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