[blog] 01/01: reproducing-r-packages: fixed the FTBFS

[Ximin Luo]

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infinity0 pushed a commit to branch master
in repository blog.

commit 59d86ff5cb3c0d77451c88a4e854b7589f6f5b43
Author: Ximin Luo <infinity0 at debian.org>
Date:   Tue May 2 19:55:09 2017 +0200

    reproducing-r-packages: fixed the FTBFS
---
 drafts/reproducing-r-packages.mdwn | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/drafts/reproducing-r-packages.mdwn b/drafts/reproducing-r-packages.mdwn
index 5d53aff..7ef1b9b 100644
--- a/drafts/reproducing-r-packages.mdwn
+++ b/drafts/reproducing-r-packages.mdwn
@@ -1,10 +1,10 @@
 [[!meta title="Reproducing R packages"]]
 
 In the past week or so, Ximin Luo worked on making R generate reproducible
-output. This is now mostly complete, a few rough edges need to be ironed out,
-then we have to convince upstream to merge the patch. Finally, there are a few
-stubborn packages that remain unreproducible, which maybe you can help with
-after reading this! Anyway, the goal is within reach and here's how he did it:
+output. This is now mostly complete, and we're waiting on feedback from
+upstream about our patch. In the meantime, there are a few packages that remain
+unreproducible, but the issue probably lies in those specific packages rather
+than the R toolchain. Perhaps you can help out with them, after reading this!
 
 ----
 
@@ -23,13 +23,16 @@ identical output for the `.rdb` files, even though they are bitwise different.
 To get to the bottom of this, we'll have to use the R debugger.
 
 Attached to this post is [a script](/blog/data/r-mini-repro-test.sh) that
-smooths this process. You can run it like `./r-mini-repro-test.sh $pkgdir
-$builddir` and it will output some hashes for you; make sure to install the
-build dependencies first. You should manually vary both `$pkgdir` and
-`$builddir` to introduce the build-path variations; `$builddir` can be an
-arbitrary string but `$pkgdir` should point to the actual R package's source
-directory, so I just copy that to two locations and point the script at each of
-them in turn.
+smooths this process. The script is meant to be run against Debian's R
+packages, but it could probably be made to work with other distros' R packages
+with minimal changes, if it doesn't already work.
+
+You run it like `./r-mini-repro-test.sh $pkgdir $builddir` and it will output
+some hashes for you; make sure to install the build dependencies first. You
+should manually vary both `$pkgdir` and `$builddir` to introduce the build-path
+variations; `$builddir` can be an arbitrary string but `$pkgdir` should point
+to the actual R package's source directory, so I just copy that to two
+locations and point the script at each of them in turn.
 
 Now, we can begin debugging. Before I did this, we had 477 unreproducible R
 packages so the biggest problem was likely with R itself. I downloaded the
@@ -405,8 +408,10 @@ packages](https://tests.reproducible-builds.org/debian/issues/unstable/randomnes
 Before the patch, all of these were unreproducible. Now 460/477 are
 reproducible, hurray!
 
-However, it seems my patch needs a bit of work, it has made 3 packages FTBFS:
-r-bioc-biobase r-cran-randomfields r-cran-shinybs
+The first version of the patch made 2 packages FTBFS, r-bioc-biobase and
+r-cran-shinybs; this was fixed in a subsequent version of the patch. 1 package,
+r-cran-randomfields, FTBFS even on an unpatched r-base, probably due to
+differences between 3.3.3 and 3.4.0
 
 Given the overwhelming proportion of packages that *did* reproduce, the other
 14 packages that are still unreproducible, are quite probably due to issues in

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/reproducible/blog.git