bug#52333: [PATCH] Remove extraneous references

bug#52333: [PATCH] Remove extraneous references

[Ricardo Wurmus]

Hi Guix,

r-minimal keeps a record of build time inputs in a comment and in a
libtool script.  I don’t know if I may remove them all, but some of them
seem to safe to remove, so that’s what the first patch does.

While I removed texlive-union references from r-minimal, I noticed that
python-nbconvert also does something undesirable: it retains references
to xelatex and bibtex, but takes these from the texlive-union of the
native-inputs.  That seems like a mistake, so I added a regular
texlive-bin input and embedded a reference to *that* instead of the
texlive-union-wrapped scripts.

-- 
Ricardo

bug#52333: [PATCH 1/2] gnu: python-nbconvert: Embed reference to texlive-bin, not texlive-union.

[Ricardo Wurmus]

* gnu/packages/python-xyz.scm (python-nbconvert)[inputs]: Add texlive-bin.
[arguments]: Embed reference to xelatex and bibtex from the texlive-bin, not
the texlive-union.
---
 gnu/packages/python-xyz.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 81b99e1d2e..602833c4f4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12117,14 +12117,15 @@ (define-public python-nbconvert
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'fix-paths-and-tests
-           (lambda _
+           (lambda* (#:key inputs #:allow-other-keys)
              ;; Use pandoc binary from input.
              (substitute* "nbconvert/utils/pandoc.py"
                (("'pandoc'") (string-append "'" (which "pandoc") "'")))
              ;; Same for LaTeX.
-             (substitute* "nbconvert/exporters/pdf.py"
-               (("\"xelatex\"") (string-append "\"" (which "xelatex") "\""))
-               (("\"bibtex\"") (string-append "\"" (which "bibtex") "\"")))
+             (let ((texlive (assoc-ref inputs "texlive-bin")))
+               (substitute* "nbconvert/exporters/pdf.py"
+                 (("\"xelatex\"") (string-append "\"" texlive "/bin/xelatex\""))
+                 (("\"bibtex\"") (string-append "\"" texlive "/bin/bibtex\""))))
              ;; Make sure tests are not skipped.
              (substitute* (find-files "." "test_.+\\.py$")
                (("@onlyif_cmds_exist\\(('(pandoc|xelatex)'(, )?)+\\)") ""))
@@ -12158,6 +12159,7 @@ (define-public python-nbconvert
                (invoke "pytest" "-vv")))))))
     (inputs
      `(("pandoc" ,pandoc)
+       ("texlive-bin" ,texlive-bin)
        ;; XXX: Disabled, needs substitute*.
        ;;("inkscape" ,inkscape)
        ))
-- 
2.34.0

bug#52333: [PATCH 2/2] gnu: r-minimal: Remove extraneous references.

[Ricardo Wurmus]

* gnu/packages/statistics.scm (r-minimal)[arguments]: Remove references to
native build-time tools.
---
 gnu/packages/statistics.scm | 39 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index cf7a64ec7a..599d6a8fc3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -403,12 +403,49 @@ (define-public r-minimal
     (arguments
      `(#:tests? #f
        ,@(substitute-keyword-arguments (package-arguments r-with-tests)
+           ((#:disallowed-references refs '())
+            (cons perl refs))
            ((#:configure-flags flags)
             ;; Do not build the recommended packages.  The build system creates
             ;; random temporary directories and embeds their names in some
             ;; package files.  We build these packages with the r-build-system
             ;; instead.
-            `(cons "--without-recommended-packages" ,flags)))))))
+            `(cons "--without-recommended-packages" ,flags))
+           ((#:phases phases '%standard-phases)
+            `(modify-phases ,phases
+               (add-after 'install 'remove-extraneous-references
+                 (lambda* (#:key inputs outputs #:allow-other-keys)
+                   (let ((out (assoc-ref outputs "out")))
+                     (substitute* (string-append out "/lib/R/etc/Makeconf")
+                       (("^# configure.*")
+                        "# Removed to avoid extraneous references\n"))
+                     (substitute* (string-append out "/lib/R/bin/libtool")
+                       (((string-append
+                          "(-L)?("
+                          (assoc-ref inputs "bzip2")
+                          "|"
+                          (assoc-ref inputs "perl")
+                          "|"
+                          (assoc-ref inputs "texlive")
+                          "|"
+                          (assoc-ref inputs "texlive-bin")
+                          "|"
+                          (assoc-ref inputs "texinfo")
+                          "|"
+                          (assoc-ref inputs "xz")
+                          "|"
+                          (format #false
+                                  "/gnu/store/[^-]+-(~{~a~^|~})-[^/]+"
+                                  '("glibc-utf8-locales"
+                                    "libselinux"
+                                    "libsepol"
+                                    "file"
+                                    "texlive-bin"
+                                    "util-macros"
+                                    "graphite2"))
+                          "|"
+                          "/gnu/store/[^-]+-glibc-[^-]+-static"
+                          ")/lib")) ""))))))))))))
 
 (define-public rmath-standalone
   (package (inherit r-minimal)
-- 
2.34.0

bug#52333: [PATCH 1/2] gnu: python-nbconvert: Embed reference to texlive-bin, not texlive-union.

[Ricardo Wurmus]

Ricardo Wurmus <rekado@elephly.net> writes:

> * gnu/packages/python-xyz.scm (python-nbconvert)[inputs]: Add texlive-bin.
> [arguments]: Embed reference to xelatex and bibtex from the texlive-bin, not
> the texlive-union.

This is a bad idea, because it breaks PDF conversion.

I still think that the texlive stuff should be a regular input, not a
native input, but however we do this: it’s not with this patch.

-- 
Ricardo

bug#52333: [PATCH] Remove extraneous references

[Ricardo Wurmus]

I applied the change to r-minimal and discarded the other one.

-- 
Ricardo