achubaty on development
GHA: add build/deploy workflow … (compare)
achubaty on development
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achubaty on development
GHA tweak (compare)
achubaty on development
update GHA coverage workflow (compare)
eliotmcintire on archivedPkg
keep known Src installs separate protect most places when intern… bugfix -- Require -- rbindlist … and 1 more (compare)
eliotmcintire on development
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eliotmcintire on archivedPkg
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achubaty on development
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eliotmcintire on archivedPkg
skip basePkgs for 'checking for… (compare)
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
it then proceeds to reinstall and reload these, which breaks and sometimes crashes the R session
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:
Require
was not installed in the new libPathpackageVersion.txt
; this changes the double folder issue @achubaty saw... 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
@achubaty I ran the Require::Require
line 2x and it worked after the 2nd time.
* DONE (usefulFuns)
All packages appear to have installed correctly
Because 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 exist
Require@development
now...
install.packages
since in most cases the latest package is compatible with a previous version.
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.