Upgrade R to 3.3.2

[charpent]

Usual reason...

This one is a bit more complicated than usual : the Windows toolchain has changed ; however, I do not have a Windows system to test this.

Original tarballs :

• ​R
• ​curl
• ​pcre

[tscrim]

cc-ing the Windows/Cygwin people.

[embray]

What is the best process for testing a new dependency update?

[charpent]

I have to forfeit on this one, or at least delay for one eek minimum (RealLife? overflow + ill health).

BTW, it seems that some of our current patches were created only for cygwin environment : I am unable to retrieve their necessity. Could their authors mtell me if they encountered their use in a Unix (Linux) environment ?

Sorry...

[jpflori]

It seems that only the large_address_aware patch is cygwin-only, upstream report:

• ​https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15643

The other patches look general purpose.

[charpent]

I've got some nonmaskable RealLife? interruptions, seriously interfering with my plans. Sorry for the delay.

I updated the description to reflect the current plans.

[charpent]

The proposed patch seems valid on Linux : it passes ptestlong with errors in two doctests :

----------------------------------------------------------------------
sage -t --long --warn-long 109.1 src/sage/homology/simplicial_complex.py  # 1 doctest failed
sage -t --long --warn-long 109.1 src/sage/misc/trace.py  # 1 doctest failed
----------------------------------------------------------------------

which both pass when run standalone :

charpent@asus16-ec:/usr/local/sage-7$ sage -t --long --warn-long 109.1 src/sage/misc/trace.py
Running doctests with ID 2016-08-20-12-45-47-583c0f71.
Git branch: t/20523/upgrade_r_to_3_3_1
Using --optional=database_gap,mpir,python2,sage,sage_mode
Doctesting 1 file.
sage -t --long --warn-long 109.1 src/sage/misc/trace.py
    [9 tests, 1.79 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 1.8 seconds
    cpu time: 0.3 seconds
    cumulative wall time: 1.8 seconds
charpent@asus16-ec:/usr/local/sage-7$ sage -t --long --warn-long 109.1 src/sage/homology/simplicial_complex.py
Running doctests with ID 2016-08-20-12-46-08-790dac8d.
Git branch: t/20523/upgrade_r_to_3_3_1
Using --optional=database_gap,mpir,python2,sage,sage_mode
Doctesting 1 file.
sage -t --long --warn-long 109.1 src/sage/homology/simplicial_complex.py
    [588 tests, 6.39 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 6.5 seconds
    cpu time: 3.0 seconds
    cumulative wall time: 6.4 seconds

I have had this kind of hiccups since about 7.2 ; reports (on sage-release, mainly) did not alarm the release maintainers ; one of them has generated a tick.

Note that the large_address_aware has been lost : R 3.3.1 no longer has cygwin-specific sections in configure.ac or Makefile.in (and therefore nothing to patch) ; maybe the cygwin-relevant problems have been fixed upstream ?

I don't have a Windows machine to port Sage to ; I leave this problem to people better(?) equipped than me.

---

New commits:

​336ee16

Upgrade R to 3.3.1 (correct on Linux).

[charpent]

On the other hand, I found this in the current ​R Installation and Administration Manual :

C.8 Cygwin

The 32-bit version has never worked well enough to pass R’s make check, and residual support from earlier experiments was removed in R 3.3.0.

The 64-bit version is completely unsupported.

Maybe we should consider to have rather an interface to system's R and make it an optional package ?

I'll broach this subject open on sage-devel (not r-devel, as I wrote incorrectly the first time...).

[tscrim]

I get a failure trying to install this on Cygwin32 with

checking for lzma_version_number in -llzma... no
configure: error: "liblzma library and headers are required"
Error configuring R.

which is the same failure I had on #20190.

[charpent]

Replying to tscrim:

I get a failure trying to install this on Cygwin32 with

checking for lzma_version_number in -llzma... no
configure: error: "liblzma library and headers are required"
Error configuring R.

which is the same failure I had on #20190.

From ​the R 3.3.0 release notes :

The previously included versions of zlib, bzip2, xz and PCRE have been removed, so suitable external (usually system) versions are required (see the ‘R Installation and Administration’ manual).

So it's either :

• add xz-tools (né lzma-utils) to the list of prerequisites for Sage (i. e. relying on system's liblzma) ;
• adding xz-tools (at least the lzma library) to sage (cluttering it with yet one more library to maintain) ;
• or relying on system's R through an interface that remains to be written...

Pick your poison...

NB : I also post this on sage-devel in the recent R thread...

[embray]

On Cygwin I needed to apt-cyg install liblzma-devel (if you have apt-cyg, otherwise use setup as normal). Without the -devel package it doesn't install the import library, so -llzma doesn't work (-llzma.dll should though).

[charpent]

Replying to embray:

On Cygwin I needed to apt-cyg install liblzma-devel (if you have apt-cyg, otherwise use setup as normal). Without the -devel package it doesn't install the import library, so -llzma doesn't work (-llzma.dll should though).

Okay. I just checked on my (Linux) system : xz is not installed in the $(SAGE_ROOT) tree, probably because I have it installed at system level and the build script detects that somehow. (BTW : it is an *optional* package.

Therefore, what is needed is :

1. ensure that xz and its development files are installed, either in the system or in the Sage package) ;
2. that this is done before the R installation begins ; and
3. that R installation depends on xz being somehow available.

This can be simplified, at the expense of making xz a standard package, just by ensuring that xz is installed before R compilation.

I have little idea on how to proceed, since the Sage build system is still a (large) bit obscure to me. What I need is a way to check in the Makefile that xz and its development files are available, install xz if not (can an optional package be installed before the compilation of standard packages is finished ?), and make the R compilation dependent on this target.

Any ideas ?

(BTW : Cc on the sage-devel thread for advice...)

[leif]

You IMHO shouldn't change patches which haven't changed at all, that's just confusing. I wouldn't even touch patches where just the offset changed, not the context.

[jpflori]

I'm working on this, especially on Cygwin as I resetuped a Cygwin install for other tickets at SD75.

[charpent]

Please see ​this post on sage-devel's discussion of this topic. I need comments from people not as concerned as we are by Sage's R's future...

Jean-Pierre : did you consider repackaging (bnew style) the old pcre package ?

[jpflori]

Nope I did not yet. I mostly made a clean set of patches.

[jpflori]

I updated the set of patches. I also slightly modiifed the options passed to configure in spkg-install.

We still need to deal with the new dependencies. It seemed to me that on top of libpcre, R also depends on libcurl...

---

New commits:

​2b7f6f4

Update patches set for R upgrade.

[jpflori]

libcurl is needed according to:

• ​https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Essential-and-useful-other-programs-under-a-Unix_002dalike

[leif]

The Cygwin patches to main/Makefile.in as well as nmath/standalone/Makefile.in, and etc/Makeconf.in have effects on non-Cygwin as well.

In the first two, the folder is changed unconditionally, the third may lead to overlinking on non-Cygwin.

I also don't like removing the documentation from SPKG.txt; at the very least, the patch descriptions should get copied into the patches. Renaming them IMHO isn't necessary either.

The patches have funny permissions; while you chmoded some a-x, the new ones again have u=rwx and go=rx.

In spkg-install, the lines with options to configure aren't consistently indented (in the diff at least => tabs vs. spaces used).

[leif]

Replying to leif:

In spkg-install, the lines with options to configure aren't consistently indented.

... and --enable-R-shlib is redundant, as it has already been added to R_CONFIGURE a couple of lines above.

[jpflori]

I'll take your comments into account or gve some justification here.

[jpflori]

Replying to leif:

The Cygwin patches to main/Makefile.in as well as nmath/standalone/Makefile.in, and etc/Makeconf.in have effects on non-Cygwin as well.

In the first two, the folder is changed unconditionally, the third may lead to overlinking on non-Cygwin.

Well spotted, I did not pay attention on that part.

From what I saw there was underlinking in all cases, I don't see how Cygwin or non-Cygwin can change anything but I'll double check.

Anyway I'll only apply this two only coniditonally.

I also don't like removing the documentation from SPKG.txt; at the very least, the patch descriptions should get copied into the patches. Renaming them IMHO isn't necessary either.

From what I remember there seemed to be a consensus on putting doc in patches themselves to modify a minimum set of files when adding/removing patches. Although each patch now has some info, I'll add more from what was removed from SPKG.txt.

The patches have funny permissions; while you chmoded some a-x, the new ones again have u=rwx and go=rx.

Windows funky choice, I'll fix it.

In spkg-install, the lines with options to configure aren't consistently indented (in the diff at least => tabs vs. spaces used).

I removed all tabs.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​893d3cb	Remove duplicated "--enable-R-shlib".
​a79ccf1	Replace tabs by spaces in R spkg-install.
​f37aedc	Apply some R patches only on Cygwin.
​0b79739	Fix permission of R patches.
​11d338e	Make description of patches more verbose.
​c7f359e	Fix SAGE_BUILDING_R patch.

[charpent]

On top of 6.4beta6+#21622 (now necessary to build Sage on Debian), this patch passes ptestlong with two failures :

----------------------------------------------------------------------
sage -t --long --warn-long 111.2 src/sage/homology/simplicial_complex.py  # 1 doctest failed
sage -t --long --warn-long 111.2 src/sage/libs/gap/assigned_names.py  # 1 doctest failed
----------------------------------------------------------------------

Both of them pass standalone. This kind of failure is a known, iterative (and annoying) problem, probably pertaining to the test infrastructure rather than to your patch.

I am sorely tempted to set this to positive_review, but I think that thios must be tested by someone testing it on Cygwin, given the changes in the R toolset on Windows.

Let me know if you think this is sufficient.

[jpflori]

Replying to charpent:

On top of 6.4beta6+#21622 (now necessary to build Sage on Debian), this patch passes ptestlong with two failures :

----------------------------------------------------------------------
sage -t --long --warn-long 111.2 src/sage/homology/simplicial_complex.py  # 1 doctest failed
sage -t --long --warn-long 111.2 src/sage/libs/gap/assigned_names.py  # 1 doctest failed
----------------------------------------------------------------------

Both of them pass standalone. This kind of failure is a known, iterative (and annoying) problem, probably pertaining to the test infrastructure rather than to your patch.

I am sorely tempted to set this to positive_review, but I think that thios must be tested by someone testing it on Cygwin, given the changes in the R toolset on Windows.

I tested that R with the patches shipped here buids on Cygwin, though not from a Sage env.

Let me know if you think this is sufficient.

IMHO this is largely sufficient as far as Cygwin is concerned. If by any chance there are some residual side effects on Cygwin they be fixed on follow up tickets.

More of a concern is the dependency on new packages... Can we list them here and I can try to package them:

• libpcre
• libcurl
• anything else?

[charpent]

Replying to jpflori:

[ ... ]

IMHO this is largely sufficient as far as Cygwin is concerned. If by any chance there are some residual side effects on Cygwin they be fixed on follow up tickets.

Okay : positive review. BTW, I think that you are the main (first) author...

More of a concern is the dependency on new packages... Can we list them here and I can try to package them:

• libpcre
• libcurl
• anything else?

• xz-tools.

Possible strategy :

1) For now, list them as supplementary dependencies in the main README.TXT.

2) Create a set of tickets to include them in Sage. These packages shuld test for existim system functionality and, if found, do nothong (how to achieve this in a Makefile ?)

3) When those tickets are tested and positively reviewed, make them standard packages, and prerequisites for R. This pulls them off the list of prerequisites.

This way, we can buy time...

BTW : Curl and xz-tools are tools of sufficient "general" interest that we should package the whole things (i. e. binaries and docs (but maybe not test utilities ?)), not just the libraries. And add the binaries to the list of candidates for small_scripts making them accessible systemwide.

[vbraun]

Hard dependency on lzma

checking for lzma_version_number in -llzma... no
configure: error: "liblzma library and headers are required"
Error configuring R.

[charpent]

lzma is already available through the optional xz package. I opened #21744 to this order.

Trivial patch to follow...

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​2875b8b

Three-keystroke patch ; depend on xz.

[charpent]

#20523 (present patch) + #21744 pass ptestlong successfully over both 7.4 and 7.5beta0.

==>needs_review

Note : I suspect that we may have to do likewise for pcre and curl. I shall package them, and open tickets to get them included as standard packages as the need arises.

[jpflori]

We need to clarify the curl and openssl issues.

[jpflori]

The good news is that R compiles against an ssl-free libcurl when configure is hacked. And it seems that nothing that fails in the test suite is related to this lacking feature.

Not sure how it affects usability though.

[charpent]

Replying to jpflori:

Not sure how it affects usability though.

Hah ! Most R repositories are switching to https:... addresses (this shown where trying to install a package without having defined a repository first : the graphical interface propose firs a list of repositories with https: addresses ; the only way to reach an http: repository is to click on the last item in that menu, which gives another list of http: repositories.

The move to such repositories parallels a similar move from various distros (starting with Debian...). I doubt that this will get reversed, and I think that, one way or another, Sage's R must keep the ability to use https:

This is true (with aggravation) of other uses of networking in applied statistics : access to remote databases is more and more frequent, and I do not see these uses accept insecure channels for a long time...

[charpent]

Changing target to 3.3.2. Meanwhile, experimenting.

Still waiting for advice (see sage-devel's sagas)...

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​6c197f6	Updating R source to 3.3.2.
​4c896a9	R's strig representation of source code has changed. Updated docstrings accordingly.

[charpent]

Minimal adjustments (package version + checksum) + fixed a couple of failing doctests due to R's change of representation of function source code.

These doctests might be usefully augmented by a doctest of a real R function. This doesn't seem to have ever been doctested. Advice ?

The resulting Sage (after merging with 7.5beta4) passes ptestlong with two transient failures (which pass with no errors when ran standalone).

The question of the new dependencies is still open (no answer to sage-devel's questions).

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​8a05b10

Depend on PCRE

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​2568ce5

Update spkg-install to conform to #20692.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​a06fc11

R-shlib is needed in configurefor the (standard) rpy2 package.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​f0ab39e

Added curl to dependencies.

[charpent]

Sage-7.6.beta4 + #20523 (this patch) + #21767 + #21770 passes ptestlong witht two transient errors :

----------------------------------------------------------------------
sage -t --long src/sage/homology/simplicial_set_morphism.py  # Bad exit: 2
sage -t --long src/sage/homology/simplicial_complex.py  # 1 doctest failed
----------------------------------------------------------------------

Both tests pass when run standalone.

This should close the R saga (for now) by allowing the current interfaces to work with R >= 3.3.x.

==>needs_review

[dimpase]

the branch is red - you need a rebase or so...

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

​c1aba6f	Fix permission of R patches.
​b05ec4b	Make description of patches more verbose.
​3b58ad0	Fix SAGE_BUILDING_R patch.
​fecbfc0	Three-keystroke patch ; depend on xz.
​3a4eb9c	Updating R source to 3.3.2.
​55a8aa4	R's strig representation of source code has changed. Updated docstrings accordingly.
​00fcc86	Depend on PCRE
​23f9471	Update spkg-install to conform to #20692.
​22974b8	R-shlib is needed in configurefor the (standard) rpy2 package.
​d873670	Added curl to dependencies.

[charpent]

Rebased on develop at 7.6.beta4

[dimpase]

A branch dependent on unmerged/under review tickets ought to include all of them, otherwise you leave it to the reviewer to do merges that might potentially be nontrivial.

[charpent]

Replying to dimpase:

A branch dependent on unmerged/under review tickets ought to include all of them, otherwise you leave it to the reviewer to do merges that might potentially be nontrivial.

If I understand you correctly,we should either :

1. merge #21767 and #21770 into develop, then merge #20523 ; OR
2. add the contents of #21767 an #21770 into #20523

1. Is this correct ?
2. What do you recommend ?

[dimpase]

I don't see a difference. Essentially it is as follows.

git checkout -b newrrr develop
git pull trac public/curl7510
git pull trac u/charpent/package_libpcre_as_a_standard_package
git pull trac public/r311
git push trac --set-upstream HEAD:public/r311

(not sure if the last push needs -f or not).

It's also a question whether these 3 branches commute, so that these 3 pull all go through without manual intervention.

[git]

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

​1588558	Packaging polish.
​81e3341	Removed patches handling.
​c02cb61	Update Curl to 7.51.0.
​d31c560	Add a fat mode to curl.
​e4e5665	Upgraded curl to 7.52.1
​43030c3	Merge branch 'public/curl7510' of git://trac.sagemath.org/sage into newrrr
​a8d77b5	Initial packaging of pcre : unconditionnal installation.
​21ce3e7	Removed patches handling.
​fb088b8	Merge branch 'u/charpent/package_libpcre_as_a_standard_package' of git://trac.sagemath.org/sage into newrrr
​3b11753	Merge branch 'public/r311' of git://trac.sagemath.org/sage into newrrr

[charpent]

Done. Added tarballs for curl and pcre, dropped the corresponding ticket dependencies.

ptestlong running.

---

Last 10 new commits:

​1588558	Packaging polish.
​81e3341	Removed patches handling.
​c02cb61	Update Curl to 7.51.0.
​d31c560	Add a fat mode to curl.
​e4e5665	Upgraded curl to 7.52.1
​43030c3	Merge branch 'public/curl7510' of git://trac.sagemath.org/sage into newrrr
​a8d77b5	Initial packaging of pcre : unconditionnal installation.
​21ce3e7	Removed patches handling.
​fb088b8	Merge branch 'u/charpent/package_libpcre_as_a_standard_package' of git://trac.sagemath.org/sage into newrrr
​3b11753	Merge branch 'public/r311' of git://trac.sagemath.org/sage into newrrr