I have a quick question, I am trying to install MicrobeR, but it is not working. I followed the instruction in the tutorials, but I get the error below.
Sorry for the dumb question, but I have never installed a package like this. I tried install.packages (biocLite(āDECIPHERā)) and just biocLite(āDECIPHERā) and it didn't work.
This should install DECIPHER. MicrobeR is a swiss-army knife of sorts to streamline certain tasks or to help visualize and as such it has quite a long list of dependencies. Running the code below might help fill in any missing dependencies. Note, if you are using an unix operating system it will also download some extra sequencing data.
I was able to instamm MicrobeR but the tutorial is based on a preinstalled data in R so it is a bit confusing to figure out how to import our own files (especially QIIME2 format) and what file to import. Can you explain that?
Iāve been using your tutorial qiime2R and it worked really great with my data, thank you so muchā¦
Iām using Version 1.2.1335 of RStudio, on MacOS Mojave Version 10.14.5 (18F132).
But Iām having trouble with installing MicrobeR. Iāve installed required philr and Decipher, that was fine, but I still get this error when I get to installation of MicrobeR (it starts fine then I get the error):
"* installing source package āMicrobeRā ā¦
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for ārjagsā, details:
call: dyn.load(file, DLLpath = DLLpath, ā¦)
error: unable to load shared object ā/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rjags/libs/rjags.soā:
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rjags/libs/rjags.so, 10): Library not loaded: /usr/local/lib/libjags.4.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rjags/libs/rjags.so
Reason: image not found
Execution halted
ERROR: lazy loading failed for package āMicrobeRā
removing ā/Library/Frameworks/R.framework/Versions/3.6/Resources/library/MicrobeRā
Error in i.p(ā¦) :
(converted from warning) installation of package ā/var/folders/pn/zcr4hs9x7c761blcsx_z0jfr0000gn/T//Rtmp9kr9yR/file93aa1f80bc50/MicrobeR_0.3.2.tar.gzā had non-zero exit status"
I suspect that this error is connected to my being unable to install tibble package, which gives me this error:
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ātibbleā
removing ā/Library/Frameworks/R.framework/Versions/3.6/Resources/library/tibbleā
Error in i.p(ā¦) :
(converted from warning) installation of package ātibbleā had non-zero exit status
But Iām not sureā¦ I had it installed, then I removed it, it gives the same error over and over again. As you can see, Iām not R savvy, but I can follow instructions.
I think it might be related to missing some part of xcode. You can download the full version from the app store, or if space is an issue, I think you can download just the command line tools via the bash terminal with xcode-select --install.
I dowloaded the Xcode and run the xcode-select --install command and installed command line tools in Terminal.
Still have the same issue:
āError in i.p(ā¦) :
(converted from warning) installation of package ā/var/folders/pn/zcr4hs9x7c761blcsx_z0jfr0000gn/T//Rtmp01CNOr/file9d9b396d3d7e/MicrobeR_0.3.2.tar.gzā had non-zero exit statusā
Thanks for the help.
Btw, I tried numerous other things, like just now I dowloaded zip file and tried to installed it locally but it gave me the same error.
Also, during install it gives me this: Skipping 4 packages not available: Biostrings, DECIPHER, philr, phyloseq.
I dowloaded all the mentioned packeges multiple times and called them with library, so I donāt get itā¦
