it's putting things into packages_1, not packages as i would expect. and packages_2 is empty. i expect that the packages get installed to the location i specify (packages).
as soon as i try to run a sim, it tries reinstalling different versions of packages even though they should be correct, and it detaches and breaks the search path, breaking all subsequent package calls
Currently, several packages are loaded that conflict with installs. Detaching:
Rcpp, crayon, magrittr, sp, fpCompare, ps, assertthat, digest, gridBase, backports, pkgconfig, withr, R.methodsS3, gtable, DBI, fs, generics, colorspace, prettyunits, R6, rstudioapi, whisker, fastdigest, bit, fansi, RcppParallel, RApiSerialize, RColorBrewer, rprojroot, R.oo, rgdal, munsell, rgeos, ellipsis, bit64, memoise, raster, R.utils, purrr, lubridate, igraph, lifecycle, stringfish, processx, callr, qs, cli, vctrs, blob, desc, sessioninfo, tidyselect, scales, pillar, tibble, RSQLite, pkgbuild, pkgload, dplyr, reproducible, testthat, googledrive, usethis, ggplot2, quickPlot, devtools, SpaDES.core
devtools is being loaded. That has A LOT of dependencies. So, don't have devtools loaded. I am running stuff now. It will take a bit to catch up to you...
@achubaty @tati-micheletti I pushed updates to Require ... running tests. Issues that I found:
Requirewas not installed in the new libPath- In my case, one package ("XML") couldn't be installed due to version of R conflict with package version. There is now a better error and suggestion about what to do.
- Suppressed some irrelevant warnings due to "locale"
- Removed base packages during installing from
packageVersion.txt; this changes the double folder issue @achubaty saw - The file ("standAloneSim.R") is not set up to be "reuseable"...:
... Do not load devtools -- it has lots of package dependencies and the versions will conflict with those versions in packageVersion.txt
... Do install Require into the new library (can do the original one too)
Require)
raster is still being re-installed to a different version than the one loaded then this new version is being forced to be loaded, which cause the same breakage i was seeing before
- By installing development branch, with devtools, you are loading devtools if you run the script as is. If you do manual intervention, then it might be fine.
- Require 0.0.9 is on CRAN as of now (I have to quickly send an update for 0.0.10 due to error on one of the flavours), so don't need dev version at all.
@achubaty I ran the Require::Require line 2x and it worked after the 2nd time.
* DONE (usefulFuns)
All packages appear to have installed correctlyBecause of transient failures with network... there used to be a message saying something to the effect of "run it again"... that seems gone now.
options(repos = c(CRAN = "https://cloud.r-project.org"),
Require.RPackageCache = "~/binaryRPackages") ## change this to your tastes
if (!requireNamespace("Require", quietly = TRUE))
install.packages("Require") # use version 0.0.9
# 0. Install working packages
library("Require")
pkgPath <- "./packages"
setLibPaths(pkgPath)
Require::Require(packageVersionFile = "./packageVersions.txt", standAlone = TRUE) # failed on some 1st tiem
Require::Require(packageVersionFile = "./packageVersions.txt", standAlone = TRUE)Require::Require(packageVersionFile = "./packageVersions.txt", standAlone = TRUE)
Error in checkPath(path, create = FALSE) :
Specified path C:/Users/HughesJo/Documents/gitprojects/NWT/packages doesn't existRequire@development now...
install.packages since in most cases the latest package is compatible with a previous version.
1 reply
covr but here are the individual coverage reports:> cov1 <- covr::package_coverage(type = "tests")
> cov2 <- covr::package_coverage(type = "examples")
> cov3 <- covr::package_coverage(type = "vignettes")
> cov1
Require Coverage: 0.20%
R/extract.R: 0.00%
R/helpers.R: 0.00%
R/pkgDep.R: 0.00%
R/pkgDepAlt.R: 0.00%
R/pkgSnapshot.R: 0.00%
R/Require-helpers.R: 0.00%
R/Require.R: 0.00%
R/RequireOptions.R: 0.00%
R/setLibPaths.R: 0.00%
R/CRAN.R: 5.26%
R/zzz.R: 5.56%
> cov2
Require Coverage: 22.62%
R/Require.R: 0.00%
R/RequireOptions.R: 0.00%
R/pkgDepAlt.R: 4.61%
R/zzz.R: 5.56%
R/Require-helpers.R: 8.01%
R/setLibPaths.R: 34.48%
R/pkgSnapshot.R: 37.50%
R/helpers.R: 59.70%
R/pkgDep.R: 61.45%
R/CRAN.R: 66.67%
R/extract.R: 89.19%
> cov3
Require Coverage: 0.09%
R/extract.R: 0.00%
R/helpers.R: 0.00%
R/pkgDep.R: 0.00%
R/pkgDepAlt.R: 0.00%
R/pkgSnapshot.R: 0.00%
R/Require-helpers.R: 0.00%
R/Require.R: 0.00%
R/RequireOptions.R: 0.00%
R/setLibPaths.R: 0.00%
R/CRAN.R: 4.17%
R/zzz.R: 5.56%Unfortunately, we see:
New things in home:
._RPackageCache
._RPackageCache/4.1
._RPackageCache/4.1/data.table_1.13.6_R_x86_64-pc-linux-gnu.tar.gz
._RPackageCache/4.1/data.table_1.13.6.tar.gz
._RPackageCache/4.1/remotes_2.2.0_R_x86_64-pc-linux-gnu.tar.gz
._RPackageCache/4.1/remotes_2.2.0.tar.gz
._RPackageCache/4.1/Require_0.0.10_R_x86_64-pc-linux-gnu.tar.gz
._RPackageCache/4.1/Require_0.0.10.tar.gzWell, clearly you caused it in :
/data/rsync/PKGS/Require$ grep -r _RPackageCache .
./R/RequireOptions.R: Require.RPackageCache = NULL,"~/._RPackageCache", # nolint
./tests/testit/test-packagesLong.R:
Require.RPackageCache = "~/._RPackageCache",
./tests/testit/test-pkgSnapshot.R: "Require.RPackageCache" =
"~/._RPackageCache/",
./tests/testit/test-1packages.R:
Require.RPackageCache = "~/._RPackageCache",And storing files there is not permitted.
Please re-read the CRAN policies that also include a suggestion:
For R version 4.0 or later (hence a version dependency is required or
only conditional use is possible), packages may store user-specific
data, configuration and cache files in their respective user
directories obtained from tools::R_user_dir(), provided that by
default sizes are kept as small as possible and the contents are
actively managed (including removing outdated material).Please fix and resubmit.