Installation Problem in RStudio

[RetnoNovvitasari]

Hi, I tried to instal metaboshiny, but find an error like this. Thanks before for your help.

Downloading GitHub repo UMCUGenetics/MetaboShiny@master These packages have more recent versions available. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: impute (1.58.0 -> 559cacdb6...) [Bioc] 5: pcaMethods (1.76.0 -> 0ae2f05a1...) [Bioc] 6: siggenes (1.58.0 -> 3cb3d040a...) [Bioc] 7: globaltest (5.38.0 -> 14fb0aa8b...) [Bioc] 8: GlobalAncova (4.2.0 -> 40f7cd29a...) [Bioc] 9: Rgraphviz (2.28.0 -> 947bd0995...) [Bioc] 10: KEGGgraph (1.44.0 -> 83fad7009...) [Bioc] 11: preproces... (1.46.0 -> 84da519db...) [Bioc] 12: genefilter (1.66.0 -> cba90ff1b...) [Bioc] 13: SSPA (2.24.0 -> 52a549f3a...) [Bioc] 14: sva (3.32.1 -> 814ff269d...) [Bioc] 15: ChemmineR (3.36.0 -> 1cbe310fa...) [Bioc] 16: KEGGREST (1.24.1 -> 56d6223ac...) [Bioc] 17: fgsea (1.10.1 -> 22c00b661...) [Bioc] 18: Rdisop (1.44.0 -> fdd73a98e...) [Bioc] 19: Biostrings (2.52.0 -> b8982e78c...) [Bioc] 20: GOSemSim (2.10.0 -> ed0884a01...) [Bioc] 21: fmcsR (1.26.0 -> 6176f38ea...) [Bioc] 22: hexbin (1.27.3 -> 1.28.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 impute (1.58.0 -> 559cacdb6...) [Bioc] pcaMethods (1.76.0 -> 0ae2f05a1...) [Bioc] siggenes (1.58.0 -> 3cb3d040a...) [Bioc] globaltest (5.38.0 -> 14fb0aa8b...) [Bioc] GlobalAncova (4.2.0 -> 40f7cd29a...) [Bioc] Rgraphviz (2.28.0 -> 947bd0995...) [Bioc] KEGGgraph (1.44.0 -> 83fad7009...) [Bioc] preproces... (1.46.0 -> 84da519db...) [Bioc] genefilter (1.66.0 -> cba90ff1b...) [Bioc] SSPA (2.24.0 -> 52a549f3a...) [Bioc] sva (3.32.1 -> 814ff269d...) [Bioc] ChemmineR (3.36.0 -> 1cbe310fa...) [Bioc] KEGGREST (1.24.1 -> 56d6223ac...) [Bioc] fgsea (1.10.1 -> 22c00b661...) [Bioc] Rdisop (1.44.0 -> fdd73a98e...) [Bioc] Biostrings (2.52.0 -> b8982e78c...) [Bioc] GOSemSim (2.10.0 -> ed0884a01...) [Bioc] fmcsR (1.26.0 -> 6176f38ea...) [Bioc] BioMedR (NA -> 1.2.1 ) [CRAN] hexbin (1.27.3 -> 1.28.0 ) [CRAN] fields (NA -> 10.0 ) [CRAN] Skipping 1 packages not available: org.Hs.eg.db Installing 3 packages: BioMedR, hexbin, fields

There are binary versions available but the source versions are later: binary source needs_compilation hexbin 1.27.3 1.28.0 TRUE fields 9.9 10.0 TRUE

Do you want to install from sources the packages which need compilation? (Yes/no/cancel) Yes installing the source packages ‘BioMedR’, ‘hexbin’, ‘fields’

essai de l'URL 'https://cran.rstudio.com/src/contrib/BioMedR_1.2.1.tar.gz' Content type 'application/x-gzip' length 2796519 bytes (2.7 MB)

downloaded 2.7 MB

essai de l'URL 'https://cran.rstudio.com/src/contrib/hexbin_1.28.0.tar.gz' Content type 'application/x-gzip' length 648771 bytes (633 KB)

downloaded 633 KB

essai de l'URL 'https://cran.rstudio.com/src/contrib/fields_10.0.tar.gz' Content type 'application/x-gzip' length 3268858 bytes (3.1 MB)

downloaded 3.1 MB

• installing source package ‘BioMedR’ ... package ‘BioMedR’ correctement décompressé et sommes MD5 vérifiées using staged installation R data * moving datasets to lazyload DB inst ** byte-compile and prepare package for lazy loading Erreur : .onLoad failed in loadNamespace() for 'rJava', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: impossible de charger l'objet partagé '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so Reason: image not found Exécution arrêtée ERROR: lazy loading failed for package ‘BioMedR’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BioMedR’ Erreur : Failed to install 'MetaboShiny' from GitHub: (converti depuis l'avis) installation of package ‘BioMedR’ had non-zero exit status

[joannawolthuis]

Hi there, thank you for your interest! Installing rJava is notoriously annoying and the solution seems to differ per computer setup :( Could you try: install.packages("rJava") library("rJava") and see if you can solve the problem with stackOverflow? Or are you on a system that supports Docker? (because that makes things a lot easier, it looks like you are on Mac :) )

[BartHee]

I'd also suggest downloading and installing Java JDK 1.2 or higher (see rJava github repository), and update Java (8 or higher). Restart RStudio in Administrator mode, and try reinstalling rJava through install.packages("rJava", dependencies = TRUE) library(rJava)