renv::activate() and renv::status() fail to recognize installed packages when library is on dual protocol drive #2058
Comments
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Thanks for the bug report. It is interesting that Some more diagnostics information that might be useful: Can you confirm that your installed packages are being loaded from the find.package("rlang")
install.packages("rlang")
library(rlang)
find.package("rlang")
getNamespaceInfo("rlang", "path")> find.package("rlang")
Error in find.package("rlang") : there is no package called ‘rlang’
> install.packages("rlang")
The following package(s) will be installed:
- rlang [1.1.4]
These packages will be installed into "~/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu".
Do you want to proceed? [Y/n]: y
# Installing packages --------------------------------------------------------
- Installing rlang ... OK [linked from cache]
Successfully installed 1 package in 29 milliseconds.
> library(rlang)
> find.package("rlang")
[1] "/home/kevin/.cache/R/renv/cache/v5/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/rlang/1.1.4/3eec01f8b1dee337674b2e34ab1f9bc1/rlang"
> getNamespaceInfo("rlang", "path")
[1] "/home/kevin/.cache/R/renv/cache/v5/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/rlang/1.1.4/3eec01f8b1dee337674b2e34ab1f9bc1/rlang"Can we also check if renv::install("dplyr", prompt = FALSE)
str(renv:::renv_package_dependencies("dplyr"))I see: > renv::install("dplyr", prompt = FALSE)
The following package(s) will be installed:
- dplyr [1.1.4]
These packages will be installed into "~/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu".
# Installing packages --------------------------------------------------------
- Installing dplyr ... OK [linked from cache]
Successfully installed 1 package in 25 milliseconds.
> str(renv:::renv_package_dependencies("dplyr"))
List of 21
$ tidyselect: chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/tidyselect"
$ R6 : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/R6"
$ magrittr : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/magrittr"
$ generics : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/generics"
$ cli : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/cli"
$ graphics : chr "/home/kevin/.cache/R/renv/sandbox/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/db5e602d/graphics"
$ withr : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/withr"
$ pillar : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/pillar"
$ glue : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/glue"
$ utils : chr "/home/kevin/.cache/R/renv/sandbox/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/db5e602d/utils"
$ dplyr : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/dplyr"
$ tibble : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/tibble"
$ grDevices : chr "/home/kevin/.cache/R/renv/sandbox/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/db5e602d/grDevices"
$ stats : chr "/home/kevin/.cache/R/renv/sandbox/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/db5e602d/stats"
$ utf8 : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/utf8"
$ fansi : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/fansi"
$ vctrs : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/vctrs"
$ methods : chr "/home/kevin/.cache/R/renv/sandbox/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/db5e602d/methods"
$ lifecycle : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/lifecycle"
$ pkgconfig : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/pkgconfig"
$ rlang : chr "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/rlang"Finally, let's also try running trace(
renv:::renv_snapshot_packages,
tracer = quote({ print(utils::ls.str()) }),
exit = quote({ utils::str(paths) })
)
trace(
renv:::renv_snapshot_dependencies,
tracer = quote({ print(utils::ls.str()) }),
exit = quote({ utils::str(packages) })
)
renv::status()I see: > renv::status()
Tracing renv_snapshot_dependencies(project, dev = dev) on entry
dev : logi FALSE
project : chr "/home/kevin/scratch/example"
type : NULL
Tracing renv_snapshot_dependencies(project, dev = dev) on exit
chr [1:2] "renv" "utils"
Tracing renv_snapshot_dependencies(project = project, type = type, dev = dev) on entry
dev : logi FALSE
project : chr "/home/kevin/scratch/example"
type : chr "all"
Tracing renv_snapshot_dependencies(project = project, type = type, dev = dev) on exit
chr [1:32] "cli" "dplyr" "fansi" "generics" "glue" "lifecycle" "magrittr" "pillar" "pkgconfig" "R6" "renv" "rlang" "tibble" "tidyselect" "utf8" "vctrs" "withr" "boot" "class" ...
Tracing renv_snapshot_packages(packages = setdiff(packages, exclude), .... on entry
libpaths : chr [1:2] "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu" ...
packages : chr [1:32] "cli" "dplyr" "fansi" "generics" "glue" "lifecycle" "magrittr" "pillar" "pkgconfig" "R6" "renv" "rlang" "tibble" "tidyselect" "utf8" "vctrs" "withr" "boot" "class" ...
project : chr "/home/kevin/scratch/example"
Tracing renv_snapshot_packages(packages = setdiff(packages, exclude), .... on exit
Named chr [1:32] "/home/kevin/scratch/example/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu/vctrs" ...
- attr(*, "names")= chr [1:32] "vctrs" "nlme" "cli" "rlang" ...
No issues found -- the project is in a consistent state. |
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All that said, this would likely need to be fixed in R Core itself; I'm not totally confident that |
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The other thing you could try would be to forcefully overwrite the file.access <- function(names, mode = 0) {
res <- if (mode == 1) {
# assume that files / folders are executable
rep.int(0L, length(names))
} else {
.Internal(file.access(names, mode))
}
names(res) <- names
res
}
environment(file.access) <- .BaseNamespaceEnv
unlockBinding("file.access", env = .BaseNamespaceEnv)
assign("file.access", file.access, env = .BaseNamespaceEnv)
lockBinding("file.access", env = .BaseNamespaceEnv)
rm("file.access")You could place this in, for example, your R installation's |
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Thanks for the response and sorry for the late answer. I tested all and here are the results: rlang is installed in the project library: > find.package("rlang")
[1] "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/rlang"
> getNamespaceInfo("rlang", "path")
[1] "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/rlang"List of installed package for dplyr: > str(renv:::renv_package_dependencies("dplyr"))
List of 21
$ tidyselect: chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/tidyselect"
$ R6 : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/R6"
$ magrittr : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/magrittr"
$ generics : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/generics"
$ cli : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/cli"
$ graphics : chr "C:/Users/malte.stein/AppData/Local/R/cache/R/renv/sandbox/R-4.2/x86_64-w64-mingw32/19d6eec0/graphics"
$ withr : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/withr"
$ pillar : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/pillar"
$ glue : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/glue"
$ utils : chr "C:/Users/malte.stein/AppData/Local/R/cache/R/renv/sandbox/R-4.2/x86_64-w64-mingw32/19d6eec0/utils"
$ dplyr : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/dplyr"
$ tibble : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/tibble"
$ grDevices : chr "C:/Users/malte.stein/AppData/Local/R/cache/R/renv/sandbox/R-4.2/x86_64-w64-mingw32/19d6eec0/grDevices"
$ stats : chr "C:/Users/malte.stein/AppData/Local/R/cache/R/renv/sandbox/R-4.2/x86_64-w64-mingw32/19d6eec0/stats"
$ fansi : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/fansi"
$ utf8 : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/utf8"
$ vctrs : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/vctrs"
$ methods : chr "C:/Users/malte.stein/AppData/Local/R/cache/R/renv/sandbox/R-4.2/x86_64-w64-mingw32/19d6eec0/methods"
$ lifecycle : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/lifecycle"
$ pkgconfig : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/pkgconfig"
$ rlang : chr "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32/rlang"These are the results with tracing the trace(
renv:::renv_snapshot_packages,
tracer = quote({ print(utils::ls.str()) }),
exit = quote({ utils::str(paths) })
)
trace(
renv:::renv_snapshot_dependencies,
tracer = quote({ print(utils::ls.str()) }),
exit = quote({ utils::str(packages) })
)
renv::status()> renv::status()
Tracing renv_snapshot_dependencies(project, dev = dev) on entry
dev : logi FALSE
project : chr "Z:/testing"
type : NULL
Tracing renv_snapshot_dependencies(project, dev = dev) on exit
chr [1:3] "renv" "dplyr" "rlang"
Tracing renv_snapshot_dependencies(project = project, type = type, dev = dev) on entry
dev : logi FALSE
project : chr "Z:/testing"
type : chr "all"
Tracing renv_snapshot_dependencies(project = project, type = type, dev = dev) on exit
chr [1:16] "boot" "class" "cluster" "codetools" "foreign" "KernSmooth" "lattice" "MASS" "Matrix" "mgcv" "nlme" "nnet" "rpart" ...
Tracing renv_snapshot_packages(packages = setdiff(packages, exclude), .... on entry
libpaths : chr [1:2] "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32" ...
packages : chr [1:16] "boot" "class" "cluster" "codetools" "foreign" "KernSmooth" "lattice" "MASS" "Matrix" "mgcv" "nlme" "nnet" "rpart" ...
project : chr "Z:/testing"
Tracing renv_snapshot_packages(packages = setdiff(packages, exclude), .... on exit
Named chr [1:16] "C:/Users/malte.stein/AppData/Local/R/cache/R/renv/sandbox/R-4.2/x86_64-w64-mingw32/19d6eec0/MASS" ...
- attr(*, "names")= chr [1:16] "MASS" "Matrix" "class" "mgcv" ...
The following package(s) are used in this project, but are not installed:
- cli
- dplyr
- fansi
- generics
- glue
- lifecycle
- magrittr
- pillar
- pkgconfig
- R6
- rlang
- tibble
- tidyselect
- utf8
- vctrs
- withr
See `?renv::status` for advice on resolving these issues. |
Results for changing the ´file.access()´ function:I had to change the your code to include also mode=5 (used in renv). Therefore I added the following code into the .Rprofile of the Rproject. file.access <- function(names, mode = 0) {
res <- numeric(length(names))
for (i in seq_along(names)) {
file_mode <- suppressWarnings(as.numeric(substr(file.mode(names[i]), 3, 3)))
res[i] <- if (!is.na(file_mode)) {
# Check mode conditions
if (mode == 7 && file_mode == 7) 0L
else if (mode == 6 && file_mode %in% c(6, 7)) 0L
else if (mode == 5 && file_mode %in% c(5, 7)) 0L
else if (mode == 4 && file_mode >= 4) 0L
else if (mode == 3 && file_mode %in% c(3, 7)) 0L
else if (mode == 2 && file_mode %in% c(2, 3, 6, 7)) 0L
else if (mode == 1 && file_mode %% 2 == 1) 0L
else if (mode == 0 && file_mode >= 4) 0L
else -1L
} else {
.Internal(file.access(names[i], mode))
}
}
names(res) <- names
res
}
environment(file.access) <- .BaseNamespaceEnv
unlockBinding("file.access", env = .BaseNamespaceEnv)
assign("file.access", file.access, env = .BaseNamespaceEnv)
lockBinding("file.access", env = .BaseNamespaceEnv)
rm("file.access")Afterwards I checked renv status again (with addition tracing) and the issue is fixed. > renv::status()
Tracing renv_snapshot_dependencies(project, dev = dev) on entry
dev : logi FALSE
project : chr "Z:/testing"
type : NULL
Tracing renv_snapshot_dependencies(project, dev = dev) on exit
chr [1:4] "renv" "dplyr" "rlang" "utils"
Tracing renv_snapshot_dependencies(project = project, type = type, dev = dev) on entry
dev : logi FALSE
project : chr "Z:/testing"
type : chr "all"
Tracing renv_snapshot_dependencies(project = project, type = type, dev = dev) on exit
chr [1:32] "cli" "dplyr" "fansi" "generics" "glue" "lifecycle" "magrittr" "pillar" "pkgconfig" "R6" "renv" "rlang" "tibble" ...
Tracing renv_snapshot_packages(packages = setdiff(packages, exclude), .... on entry
libpaths : chr [1:2] "Z:/testing/renv/library/R-4.2/x86_64-w64-mingw32" ...
packages : chr [1:32] "cli" "dplyr" "fansi" "generics" "glue" "lifecycle" "magrittr" "pillar" "pkgconfig" "R6" "renv" "rlang" "tibble" ...
project : chr "Z:/testing"
Tracing renv_snapshot_packages(packages = setdiff(packages, exclude), .... on exit
Named chr [1:32] "C:/Users/malte.stein/AppData/Local/R/cache/R/renv/sandbox/R-4.2/x86_64-w64-mingw32/19d6eec0/cluster" ...
- attr(*, "names")= chr [1:32] "cluster" "magrittr" "MASS" "tidyselect" ...
No issues found -- the project is in a consistent state. |
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That's great! Hopefully this is sufficient as a workaround. If I understand correctly, the real fix here would require changes to R's own internals. If so, you could also consider filing a bug report at https://bugs.r-project.org and see if there are any R Core members who would be willing to investigate. |
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We are using a dual protocol drive (SMB+NFS), and security is controlled in Unix style. But we are facing issues with using Windows R. I raised a similar issue #1625. This was solving in new renv version. Now renv installation is detected correctly, but not the installation of any other R package.
The renv project library path will be assumed as not executable. Therefore the installed R package in the renv project library will not be considers as available/installed, which is causing renv::activate() and renv::status() raising an error of "The following package(s) are used in this project, but are not installed:"
Package can be installed in renv project library and be used (e.g. with library() or in the code itself) and renv::snapshot() is working as expected.
Note: Using same R project with Linux R is causing no issues and renv is working as expected.
Main issue
I did a root cause analysis on it:
It is coming from the winAccessW functions of base R version:
https://github.com/SurajGupta/r-source/blob/a28e609e72ed7c47f6ddfbb86c85279a0750f0b7/src/gnuwin32/extra.c#L654
It is using the GetFileSecurityW function from windows.h.
On the dual drive folders R is not able to check the security descriptor. Therefore, R assuming every file on dual drive as not executable, which is causing issues (e.g. in detecting installed R packages in library). Files or folder will get from file.access(path="XX", mode=1) the result -1 (= no execution access), even if the detected mode bit is 777 from file.info()
I'm in contact with POSIT on the root issue, but was asked to raise this issue here as well.
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