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r: improve relocatability (#42030)

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R embeds an absolute path to the `which` executable in the sources for
`Sys.which`. This gets ultimately stored as serialized byte code in some
custom database format, which uses compression for entries.

As a result, Spack cannot relocate `<prefix which>/bin/which` when
installing from a build cache.

The patch works around this by making R create a symlink to `which` in
its own prefix, have the R sources call that, so that relocation works
again.

See https://github.com/r-devel/r-svn/pull/151
This commit is contained in:
Harmen Stoppels 2024-01-16 13:37:25 +01:00 committed by GitHub
parent f0c69ff3bf
commit bc9b39cb73
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2 changed files with 56 additions and 0 deletions
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4
var/spack/repos/builtin/packages/r/package.py
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@ -108,6 +108,10 @@ class R(AutotoolsPackage):
# temporary fix to lower the optimization level.
patch("change_optflags_tmp.patch", when="%fj@4.1.0")
# Make R use a symlink to which in Sys.which, otherwise an absolute path
# gets stored as compressed byte code, which is not relocatable
patch("relocate-which.patch")
build_directory = "spack-build"
# R custom URL version

52
var/spack/repos/builtin/packages/r/relocate-which.patch Normal file
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@ -0,0 +1,52 @@
From 3f2b1b6c94460fd4d3e9f03c9f17a25db2d2b473 Mon Sep 17 00:00:00 2001
From: Harmen Stoppels <me@harmenstoppels.nl>
Date: Wed, 10 Jan 2024 12:40:40 +0100
Subject: [PATCH] base: use a symlink for which instead of hard-coded string
---
share/make/basepkg.mk | 8 ++++----
src/library/base/R/unix/system.unix.R | 6 +++---
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/share/make/basepkg.mk b/share/make/basepkg.mk
index c0a69c8a0af338ec002156236e47b9d7efea8165..4cf6387870915001cbb8b1439509ff4955cc67b1 100644
--- a/share/make/basepkg.mk
+++ b/share/make/basepkg.mk
@@ -72,16 +72,16 @@ mkRbase:
else \
cat $(RSRC) > "$${f}"; \
fi; \
- f2=$${TMPDIR:-/tmp}/R2$$$$; \
- sed -e "s:@WHICH@:${WHICH}:" "$${f}" > "$${f2}"; \
- rm -f "$${f}"; \
- $(SHELL) $(top_srcdir)/tools/move-if-change "$${f2}" all.R)
+ $(SHELL) $(top_srcdir)/tools/move-if-change "$${f}" all.R)
@if ! test -f $(top_builddir)/library/$(pkg)/R/$(pkg); then \
$(INSTALL_DATA) all.R $(top_builddir)/library/$(pkg)/R/$(pkg); \
else if test all.R -nt $(top_builddir)/library/$(pkg)/R/$(pkg); then \
$(INSTALL_DATA) all.R $(top_builddir)/library/$(pkg)/R/$(pkg); \
fi \
fi
+ @if ! test -f $(top_builddir)/library/$(pkg)/R/which; then \
+ cd $(top_builddir)/library/$(pkg)/R/ && $(LN_S) $(WHICH) which; \
+ fi
mkdesc:
@if test -f DESCRIPTION; then \
diff --git a/src/library/base/R/unix/system.unix.R b/src/library/base/R/unix/system.unix.R
index 3bb7d0cb27cc73a024bcea3e41e2e0c5c7e9648a..78271c8c12cb3217bc068e9d53ef9e3060e8dcc9 100644
--- a/src/library/base/R/unix/system.unix.R
+++ b/src/library/base/R/unix/system.unix.R
@@ -114,9 +114,9 @@ system2 <- function(command, args = character(),
Sys.which <- function(names)
{
res <- character(length(names)); names(res) <- names
- ## hopefully configure found [/usr]/bin/which
- which <- "@WHICH@"
- if (!nzchar(which)) {
+ which <- file.path(R.home(), "library", "base", "R", "which")
+ ## which should be a symlink to the system's which
+ if (!file.exists(which)) {
warning("'which' was not found on this platform")
return(res)
}