Hello,
First, I appreciate the work that goes into maintaining the R ecosystem. But there is now a problem that I don't think people would allow in other languages. Namely, the recently pushed R-3.4 update breaks the whole world. Something this disruptive usually has to wait for a new Fedora release to get pushed out. I really think the same thing has to apply for R.
For example, when I run RStudio, I get:
R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.
Also:
Warning: Error in library: there is no package called ‘shinyjs’ Stack trace (innermost first): 41: library 1: shiny::runApp Error : there is no package called ‘shinyjs’
So, basically, anyone updating to the new R is dead in the water. It really needs to be rolled back to 3.3.3 in F24 & F25. Which leads to another issue...where is R in the bugzilla database? I can't find it.
-Steve
On Sunday, 25 June 2017 16.38.00 WEST Steve Grubb wrote:
For example, when I run RStudio, I get:
R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.
You need to update Rstudio to a newer version. That fixes this issue.
Also:
Warning: Error in library: there is no package called ‘shinyjs’ Stack trace (innermost first): 41: library 1: shiny::runApp Error : there is no package called ‘shinyjs’
So, basically, anyone updating to the new R is dead in the water. It really needs to be rolled back to 3.3.3 in F24 & F25. Which leads to another issue...where is R in the bugzilla database? I can't find it.
The only packages that needed to be rebuild are those that rebuild packages that register C or Fortran functions:
From https://cran.r-project.org/doc/manuals/r-release/NEWS.html
""" PACKAGE INSTALLATION ... Packages which register native routines for .C or .Fortran need to be re- installed for this version (unless installed with R-devel SVN revision r72375 or later). ... """
This issue does not seem to be related, but I have not tested.
On Sunday, June 25, 2017 12:08:29 PM EDT José Abílio Matos wrote:
On Sunday, 25 June 2017 16.38.00 WEST Steve Grubb wrote:
For example, when I run RStudio, I get:
R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.
You need to update Rstudio to a newer version. That fixes this issue.
There isn't an easy to build newer version right at the moment. The issue is really that a major ABI change occurred and it was pushed to a shipped OS. Do we do things like go from python 2 to 3 after Fedora ships? No. Major version changes for R need to be tied to an OS release like every other language. Or a compat package created.
Also:
Warning: Error in library: there is no package called ‘shinyjs’ Stack trace (innermost first):
41: library 1: shiny::runAppError : there is no package called ‘shinyjs’
So, basically, anyone updating to the new R is dead in the water. It really needs to be rolled back to 3.3.3 in F24 & F25. Which leads to another issue...where is R in the bugzilla database? I can't find it.
The only packages that needed to be rebuild are those that rebuild packages that register C or Fortran functions:
From https://cran.r-project.org/doc/manuals/r-release/NEWS.html
""" PACKAGE INSTALLATION ... Packages which register native routines for .C or .Fortran need to be re- installed for this version (unless installed with R-devel SVN revision r72375 or later). ... """
We don't do incompatible changes for python within a Fedora version release. Major changes should be tied to an OS release. IOW, F26 can have 3.4 just fine since its not shipped. F25 has already shipped and rebuilding EVERYTHING is just not nice to push on people.
-Steve
On Sun, Jun 25, 2017 at 08:28:15PM -0400, Steve Grubb wrote:
We don't do incompatible changes for python within a Fedora version release. Major changes should be tied to an OS release. IOW, F26 can have 3.4 just fine since its not shipped. F25 has already shipped and rebuilding EVERYTHING is just not nice to push on people.
Yeah, I'd _really_ like to encourage sticking to the policy. It can be more work for packagers when there are big bugs to fix going back to older releases, but the ability to digest change on different streams is a big benefit to our users. If you'd like to make newer versions of something like R available for shipped releases for people who want to opt-in, we have Copr which makes that easy.
On Sun, 2017-06-25 at 20:28 -0400, Steve Grubb wrote:
IOW, F26 can have 3.4 just fine since its not shipped.
Well, it's not quite that clear cut. Even if we ignore the Final freeze which just kicked in (a significant version update would not be a great candidate for a freeze exception, in most cases), consider the updates policy during the 'Beta to Pre Release' period (which is after the Beta is released but before the Final freeze kicks in):
https://fedoraproject.org/wiki/Updates_Policy#Beta_to_Pre_Release
"From this point onwards maintainers MUST[1]:
Avoid Major version updates, ABI breakage or API changes if at all possible."
On Sun, 2017-06-25 at 17:08 +0100, José Abílio Matos wrote:
On Sunday, 25 June 2017 16.38.00 WEST Steve Grubb wrote:
For example, when I run RStudio, I get:
R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.
You need to update Rstudio to a newer version. That fixes this issue.
Also:
Warning: Error in library: there is no package called ‘shinyjs’ Stack trace (innermost first): 41: library 1: shiny::runApp Error : there is no package called ‘shinyjs’
So, basically, anyone updating to the new R is dead in the water. It really needs to be rolled back to 3.3.3 in F24 & F25. Which leads to another issue...where is R in the bugzilla database? I can't find it.
The only packages that needed to be rebuild are those that rebuild packages that register C or Fortran functions:
By policy, the Rstudio update and updates for all those packages should have been included with the update to R itself:
https://fedoraproject.org/wiki/Updates_Policy#Updating_inter-dependent_packa...
"When one updated package requires another (or more than one other), the packages should be submitted together as a single update. For instance, if package A depends on packages B and C, and you want to update to a new version of package A which requires new versions of B and C, you must submit a single update containing the updated versions of all three packages. It is a bad idea to submit three separate updates, because if the update for package A is pushed stable before the updates for packages B and C, it will cause dependency problems."
Also, it may be worth considering whether updating R to 3.4 is in line with these parts of the policy:
"Releases of the Fedora distribution are like releases of the individual packages that compose it. A major version number reflects a more-or-less stable set of features and functionality. As a result, we should avoid major updates of packages within a stable release. Updates should aim to fix bugs, and not introduce features, particularly when those features would materially affect the user or developer experience. The update rate for any given release should drop off over time, approaching zero near release end-of-life; since updates are primarily bugfixes, fewer and fewer should be needed over time."
"Package maintainers MUST:
Avoid Major version updates, ABI breakage or API changes if at all possible. Avoid changing the user experience if at all possible. Avoid updates that are trivial or don't affect any Fedora users."
It would be great if the relevant maintainers could take these points into consideration for future updates. Thanks!
On Tuesday, June 27, 2017 3:47:42 PM EDT Adam Williamson wrote:
On Sun, 2017-06-25 at 17:08 +0100, José Abílio Matos wrote:
On Sunday, 25 June 2017 16.38.00 WEST Steve Grubb wrote:
For example, when I run RStudio, I get:
R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.
You need to update Rstudio to a newer version. That fixes this issue.
Also:
Warning: Error in library: there is no package called ‘shinyjs’ Stack trace (innermost first):
41: library 1: shiny::runAppError : there is no package called ‘shinyjs’
So, basically, anyone updating to the new R is dead in the water. It really needs to be rolled back to 3.3.3 in F24 & F25. Which leads to another issue...where is R in the bugzilla database? I can't find it.
The only packages that needed to be rebuild are those that rebuild packages that register C or Fortran functions:
By policy, the Rstudio update and updates for all those packages should have been included with the update to R itself:
https://fedoraproject.org/wiki/Updates_Policy#Updating_inter-dependent_packa ges
There really is no way to do this. We don't ship RStudio because its so hard to package. I've tried creating a spec file and putting all the pieces where it belongs but it doesn't work unless its installed to /usr/local which is against Fedora policies. The best I could come up with is to create a blog to tell everyone how to build it for themselves.
There just simply needs to be a rule of no update to a major release during a shipped Fedora OS. R 3.3 -> 3.3.1 is fine as that's bug fixes. R 3.3.3 -> 3.4 has potential to wreck things on already shipped OS.
"When one updated package requires another (or more than one other), the packages should be submitted together as a single update. For instance, if package A depends on packages B and C, and you want to update to a new version of package A which requires new versions of B and C, you must submit a single update containing the updated versions of all three packages. It is a bad idea to submit three separate updates, because if the update for package A is pushed stable before the updates for packages B and C, it will cause dependency problems."
Also, it may be worth considering whether updating R to 3.4 is in line with these parts of the policy:
"Releases of the Fedora distribution are like releases of the individual packages that compose it. A major version number reflects a more-or-less stable set of features and functionality. As a result, we should avoid major updates of packages within a stable release. Updates should aim to fix bugs, and not introduce features, particularly when those features would materially affect the user or developer experience. The update rate for any given release should drop off over time, approaching zero near release end-of-life; since updates are primarily bugfixes, fewer and fewer should be needed over time."
It sounds like this ^^^ fits best.
"Package maintainers MUST:
Avoid Major version updates, ABI breakage or API changes if at allpossible. Avoid changing the user experience if at all possible. Avoid updates that are trivial or don't affect any Fedora users."
It would be great if the relevant maintainers could take these points into consideration for future updates. Thanks!
I'm trying to consider what to do to get a working RStudio again. I suppose I can find the packages in the build system and do it manually. But it pulled in a little over 20 dependency packages.
Also, what about the missing bz entry? I'd file a bug but I can't find an "R" component to file a bug against. Try it.
Thanks, -Steve
On Tue, 2017-06-27 at 16:09 -0400, Steve Grubb wrote:
On Tuesday, June 27, 2017 3:47:42 PM EDT Adam Williamson wrote:
On Sun, 2017-06-25 at 17:08 +0100, José Abílio Matos wrote:
On Sunday, 25 June 2017 16.38.00 WEST Steve Grubb wrote:
For example, when I run RStudio, I get:
R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.
You need to update Rstudio to a newer version. That fixes this issue.
Also:
Warning: Error in library: there is no package called ‘shinyjs’ Stack trace (innermost first):
41: library 1: shiny::runAppError : there is no package called ‘shinyjs’
So, basically, anyone updating to the new R is dead in the water. It really needs to be rolled back to 3.3.3 in F24 & F25. Which leads to another issue...where is R in the bugzilla database? I can't find it.
The only packages that needed to be rebuild are those that rebuild packages that register C or Fortran functions:
By policy, the Rstudio update and updates for all those packages should have been included with the update to R itself:
https://fedoraproject.org/wiki/Updates_Policy#Updating_inter-dependent_packa ges
There really is no way to do this. We don't ship RStudio because its so hard to package. I've tried creating a spec file and putting all the pieces where it belongs but it doesn't work unless its installed to /usr/local which is against Fedora policies. The best I could come up with is to create a blog to tell everyone how to build it for themselves.
Ah, I see. Sorry, I realize I was making an unwarranted assumption that it was packaged.
Also, what about the missing bz entry? I'd file a bug but I can't find an "R" component to file a bug against. Try it.
Try this:
https://bugzilla.redhat.com/enter_bug.cgi?product=Fedora&component=R
I do indeed confirm the bug, when trying to find the component using the 'search-as-you-type' implementation. It looks to me like it doesn't even attempt to find a match until you've typed two characters. I tried typing ' R' (space, then R) and that *does* cause it to search and find a bunch of components with 'R' in their name, but it doesn't find R itself. I'd suggest reporting this against the Bugzilla product.
On Tuesday, June 27, 2017 4:09:54 PM EDT Steve Grubb wrote:
On Tuesday, June 27, 2017 3:47:42 PM EDT Adam Williamson wrote:
On Sun, 2017-06-25 at 17:08 +0100, José Abílio Matos wrote:
On Sunday, 25 June 2017 16.38.00 WEST Steve Grubb wrote:
For example, when I run RStudio, I get:
R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.
You need to update Rstudio to a newer version. That fixes this issue.
Also:
Warning: Error in library: there is no package called ‘shinyjs’ Stack trace (innermost first): 41: library 1: shiny::runApp Error : there is no package called ‘shinyjs’
So, basically, anyone updating to the new R is dead in the water. It really needs to be rolled back to 3.3.3 in F24 & F25. Which leads to another issue...where is R in the bugzilla database? I can't find it.
The only packages that needed to be rebuild are those that rebuild packages that register C or Fortran functions:
By policy, the Rstudio update and updates for all those packages should have been included with the update to R itself:
https://fedoraproject.org/wiki/Updates_Policy#Updating_inter-dependent_pac kages
There really is no way to do this. We don't ship RStudio because its so hard to package. I've tried creating a spec file and putting all the pieces where it belongs but it doesn't work unless its installed to /usr/local which is against Fedora policies. The best I could come up with is to create a blog to tell everyone how to build it for themselves.
For anyone following along...since this completely stopped work on my projects, I took the time to upgrade to a newer version of Rstudio which works with R 3.4. A link to the srpm and some basic instructions can be found here:
http://security-plus-data-science.blogspot.com/2017/06/updated-rstudio-srpm-...
-Steve
There just simply needs to be a rule of no update to a major release during a shipped Fedora OS. R 3.3 -> 3.3.1 is fine as that's bug fixes. R 3.3.3 -> 3.4 has potential to wreck things on already shipped OS.
"When one updated package requires another (or more than one other), the packages should be submitted together as a single update. For instance, if package A depends on packages B and C, and you want to update to a new version of package A which requires new versions of B and C, you must submit a single update containing the updated versions of all three packages. It is a bad idea to submit three separate updates, because if the update for package A is pushed stable before the updates for packages B and C, it will cause dependency problems."
Also, it may be worth considering whether updating R to 3.4 is in line with these parts of the policy:
"Releases of the Fedora distribution are like releases of the individual packages that compose it. A major version number reflects a more-or-less stable set of features and functionality. As a result, we should avoid major updates of packages within a stable release. Updates should aim to fix bugs, and not introduce features, particularly when those features would materially affect the user or developer experience. The update rate for any given release should drop off over time, approaching zero near release end-of-life; since updates are primarily bugfixes, fewer and fewer should be needed over time."
It sounds like this ^^^ fits best.
"Package maintainers MUST:
Avoid Major version updates, ABI breakage or API changes if at allpossible.
Avoid changing the user experience if at all possible. Avoid updates that are trivial or don't affect any Fedora users."It would be great if the relevant maintainers could take these points into consideration for future updates. Thanks!
I'm trying to consider what to do to get a working RStudio again. I suppose I
can find the packages in the build system and do it manually. But it
pulled in a little over 20 dependency packages.
Also, what about the missing bz entry? I'd file a bug but I can't find an "R"
component to file a bug against. Try it.
Thanks, -Steve _______________________________________________ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-leave@lists.fedoraproject.org
On Sun, Jun 25, 2017 at 11:38:00AM -0400, Steve Grubb wrote:
First, I appreciate the work that goes into maintaining the R ecosystem. But there is now a problem that I don't think people would allow in other languages. Namely, the recently pushed R-3.4 update breaks the whole world. Something this disruptive usually has to wait for a new Fedora release to get pushed out. I really think the same thing has to apply for R.
FWIW, here is another example where this caused problems: https://stackoverflow.com/q/44834208/479426
From: Matthew Miller mattdm@fedoraproject.org To: Development discussions related to Fedora devel@lists.fedoraproject.org Sent: Friday, June 30, 2017 10:57 AM Subject: Re: R 3.4 update
On Sun, Jun 25, 2017 at 11:38:00AM -0400, Steve Grubb wrote:
First, I appreciate the work that goes into maintaining the R ecosystem. But there is now a problem that I don't think people would allow in other languages. Namely, the recently pushed R-3.4 update breaks the whole world. Something this disruptive usually has to wait for a new Fedora release to get pushed out. I really think the same thing has to apply for R.
FWIW, here is another example where this caused problems: https://stackoverflow.com/q/44834208/479426
-- Respectfully, the above package is not from R, but R-forge. If contributors who are not part of the R ecosystem do not want to update their packages, then not much more can be done and the issue is not resolved even if you wait for the move to a later version of Fedora.
I have not had a single package break by the move to R 3.4 (and I have a few 100s of them installed). Indeed, all are updated. In any case, with Fedora supposed to be a leading-edge system, I feel that we should keep updates happening promptly. Of course, one could also have a R-prev or something like that in case someone wanted to keep the older version. I prefer having the latest versions in R.
On the other hand, conveniently, R releases just a few weeks before a Fedora release. This term it is much longer because Fedora 26 slipped schedules pretty badly. Thanks!
On Fri, Jun 30, 2017 at 04:27:25PM +0000, Globe Trotter wrote:
FWIW, here is another example where this caused problems: https://stackoverflow.com/q/44834208/479426
-- Respectfully, the above package is not from R, but R-forge. If contributors who are not part of the R ecosystem do not want to update their packages, then not much more can be done and the issue is not resolved even if you wait for the move to a later version of Fedora.
This is the whole point of having versions of Fedora, though.
In any case, with Fedora supposed to be a leading-edge system, I feel that we should keep updates happening promptly. Of course, one could also have a R-prev or something like that in case someone wanted to keep the older version. I prefer having the latest versions in R.
We _are_ a leading edge system, but leading edge of stuff that works, with the newest stuff in the latest version. This is and has been Fedora policy for a long time.
On the other hand, conveniently, R releases just a few weeks before a Fedora release. This term it is much longer because Fedora 26 slipped schedules pretty badly.
Right -- this is one of the reasons to keep to the schedule.
-
Adam Williamson -
Globe Trotter -
José Abílio Matos -
Matthew Miller -
Steve Grubb