So your Git repository is getting ungainly large. What's causing it? Are the problem files still being updated, or are they the deleted ghosts of old binaries?
git cat-file --batch-check --batch-all-objects --unordered \
| sort --numeric-sort --key=3 \
| tail -n10 \
| xargs -L1 sh -c \
'pth=`git describe --always $0`; \
printf "%s %s %s %s\n" $0 $1 $2 $pth'
Have: several treatments measured across time, many parameters recorded
dat <- expand.grid(
time = 1:3,
trt = letters[1:2],
param = LETTERS[1:3])
dat$value <- c(
rep(1.0, 6), # A: constant, should drop
rep(c(1.0, 1.5, 2.0), 2), # B: trts identical within days, should drop
| # Do R packages on GitHub commit their Rd files? | |
| # Searched all of GitHub for "RoxygenNote", ordered by recently indexed, | |
| # clicked through on all DESCRIPTION files in first five pages of results, | |
| # if a fork clicked through to source, if a source then | |
| # checked whether man/ directory contains Rd files | |
| pik-piam/madrat, n (Rd files are gitignored) | |
| hemberg-lab/scfind, y | |
| daewoooo/primatR, y | |
| dleutnant/muasdown, y |
| # selflibrary/showsearch.R: | |
| showsearch_lib <- function(){ | |
| print(search()) | |
| library(selflibrary) | |
| print(search()) | |
| } | |
| $ R -q -e 'selflibrary::showsearch_lib()' chrisb@morus:~/Desktop/selflibrary | |
| > selflibrary::showsearch_lib() | |
| [1] ".GlobalEnv" "package:stats" "package:graphics" |
| root@7c782f3c2892:~# cat Makefile | |
| all: | |
| Rscript -e 'install.packages("getPass", type = "source")' | |
| root@7c782f3c2892:~# make | |
| Rscript -e 'install.packages("getPass", type = "source")' | |
| Installing package into '/usr/local/lib/R/site-library' | |
| (as 'lib' is unspecified) | |
| trying URL 'https://cloud.r-project.org/src/contrib/getPass_0.2-2.tar.gz' | |
| Content type 'application/x-gzip' length 252439 bytes (246 KB) |
Great question. Let's find out, with two big caveats.
This approach will find components formally required by one or more of the PEcAn R packages. It will not tell us what dependencies are missing from the package descriptions, nor about any of PEcAn's non-R dependencies -- notably, the list it produces will not contain Postgres or any of the components of Bety. But we will get a list of the system libraries needed by each R package (e.g. RCurl depends on your OS's libcurl), at least to the extent that the packages declare them.
Ironically, it only works on a system that already has all of PEcAn installed. If your machine is already in dependency hell, this probably won't help because R won't know how to find and recursively check the dependencies it doesn't yet have. But with some refinements, this approach could probably autogenerate a list of dependencies so that we can, say, mention new ones in the changelog.
For th
| # OS X 10.13.4, Postgres 10.4 | |
| 0> curl -o bety.sql.gz http://pecan.ncsa.illinois.edu/dump/betydump.psql.gz | |
| % Total % Received % Xferd Average Speed Time Time Time Current | |
| Dload Upload Total Spent Left Speed | |
| 100 167M 100 167M 0 0 7790k 0 0:00:21 0:00:21 --:--:-- 8289k | |
| library(tidyverse) | |
| # local df works as expected with or without .data | |
| mtcars %>% select(mpg) %>% filter(mpg > 33) | |
| # mpg | |
| # 1 33.9 | |
| mtcars %>% select(.data$mpg) %>% filter(.data$mpg > 33) | |
| # mpg | |
| # 1 33.9 |
| library(dplyr) | |
| a = data.frame(id=1:3, x=1:3) | |
| ## local join: works as expected | |
| inner_join(a, a, by="id", suffix=c(".1", ".2")) | |
| # id x.1 x.2 | |
| # 1 1 1 1 | |
| # 2 2 2 2 |
| library(dplyr) | |
| # invent some data | |
| budget_min = 2e4 | |
| budget_max = 2.5e4 | |
| costs = round(rnorm(n=20, mean=1e4, sd=3e3)) | |
| names(costs) = LETTERS[1:20] | |