Hello all,

I have been having issues installing packages that I really need to use. Basically, I cannot download either Phyloseq or dada2 and I believe it's because I don't have GenomeInfoDbData. But at the same time, I cannot install GenomeInfoDbData because I can't seem to update the dependencies ("fansi" in my case is causing the problems). Which leads me to think I've incorrectly installed Rtools, but I followed the instructions and if i fun devtools::find_rtools(), the output is always TRUE. However, when I follow the installation guide and try to install jslonlite by source, I get an error.

I apologise if this isn't really a BioConductor problem, but I've tried very hard to solve my issue, and still can't figure it out. I really need access to the packages and I'm not sure what else to do. Any help would be very much appreciated.

install.packages("jsonlite", type = "source")
install.packages("jsonlite", type = "source")
Installing package into ‘C:/Users/ymt89/OneDrive/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_1.7.2.tar.gz'
Content type 'application/x-gzip' length 421716 bytes (411 KB)
downloaded 411 KB

& was unexpected at this time.

The downloaded source packages are in
        ‘C:\Users\ymt89\AppData\Local\Temp\RtmpWGM5Eg\downloaded_packages’
Warning message:
In install.packages("jsonlite", type = "source") :
  installation of package ‘jsonlite’ had non-zero exit status
>

BiocManager::install("GenomeInfoDbData")
Bioconductor version 3.12 (BiocManager 1.30.16), R 4.0.0 (2020-04-24)
Installing package(s) 'BiocVersion', 'GenomeInfoDbData'
trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/BiocVersion_3.12.0.zip'
Content type 'application/zip' length 8889 bytes
downloaded 8889 bytes

package ‘BiocVersion’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\ymt89\AppData\Local\Temp\RtmpWGM5Eg\downloaded_packages
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/GenomeInfoDbData_1.2.4.tar.gz'
Content type 'application/x-gzip' length 10673545 bytes (10.2 MB)
downloaded 10.2 MB

& was unexpected at this time.

The downloaded source packages are in
        ‘C:\Users\ymt89\AppData\Local\Temp\RtmpWGM5Eg\downloaded_packages’
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.0.0/library
  packages:
    boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, spatial, survival
Old packages: 'fansi'
Update all/some/none? [a/s/n]: a

  There is a binary version available but the source version is later:
      binary source needs_compilation
fansi  0.5.0  1.0.2              TRUE

installing the source package ‘fansi’

trying URL 'https://cloud.r-project.org/src/contrib/fansi_1.0.2.tar.gz'
Content type 'application/x-gzip' length 480902 bytes (469 KB)
downloaded 469 KB

& was unexpected at this time.

The downloaded source packages are in
        ‘C:\Users\ymt89\AppData\Local\Temp\RtmpWGM5Eg\downloaded_packages’
Warning messages:
1: In .inet_warning(msg) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘fansi’ had non-zero exit status

Thank you.

I'm worried by the repeated line with & was unexpected at this time.

When you're installing a source package you'd expect the line after the "downloaded XX KB" to start with "* installing \*source\* package .."

I've no idea where the message you're seeing is coming from, but it looks wrong to me and is probably the root of your issues.