SRAdbV2 attempt

gistfile1.txt

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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  Natural language support but running in an English locale

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Warning: namespace ‘ggplot2’ is not available and has been replaced
by .GlobalEnv when processing object ‘zoom’
Warning: namespace ‘scales’ is not available and has been replaced
by .GlobalEnv when processing object ‘zoom’
[Workspace loaded from ~/.RData]

> 
> 
> source('https://bioconductor.org/biocLite.R')
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/macosx/el-capitan/contrib/3.5/BiocInstaller_1.30.0.tgz'
Content type 'application/x-gzip' length 84646 bytes (82 KB)
==================================================
downloaded 82 KB


The downloaded binary packages are in
	/var/folders/zh/z1jv_t3167xdntk02mxwc2580000gn/T//Rtmp8FAEwQ/downloaded_packages
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
> biocLite('seandavi/SRAdbV2')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing github package(s) ‘seandavi/SRAdbV2’
Error: there is no package called ‘remotes’
    package 'remotes' not installed in library path(s)
        /Library/Frameworks/R.framework/Versions/3.5/Resources/library
    install with 'biocLite("remotes")', and re-run your biocLite() command
> biocLite("remotes")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘remotes’
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/remotes_1.1.1.tgz'
Content type 'application/x-gzip' length 137381 bytes (134 KB)
==================================================
downloaded 134 KB


The downloaded binary packages are in
	/var/folders/zh/z1jv_t3167xdntk02mxwc2580000gn/T//Rtmp8FAEwQ/downloaded_packages
Old packages: 'MASS', 'survival'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/MASS_7.3-50.tgz'
Content type 'application/x-gzip' length 1163764 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/survival_2.42-3.tgz'
Content type 'application/x-gzip' length 4647766 bytes (4.4 MB)
==================================================
downloaded 4.4 MB


The downloaded binary packages are in
	/var/folders/zh/z1jv_t3167xdntk02mxwc2580000gn/T//Rtmp8FAEwQ/downloaded_packages
> biocLite('seandavi/SRAdbV2')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing github package(s) ‘seandavi/SRAdbV2’
Downloading GitHub repo seandavi/SRAdbV2@master
Installing 14 packages: assertthat, cli, crayon, curl, httr, jsonlite, mime, openssl, pillar, R6, rapiclient, rlang, tibble, utf8
* installing *source* package ‘SRAdbV2’ ...
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘lubridate’
ERROR: lazy loading failed for package ‘SRAdbV2’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/SRAdbV2’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/zh/z1jv_t3167xdntk02mxwc2580000gn/T//Rtmp8FAEwQ/remotes70a4176d9b1/seandavi-SRAdbV2-484dc73’ had non-zero exit status


> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0    remotes_1.1.1