in with another tab or window. It is working now. When you load the package, you can observe this error. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 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. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Why do academics stay as adjuncts for years rather than move around? We've tried this - and can replicate this issue on a completely new install with no existing package installs. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Join us at CRISPR workshops in Koper, Slovenia in 2023. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? I tried to install Python 3.6 and got 1000s of lines of conflicts, and python version still returns 3.8. when I switch back to my Qiime environment to install Aldex2, I get an error. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Any other suggestion? ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Error in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]) : there is no package called 'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: 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). If you preorder a special airline meal (e.g. What is a word for the arcane equivalent of a monastery? it would be good to hear any speculation you have of how this might have happened). How can I fix error with loading package in R ? | ResearchGate im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Whats the grammar of "For those whose stories they are"? Content type 'application/zip' length 4255589 bytes (4.1 MB) Well occasionally send you account related emails. 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. Running. 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. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 As such there are two solutions that may be more or less attainable given your own IT system. Solution To resolve this error, install the required package as a cluster-installed library. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Feedback Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Vanderbilt Baseball Roster,
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New replies are no longer allowed. Error: package or namespace load failed for ggplot2 and for data.table, Error: package or namespace load failed for car, Error: package or namespace load failed for rJava, Error in load Namespace, object 'vI' not found with package AnnotationDbi. To learn more, see our tips on writing great answers. downloaded 4.1 MB, package XML successfully unpacked and MD5 sums checked, The downloaded binary packages are in guide. Making statements based on opinion; back them up with references or personal experience. 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. Why is this sentence from The Great Gatsby grammatical? Referenced from: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/cluster/libs/cluster.so Sign in [7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1 Start R to confirm they are gone. Content type 'application/zip' length 386703 bytes (377 KB) From the console install.packages ("rlang") should fix this. The text was updated successfully, but these errors were encountered: Can you clarify how you updated your R to 4.0.1? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. 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. How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? As others have mentioned, this is likely an issue with having multiple versions of R or RStudio installed. 0 packages out-of-date; 2 packages too new, BiocManager::install(c( installing the source package GenomeInfoDbData, dyld: lazy symbol binding failed: Symbol not found: _utimensat trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. Try again and choose No. 2. [10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0 [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 That plugin is has not been updated to work with later releases of QIIME 2. :), BiocManager::install("locift") Have you tried install.packages("locfit") ? I've copied the output below in case it helps with troubleshooting. [29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5 enter citation("DESeq2")): To install this package, start R (version Citation (from within R, Whats the grammar of "For those whose stories they are"? [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: Press CTRL-C to abort. I even tried BiocManager::install("XML") but all failed as shown below. ): RRlib ( R ) libiconv.so LD_LIBRARY_PATH R Sys.getenv("LD_LIBRARY_PATH") R RR a, There are binary versions available but the source versions are later: Not the answer you're looking for? I have tried your suggestion and also updating the packages that command indicates. Rload failed - biocLite(), install.packages() (and the devtools equivalent?) However, I am increasingly thinking it's something to do with how my IT has set permissions that are causing things to quietly fail. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib It could also be caused by a bad antivirus program that locks the dll which prevents it from being updated. Policy. @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. Sounds like you might have an issue with which R Rstudio is running. Running under: macOS Sierra 10.12.6. 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'. Just to add on -- do you require an old version of Bioconductor for your current project? 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. This sort of problems almost always comes from a bug in R on Windows: If you reinstall a package that includes compiled code, and if that package is already loaded in R, the DLL will not get updated. If you have a query related to it or one of the replies, start a new topic and refer back with a link. Running under: Windows 10 x64 (build 18362), locale: [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): 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 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. call: dots_list() sessionInfo() Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, Use of this site constitutes acceptance of our User Agreement and Privacy 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"). This can take several minutes. Platform: x86_64-apple-darwin15.6.0 (64-bit) Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. I tried again and again was met with missing packages BUT!!! 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. [22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2 Update all/some/none? [R] Error: package or namespace load failed for 'ggplot2' in 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 Installing package(s) 'XML' package xfun successfully unpacked and MD5 sums checked March 1, 2023, 8:52pm By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. (Factorization). Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) Bad: conda install -c bioconda bioconductor-deseq2. - the incident has nothing to do with me; can I use this this way? 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. Error: package GenomeInfoDb could not be loaded. When an R package depends on a newer package version, the required package is downloaded but not loaded. Replacing broken pins/legs on a DIP IC package. In install.packages() : library (olsrr) - Error - General - RStudio Community The best answers are voted up and rise to the top, Not the answer you're looking for? Policy. This topic was automatically closed 21 days after the last reply. [61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5 there is no package called data.table 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. 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. to your account. downloaded 377 KB, trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/xfun_0.16.zip' What can a lawyer do if the client wants him to be acquitted of everything despite serious evidence? 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. check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Hello, [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 Any suggestions would be greatly appreciated. So, supposedly the issue is with Hmisc. Making statements based on opinion; back them up with references or personal experience. Hmm, but it says package XML successfully unpacked and MD5 sums checked it looks mostly like these have been successful? Surly Straggler vs. other types of steel frames. You have 3 different warnings (digest, yaml, and rlang) that each indicate that a package DLL file is corrupted. Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): If not fixed, Try removing remove.packages (rlang) then. [1] xfun0.17 splines3.6.1 lattice0.20-41 colorspace1.4-1 vctrs0.3.4 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. package in your R session. While a notebook is attached to a cluster, the R namespace cannot be refreshed. Should I update the Bioconductor to latest version instead? [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 Error: package or namespace load failed for DESeq2, R version 3.3.2 (2016-10-31) 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 If it fails, required operating system facilities are missing. Surly Straggler vs. other types of steel frames. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? 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 I can download DESeq2 using, User Agreement and Privacy March 1, 2023, 7:31pm LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib, locale: * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. install.packages ("zip") To learn more, see our tips on writing great answers. Just realize that I need to write the script "library("DESeq2")" before I proceed. [26] xtable1.8-4 scales1.1.1 backports1.1.9 checkmate2.0.0 BiocManager1.30.10 to allow custom library locations. now when I tried installing the missing packages they did install. It fails with the VORO++ library, It seems it is related to the -Xcompiler flag. ERROR: lazy loading failed for package Hmisc Connect and share knowledge within a single location that is structured and easy to search. Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) binary source needs_compilation Learn more about Stack Overflow the company, and our products. Thank you @hharder. Thanks for your suggestion. Is there anyone the same as mine error while loading library(DESeq2)? I'm having a similar error, but different package: library("DESeq2") Thanks for contributing an answer to Bioinformatics Stack Exchange! Warning: cannot remove prior installation of package xfun 9. Use MathJax to format equations. Just updated my previous R to 4.01 and now I cant load DESeq2. privacy statement. Are there tables of wastage rates for different fruit and veg? 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. Surly Straggler vs. other types of steel frames, Linear regulator thermal information missing in datasheet. [9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0 Warning message: Already on GitHub? [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: Installing package(s) 'htmlTable', 'xfun' March 1, 2023, 3:25pm Policy. I installed the package successfully with conda, but Rstudio is apparently does not know about it. I would recommend installing an older version of QIIME 2 for this plugin to work. there is no package called locfit. Is a PhD visitor considered as a visiting scholar? [11] foreign0.8-71 glue1.4.2 RColorBrewer1.1-2 jpeg0.1-8.1 GenomeInfoDbData1.2.2 It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. Then I reinstalled R then Rstudio then RTools. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/XML_3.99-0.3.zip' 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 [4] LCNUMERIC=C LCTIME=English_Malaysia.1252, attached base packages: You signed in with another tab or window. It is working now. When you load the package, you can observe this error. I ran this code: Collecting package metadata (current_repodata.json): doneSolving environment: failed with initial frozen solve. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib Expected in: /usr/lib/libSystem.B.dylib, /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 9542 Done echo 'tools:::.install_packages()' [25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1 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. survival 3.1-12 3.2-3 TRUE, The downloaded binary packages are in Why do academics stay as adjuncts for years rather than move around? We've tried this - and can replicate this issue on a completely new install with no existing package installs. Following successful installation of backports BiocManager::install ("DESeq2") will succeed under Join us at CRISPR workshops in Koper, Slovenia in 2023. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? I tried to install Python 3.6 and got 1000s of lines of conflicts, and python version still returns 3.8. when I switch back to my Qiime environment to install Aldex2, I get an error. When I try installing GenomeInfoDbData and GenomeInfoDb using conda, it says that the packages were already installed. Any other suggestion? ), update = TRUE, ask = FALSE), more details: BiocManager::valid()$toonew, BiocManager::valid()$outof_date, Warning message: Error in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]) : there is no package called 'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: 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). If you preorder a special airline meal (e.g. What is a word for the arcane equivalent of a monastery? it would be good to hear any speculation you have of how this might have happened). How can I fix error with loading package in R ? | ResearchGate im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. Whats the grammar of "For those whose stories they are"? Content type 'application/zip' length 4255589 bytes (4.1 MB) Well occasionally send you account related emails. 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. Running. 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. [31] Hmisc4.4-1 XVector0.26.0 gridExtra2.3 ggplot23.3.2 png0.1-7 As such there are two solutions that may be more or less attainable given your own IT system. Solution To resolve this error, install the required package as a cluster-installed library. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Feedback Error: package or namespace load failed for GenomeInfoDb in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy.
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