Bug#617296: RFP: rstudio -- IDE for GNU R

[Neal Fultz]

Hello,

I've made an initial attempt at compiling rstudio "the debian way" with
debuild. Luckily I could start from the Arch package instead of nothing.

In hindsight, this was probably too complicated of a project to be my first
debian package, because it requires cmake, (old) java, R and node.js in
addition to figuring out the various debian tools. The New Maintainer's
Guide didn't have much to say about any of those.

I finally got debuild to run all the way through, but there's lots of
warnings; some are easy (templates etc) but many of them I would have no
idea what to do. If someone could skim the warnings I would appreciate any
pointers, even just "here's what you should google for dh_dwz errors" would
be really helpful -  https://mentors.debian.net/package/rstudio/

I put some of my notes/questions into
https://github.com/nfultz/rstudio-debian/blob/main/README.md

Kind of a frustrating project, so I'm going to step away for a while, but
hopefully can move the ball forward in coming months. Also thanks much to
Dirk for pointing me to this thread.

Best,

Neal Fultz

Bug#617296: RFP: rstudio -- IDE for GNU R

[Jan Groenewald]

Hi

Just an update. I have received an request from users to update the PPA to
copy the rstudio package from Ubuntu 14.04 trusty to Ubuntu 16.04 xenial.
They will be testing it.

https://launchpad.net/~aims/+archive/ubuntu/aims-desktop/+files/rstudio-upstream-deb_1.0.136~ppa1_amd64.deb

In the meantime my own institution is migrating from Ubuntu 14.04 trusty to
Debian 9 stretch. Installing rstudio 1.0.136 depends on 3 packages from
Debian 8 jessie:

libgstreamer0.10-0
libgstreamer-plugins-base0.10-0
libssl1.0.0

(As far as I can see via search, other users are running rstudio on Ubuntu
16.04 xenial without additional dependencies from elsewhere.)

As it is "version 1" now, perhaps it has stabilized enough for inclusion in
Debian?

(My users need new R packages, but a version 1 of rstudio will be useful
for a year or two without updates; but that could also go in backports if
possible.)

Regards,
Jan



-- 
  .~.
  /V\ Jan Groenewald
 /( )\www.aims.ac.za
 ^^-^^

Bug#617296: RFP: rstudio -- IDE for GNU R

[Iain R. Learmonth]

Hi,

On Mon, Sep 21, 2015 at 08:25:26AM +0200, Andreas Tille wrote:
> I hope we could settle with RStudio maintained in Debian Science
> repository.  Chen, I accepted your application and it would be great if
> you could merge the repository from collab-maint into the repository in
> Debian Science.  I also kept Debian Med list in CC since there was also
> some interest in RStudio.  If anybody from Debian Med needs commit
> permissions in Debian Science I could easily add these.

Debian Science makes good sense. +1

> Regarding sponsering:  I'd happily sponsor RStudio.  I do not require
> any upload to mentors.debian.net since I build from Debian Science Git
> repository anyway.

Andreas - if you're too busy once the package is ready, I'm also happy to
look at sponsoring this.

Does this RFP include the web-based frontend? I've been looking at getting a
service set up at my University and it would be great if I can do it on a
Pure Debian system.

Thanks,
Iain.

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Bug#617296: RFP: rstudio -- IDE for GNU R

[Andreas Tille]

On Mon, Sep 21, 2015 at 08:41:39AM +0100, Iain R. Learmonth wrote:
> 
> > Regarding sponsering:  I'd happily sponsor RStudio.  I do not require
> > any upload to mentors.debian.net since I build from Debian Science Git
> > repository anyway.
> 
> Andreas - if you're too busy once the package is ready, I'm also happy to
> look at sponsoring this.

Cool.  Any helping hand is welcome.
 
> Does this RFP include the web-based frontend? I've been looking at getting a
> service set up at my University and it would be great if I can do it on a
> Pure Debian system.

I did not checked the packaging - may be you should have a look into the
packaging Git.  My colleagues also need rstudio_server.

Kind regards

Andreas.

-- 
http://fam-tille.de

Bug#617296: RFP: rstudio -- IDE for GNU R

[Andreas Tille]

Hi,

On Mon, Sep 21, 2015 at 02:05:44AM +, nore...@alioth.debian.org wrote:
> ChangZhuo Chen (czchen) has requested to join your project. 
> You can approve this request here: 
> https://alioth.debian.org/project/admin/users.php?group_id=100159 
> 
> Comments by the user:
> I could like to join Debian Science for rstudio.

I guess this request to join Debian Science is a reaction to Bertrand's
hint:

> Thanks ! I just found out there was an other git repository [1]. We
> should have a look and make sure there is no duplicate effort.
> ..
> [1] http://anonscm.debian.org/cgit/debian-science/packages/rstudio.git/

I hope we could settle with RStudio maintained in Debian Science
repository.  Chen, I accepted your application and it would be great if
you could merge the repository from collab-maint into the repository in
Debian Science.  I also kept Debian Med list in CC since there was also
some interest in RStudio.  If anybody from Debian Med needs commit
permissions in Debian Science I could easily add these.

Regarding sponsering:  I'd happily sponsor RStudio.  I do not require
any upload to mentors.debian.net since I build from Debian Science Git
repository anyway.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Bug#617296: RFP: rstudio -- IDE for GNU R

[ChangZhuo Chen]

On Mon, Sep 21, 2015 at 08:25:26AM +0200, Andreas Tille wrote:
> Hi,
> 
> On Mon, Sep 21, 2015 at 02:05:44AM +, nore...@alioth.debian.org wrote:
> > ChangZhuo Chen (czchen) has requested to join your project. 
> > You can approve this request here: 
> > https://alioth.debian.org/project/admin/users.php?group_id=100159 
> > 
> > Comments by the user:
> > I could like to join Debian Science for rstudio.
> 
> I guess this request to join Debian Science is a reaction to Bertrand's
> hint:
> 
> > Thanks ! I just found out there was an other git repository [1]. We
> > should have a look and make sure there is no duplicate effort.
> > ..
> > [1] http://anonscm.debian.org/cgit/debian-science/packages/rstudio.git/
> 
> I hope we could settle with RStudio maintained in Debian Science
> repository.  Chen, I accepted your application and it would be great if
> you could merge the repository from collab-maint into the repository in
> Debian Science.  I also kept Debian Med list in CC since there was also
> some interest in RStudio.  If anybody from Debian Med needs commit
> permissions in Debian Science I could easily add these.

Sure, putting rstudio into Debian Science is better than collab-maint. I
will remove the repository in collab-maint and check the package in
Debian Science repository.

> 
> Regarding sponsering:  I'd happily sponsor RStudio.  I do not require
> any upload to mentors.debian.net since I build from Debian Science Git
> repository anyway.
> 
> Kind regards
> 
>   Andreas.
> 
> -- 
> http://fam-tille.de

-- 
ChangZhuo Chen (陳昌倬) 
Debian Developer
Key fingerprint = EC9F 905D 866D BE46 A896  C827 BE0C 9242 03F4 552D


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Bug#617296: RFP: rstudio -- IDE for GNU R

[Dirk Eddelbuettel]

FWIW I am very good and close friends with the RStudio founders and several
of their engineers.  But most (power R) users I know (myself included)
happily use their dailies from http://www.rstudio.org/download/daily/

It would be a lot of work to get (and keep) this packaged as RStudio found
over the years to often require newer-than-packaged tools like Qt, Boost,
and more. While it would be nice to see it packaged, maybe we have other more
urgent tasks.  Not sure.

Good luck anyway!

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#617296: RFP: rstudio -- IDE for GNU R

[Jan Groenewald]

FWIW I repackage the stable debs (built on Ubuntu 1204) from
https://www.rstudio.com/products/rstudio/  into a PPA here
https://launchpad.net/~aims/+archive/ubuntu/aims-desktop so that my users
install via apt and get updates. I just unpack their deb and repack it as a
binary package with dependencies added. Only the desktop version (not
server version) as we need this to work on student laptops while offline.

Would love to see rstudio in Debian.

Regards,
Jan

On 21 September 2015 at 13:26, Dirk Eddelbuettel  wrote:

>
> FWIW I am very good and close friends with the RStudio founders and several
> of their engineers.  But most (power R) users I know (myself included)
> happily use their dailies from http://www.rstudio.org/download/daily/
>
> It would be a lot of work to get (and keep) this packaged as RStudio found
> over the years to often require newer-than-packaged tools like Qt, Boost,
> and more. While it would be nice to see it packaged, maybe we have other
> more
> urgent tasks.  Not sure.
>
> Good luck anyway!
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>
>


-- 
  .~.
  /V\ Jan Groenewald
 /( )\www.aims.ac.za
 ^^-^^

Bug#617296: RFP: rstudio -- IDE for GNU R

[Bertrand Marc]

Hello Chen,

Thanks ! I just found out there was an other git repository [1]. We
should have a look and make sure there is no duplicate effort.

Regards,
Bertrand


[1] http://anonscm.debian.org/cgit/debian-science/packages/rstudio.git/



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Bug#617296: RFP: rstudio -- IDE for GNU R

[ChangZhuo Chen]

On Sat, Sep 19, 2015 at 02:28:10PM +0200, Bertrand Marc wrote:
> Hi Chen,
> 
> I did not build a complete debian package. I only built rstudio from
> source, using only debian packages as build-dependencies (listed in the
> control file attached to my previous message).
> 
> I needed to tweak a file (see patch attached) to build it without
> downloading external dependencies.
> 
> We still need to check the resources directory and find a way to make
> rstudio use system librairies instead of downloading everything. This
> should probably be asked upstream.

Hi,

I just put all the code from Bertrand to [0]. Need some tweak to make it
buildable.


[0] git://anonscm.debian.org/collab-maint/rstudio.git

> 
> Good luck !
> Bertrand
> 
> Le 19/09/2015 05:45, ChangZhuo Chen a écrit :
> > Hi Bertrand,
> > 
> > Could you provide the full buildable source for rstudio? It will be very
> > useful to make rstudio into Debian. You can upload it to mentor [0] or
> > other source repository.
> > 
> > [0] https://mentors.debian.net/
> > 
> 

> --- CMakeLists.txt2015-09-12 00:51:17.0 +0200
> +++ rstudio-0.99.682/src/cpp/session/CMakeLists.txt   2015-09-16 
> 22:01:49.925022916 +0200
> @@ -19,18 +19,6 @@
>  
>  # verify that install-dictionaries, install-mathjax, install-pandoc,
>  # and install-rmarkdown have been run
> -if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries")
> -  message(FATAL_ERROR "Dictionaries not found (re-run install-dependencies 
> script to install)")
> -endif()
> -if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23")
> -  message(FATAL_ERROR "Mathjax 2.3 not found (re-run install-dependencies 
> script to install)")
> -endif()
> -if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
> -  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script 
> to install)")
> -endif()
> -if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/rsconnect")
> -  message(FATAL_ERROR "rsconnect package not found (re-run 
> install-dependencies script to install)")
> -endif()
>  
>  
>  # verify libclang is installed
> @@ -39,11 +27,11 @@
>  else()
> set(LIBCLANG_VERSION "3.5")
>  endif()
> -set(LIBCLANG_DIR 
> "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
> +set(LIBCLANG_DIR "/usr/lib/llvm-3.5/include/clang/")
>  if(NOT EXISTS "${LIBCLANG_DIR}")
>message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run 
> install-dependencies script to install)")
>  endif()
> -set(LIBCLANG_HEADERS_DIR 
> "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
> +set(LIBCLANG_HEADERS_DIR "/usr/lib/llvm-3.5/include/clang/")
>  if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
>message(FATAL_ERROR "libclang builtin-headers not found  (re-run 
> install-dependencies script to install)")
>  endif()
> @@ -390,14 +378,6 @@
> install(FILES ${R_MODULE_SRC_FILES}
> DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/R/modules)
>  
> -   # install hunspell dictionaries
> -   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries"
> -   DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
> -
> -   # install mathjax for local html preview
> -   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23"
> -   DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
> -
> # install pandoc
> if(RSTUDIO_PACKAGE_BUILD_SLES)
># when producing a SUSE Linux Enterpise build, we want to install the 
> @@ -415,10 +395,6 @@
> install(FILES ${RSCONNECT_PACKAGE}
> DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/R/packages)
>  
> -   # install PDF.js
> -   install(DIRECTORY "resources/pdfjs"
> -   DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
> -
> # install DataTables
> install(DIRECTORY "resources/grid"
> DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
> @@ -427,24 +403,6 @@
> install(DIRECTORY "resources/help_resources"
> DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
>  
> -   # install libclang
> -   if(WIN32)
> -  file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
> -  install(PROGRAMS ${LIBCLANG_32_FILES}
> -  DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
> -  file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
> -  install(PROGRAMS ${LIBCLANG_64_FILES}
> -  DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
> -   else()
> -  file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
> -  install(PROGRAMS ${LIBCLANG_FILES}
> -  DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
> -   endif()
> -
> -   # install libclang builtin-headers
> -   install(DIRECTORY 
> "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
> -   DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
> -
> # install 64 bit binaries if we are on win64
> if(WIN32)
>if(NOT ("$ENV{PROGRAMW6432}" STREQUAL ""))




-- 
ChangZhuo Chen (陳昌倬) 

Bug#617296: RFP: rstudio -- IDE for GNU R

[Bertrand Marc]

Hi Chen,

I did not build a complete debian package. I only built rstudio from
source, using only debian packages as build-dependencies (listed in the
control file attached to my previous message).

I needed to tweak a file (see patch attached) to build it without
downloading external dependencies.

We still need to check the resources directory and find a way to make
rstudio use system librairies instead of downloading everything. This
should probably be asked upstream.

Good luck !
Bertrand

Le 19/09/2015 05:45, ChangZhuo Chen a écrit :
> Hi Bertrand,
> 
> Could you provide the full buildable source for rstudio? It will be very
> useful to make rstudio into Debian. You can upload it to mentor [0] or
> other source repository.
> 
> [0] https://mentors.debian.net/
> 

--- CMakeLists.txt	2015-09-12 00:51:17.0 +0200
+++ rstudio-0.99.682/src/cpp/session/CMakeLists.txt	2015-09-16 22:01:49.925022916 +0200
@@ -19,18 +19,6 @@
 
 # verify that install-dictionaries, install-mathjax, install-pandoc,
 # and install-rmarkdown have been run
-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries")
-  message(FATAL_ERROR "Dictionaries not found (re-run install-dependencies script to install)")
-endif()
-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23")
-  message(FATAL_ERROR "Mathjax 2.3 not found (re-run install-dependencies script to install)")
-endif()
-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
-endif()
-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/rsconnect")
-  message(FATAL_ERROR "rsconnect package not found (re-run install-dependencies script to install)")
-endif()
 
 
 # verify libclang is installed
@@ -39,11 +27,11 @@
 else()
set(LIBCLANG_VERSION "3.5")
 endif()
-set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
+set(LIBCLANG_DIR "/usr/lib/llvm-3.5/include/clang/")
 if(NOT EXISTS "${LIBCLANG_DIR}")
   message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run install-dependencies script to install)")
 endif()
-set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
+set(LIBCLANG_HEADERS_DIR "/usr/lib/llvm-3.5/include/clang/")
 if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
   message(FATAL_ERROR "libclang builtin-headers not found  (re-run install-dependencies script to install)")
 endif()
@@ -390,14 +378,6 @@
install(FILES ${R_MODULE_SRC_FILES}
DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/R/modules)
 
-   # install hunspell dictionaries
-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries"
-   DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
-
-   # install mathjax for local html preview
-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23"
-   DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
-
# install pandoc
if(RSTUDIO_PACKAGE_BUILD_SLES)
   # when producing a SUSE Linux Enterpise build, we want to install the 
@@ -415,10 +395,6 @@
install(FILES ${RSCONNECT_PACKAGE}
DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/R/packages)
 
-   # install PDF.js
-   install(DIRECTORY "resources/pdfjs"
-   DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
-
# install DataTables
install(DIRECTORY "resources/grid"
DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
@@ -427,24 +403,6 @@
install(DIRECTORY "resources/help_resources"
DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
 
-   # install libclang
-   if(WIN32)
-  file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
-  install(PROGRAMS ${LIBCLANG_32_FILES}
-  DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
-  file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
-  install(PROGRAMS ${LIBCLANG_64_FILES}
-  DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
-   else()
-  file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
-  install(PROGRAMS ${LIBCLANG_FILES}
-  DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
-   endif()
-
-   # install libclang builtin-headers
-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
-   DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
-
# install 64 bit binaries if we are on win64
if(WIN32)
   if(NOT ("$ENV{PROGRAMW6432}" STREQUAL ""))


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Bug#617296: RFP: rstudio -- IDE for GNU R

[ChangZhuo Chen]

Hi Bertrand,

Could you provide the full buildable source for rstudio? It will be very
useful to make rstudio into Debian. You can upload it to mentor [0] or
other source repository.

[0] https://mentors.debian.net/

-- 
ChangZhuo Chen (陳昌倬) 
Debian Developer
Key fingerprint = EC9F 905D 866D BE46 A896  C827 BE0C 9242 03F4 552D


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Bug#617296: RFP: rstudio -- IDE for GNU R

[Bertrand Marc]

Hi,

I tried to start from scratch, and was able to build rstudio without
downloading any additional resources. It still needs GWT to run though,
and a way to configure every path to system libraries, dictionaries...

You'll find attached a minimal control file to list the debian
build-deps (and use mk-build-deps). You could configure it with
cmake .. -DCMAKE_BUILD_TYPE=Release -DQT_QMAKE_EXECUTABLE=qmake
-DCMAKE_INSTALL_PREFIX=/usr/lib/

And you need to tweak src/cpp/session/CMakeLists.txt to remove
dependency checking and install.

Regards,
Bertrand

Source: rstudio
Section: gnu-r
Priority: optional
Maintainer: Bertrand Marc 
Build-Depends: debhelper (>= 9), build-essential, pkg-config, fakeroot, cmake,
 uuid-dev, libssl-dev, libbz2-dev, zlib1g-dev, libpam-dev, libxslt1-dev,
 libapparmor1, apparmor-utils, libboost-all-dev (>=1.50), libpango1.0-dev,
 unzip, qt-sdk, qtbase5-dev, libqt5webkit5-dev, qtpositioning5-dev,
 libqt5sensors5-dev, libqt5svg5-dev, libqt5xmlpatterns5-dev,
 libjs-mathjax, libclang-dev, pandoc, hunspell-dictionnaries
Standards-Version: 3.9.6