subject:"Re\: \[Bioc\-devel\] xps build problem on veracruz2"

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-23 Thread cstrato

iginal Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "Dan Tenenbaum"
<dtene...@fredhutch.org>
Cc: "bioc-devel" <bioc-devel@r-project.org>
Sent: Thursday, April 20, 2017 3:17:23 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2

On 04/20/2017 03:01 PM, cstrato wrote:

Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=

This means, that users of xps seem to be willing to disable
csrutil.

I'm not a statistician but I wouldn't draw conclusions from a
sample
of size 1. Mac users who cannot install xps on their machine will
use something else, or, if they desperately need xps, they will
grab a Linux box.

Sorry but disabling SIP on our Mac builders is not an option.

However, I just realized that there may be an even greater
problem,
namely, which version of ROOT should a user install?

People can download ROOT binaries built with XCode 7.x from:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=

for OS X 10.10 and 10.11.

Thus for El Capitan they can download the following binaries:
- root_v5.34.36.macosx64-10.11-clang70.dmg
- root_v5.34.36.macosx64-10.11-clang70.tar.gz

Did you install one of those binaries or did you compile ROOT
from
source?

As I said earlier, I compiled ROOT 5 from source on veracruz2.

With the help of my README file people could compile ROOT from
source
for XCode 8.x.

However, you have mentioned that the CRAN people are using clang
4.0.0
for producing the Mac binaries of R and CRAN packages and thus
you
are
using the same on veracruz2.

Yes.

Did you compile ROOT with XCode 7 or 8 or did you use clang
4.0.0,
which
is not officially supported by Apple?

With clang 4.0.0.

The question is whether xps built with this version of ROOT will
work
with the ROOT binaries which people can download from ROOT?

I guess someone will need to figure this out.

Note that if people need to compile their own ROOT anyway in
order to
be able to use the xps binary we distribute, then they should
also be
able to install xps from source. So that defeats the purpose of
providing a binary in the first place.

Cheers,
H.

Best regards,
Christian

On 04/20/17 20:00, Hervé Pagès wrote:

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but
that

  ^^
oops, no double negative intended here. I meant, doing 'csrutil
disable'
might help... etc

H.

won't help your end users.

I'm no expert in developing a package on Mac but other
people on
this list are. Also R-SIG-Mac might be a good place to seek
help
for this.

Cheers,
H.

On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am
glad to
hear
that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of
people
(when
googling around).

I will try to change the build process and will see if I
succeed.
However, at the moment I have a couple of questions:

1, Is there any reason that you do not want to 'csrutil
disable'?

2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the
'Makefile'.

Since you say that the problem can be solved by adding the
-rpath
flag
when linking, I assume that I have to change  the following
line
in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint
how to
change
it?

3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=

Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the
environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?

4, Googling for the DYLD_LIBRARY_PATH problem I have also
found
the
following discussion:
https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_t

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-23 Thread Hervé Pagès

um"
<dtene...@fredhutch.org>
Cc: "bioc-devel" <bioc-devel@r-project.org>
Sent: Thursday, April 20, 2017 3:17:23 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2

On 04/20/2017 03:01 PM, cstrato wrote:

Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=

This means, that users of xps seem to be willing to disable
csrutil.

I'm not a statistician but I wouldn't draw conclusions from a
sample
of size 1. Mac users who cannot install xps on their machine will
use something else, or, if they desperately need xps, they will
grab a Linux box.

Sorry but disabling SIP on our Mac builders is not an option.

However, I just realized that there may be an even greater
problem,
namely, which version of ROOT should a user install?

People can download ROOT binaries built with XCode 7.x from:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=

for OS X 10.10 and 10.11.

Thus for El Capitan they can download the following binaries:
- root_v5.34.36.macosx64-10.11-clang70.dmg
- root_v5.34.36.macosx64-10.11-clang70.tar.gz

Did you install one of those binaries or did you compile ROOT
from
source?

As I said earlier, I compiled ROOT 5 from source on veracruz2.

With the help of my README file people could compile ROOT from
source
for XCode 8.x.

However, you have mentioned that the CRAN people are using clang
4.0.0
for producing the Mac binaries of R and CRAN packages and thus
you
are
using the same on veracruz2.

Yes.

Did you compile ROOT with XCode 7 or 8 or did you use clang
4.0.0,
which
is not officially supported by Apple?

With clang 4.0.0.

The question is whether xps built with this version of ROOT will
work
with the ROOT binaries which people can download from ROOT?

I guess someone will need to figure this out.

Note that if people need to compile their own ROOT anyway in
order to
be able to use the xps binary we distribute, then they should
also be
able to install xps from source. So that defeats the purpose of
providing a binary in the first place.

Cheers,
H.

Best regards,
Christian

On 04/20/17 20:00, Hervé Pagès wrote:

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but
that

  ^^
oops, no double negative intended here. I meant, doing 'csrutil
disable'
might help... etc

H.

won't help your end users.

I'm no expert in developing a package on Mac but other
people on
this list are. Also R-SIG-Mac might be a good place to seek
help
for this.

Cheers,
H.

On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to
hear
that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of
people
(when
googling around).

I will try to change the build process and will see if I
succeed.
However, at the moment I have a couple of questions:

1, Is there any reason that you do not want to 'csrutil
disable'?

2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the
'Makefile'.

Since you say that the problem can be solved by adding the
-rpath
flag
when linking, I assume that I have to change  the following
line
in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint
how to
change
it?

3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=

Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the
environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?

4, Googling for the DYLD_LIBRARY_PATH problem I have also
found
the
following discussion:
https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_=DwIDaQ=eRAMFD

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-22 Thread Hervé Pagès


Hi Christian,

Thanks for the update. Glad it works for you.

One small thing is that, if CMAKE_INSTALL_PREFIX is specified
when configuring ROOT, the ROOT libs get installed under
/lib/root, not under /lib. I was surprised by
this, but that's what I got when I installed ROOT on veracruz2.
I configured with:

export CC=/usr/local/clang4/bin/clang
export CXX=/usr/local/clang4/bin/clang++
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/root -Dgnuinstall=ON 
-Dfortran=OFF -Dmysql=OFF -Dsqlite=OFF ../root


Then built with:

cmake --build . -- -j4

Then installed with:

sudo cmake --build . --target install

And the libraries got installed under /usr/local/root/lib/root

So when trying to install the latest xps, loading xps.so failed for
me because the ROOT libraries were not found. The following change
to Makefile.arch fixed the problem:

$ svn diff Makefile.arch
Index: Makefile.arch
===
--- Makefile.arch   (revision 129046)
+++ Makefile.arch   (working copy)
@@ -261,7 +261,7 @@
 CXXFLAGS  = $(OPT2) -pipe -Wall -W -Woverloaded-virtual
 LD= $(MACOSXTARGET) g++
 #LDFLAGS   = $(OPT2)
-LDFLAGS   = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib
+LDFLAGS   = $(OPT2) -rpath $(shell $(ROOTCONFIG) --prefix)/lib 
-rpath $(shell $(ROOTCONFIG) --prefix)/lib/root

 UNDEFOPT  = dynamic_lookup
 # The SOFLAGS will be used to create the .dylib,
 # the .so will be created separately

Also note that the rpaths specified at linking time get hardcoded in
xps.so:

veracruz2:src biocbuild$ otool -l xps.so | tail -n 18
Load command 31
  cmd LC_RPATH
  cmdsize 32
 path /usr/local/root/lib (offset 12)
Load command 32
  cmd LC_RPATH
  cmdsize 40
 path /usr/local/root/lib/root (offset 12)
Load command 33
  cmd LC_FUNCTION_STARTS
  cmdsize 16
  dataoff 4141784
 datasize 14336
Load command 34
  cmd LC_DATA_IN_CODE
  cmdsize 16
  dataoff 4156120
 datasize 904

So the end user will need to have the ROOT libraries at these locations
too (unless s/he installs from source of course). This would need to be
explained in xps README file (which BTW should preferably be named
INSTALL).

Thanks,
H.


On 04/22/2017 05:15 AM, cstrato wrote:

Dear Herve,

I am glad to inform you that I have just uploaded version xps_1.35.3 to
BioC-dev branch. I have followed your suggestion to use -rpath and have
eliminated the environment variables DYLD_LIBRARY_PATH and LD_LIBRARY_PATH.

I have tested the new version on both Yosemite and on Sierra with
csrutil enabled! Thus I assume that it will also run on El Capitan.

Best regards,
Christian

P.S.:
Please allow me to comment on your note on [DY]LD_LIBRARY_PATH.
As you know xps was uploaded to Bioc 10 years ago (with your kind help)
and is available on BioC since 9 years.
At that time the environment variables [DY]LD_LIBRARY_PATH were
necessary, and for many years required by ROOT. Since xps did run on the
Mac on all systems from Leopard till Yosemite w/o problems I had no need
to change it.
Furthermore, I had not heard that the use of these variables have been
discouraged, just like many other developers who only now realize that
they have to use rpath or simply disable csrutil (I have realized this
when googling around).



On 04/21/17 00:29, Hervé Pagès wrote:

Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and
has been discouraged for years. xps is the only Bioconductor package
that relies on these variables for its configure/build process.

H.

On 04/20/2017 03:24 PM, Dan Tenenbaum wrote:

Disabling SIP should not be done anywhere. Every page I've read on
this topic strongly discourages doing this.


- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "Dan Tenenbaum"
<dtene...@fredhutch.org>
Cc: "bioc-devel" <bioc-devel@r-project.org>
Sent: Thursday, April 20, 2017 3:17:23 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 04/20/2017 03:01 PM, cstrato wrote:

Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=



This means, that users of xps seem to be willing to disable csrutil.


I'm not a statistician but I wouldn't draw conclusions from a sample
of size 1. Mac users who cannot install xps on their machine will
use something else, or, if they desperately need xps, they will
grab a Linux box.

Sorry but disabling SIP on our Mac builders is not an option.





However, I just realized that there may be an e

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-22 Thread cstrato


Dear Herve,

I am glad to inform you that I have just uploaded version xps_1.35.3 to 
BioC-dev branch. I have followed your suggestion to use -rpath and have 
eliminated the environment variables DYLD_LIBRARY_PATH and LD_LIBRARY_PATH.


I have tested the new version on both Yosemite and on Sierra with 
csrutil enabled! Thus I assume that it will also run on El Capitan.


Best regards,
Christian

P.S.:
Please allow me to comment on your note on [DY]LD_LIBRARY_PATH.
As you know xps was uploaded to Bioc 10 years ago (with your kind help) 
and is available on BioC since 9 years.
At that time the environment variables [DY]LD_LIBRARY_PATH were 
necessary, and for many years required by ROOT. Since xps did run on the 
Mac on all systems from Leopard till Yosemite w/o problems I had no need 
to change it.
Furthermore, I had not heard that the use of these variables have been 
discouraged, just like many other developers who only now realize that 
they have to use rpath or simply disable csrutil (I have realized this 
when googling around).




On 04/21/17 00:29, Hervé Pagès wrote:

Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and
has been discouraged for years. xps is the only Bioconductor package
that relies on these variables for its configure/build process.

H.

On 04/20/2017 03:24 PM, Dan Tenenbaum wrote:

Disabling SIP should not be done anywhere. Every page I've read on
this topic strongly discourages doing this.


- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "Dan Tenenbaum" <dtene...@fredhutch.org>
Cc: "bioc-devel" <bioc-devel@r-project.org>
Sent: Thursday, April 20, 2017 3:17:23 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 04/20/2017 03:01 PM, cstrato wrote:

Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=


This means, that users of xps seem to be willing to disable csrutil.


I'm not a statistician but I wouldn't draw conclusions from a sample
of size 1. Mac users who cannot install xps on their machine will
use something else, or, if they desperately need xps, they will
grab a Linux box.

Sorry but disabling SIP on our Mac builders is not an option.





However, I just realized that there may be an even greater problem,
namely, which version of ROOT should a user install?

People can download ROOT binaries built with XCode 7.x from:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=

for OS X 10.10 and 10.11.

Thus for El Capitan they can download the following binaries:
- root_v5.34.36.macosx64-10.11-clang70.dmg
- root_v5.34.36.macosx64-10.11-clang70.tar.gz

Did you install one of those binaries or did you compile ROOT from
source?


As I said earlier, I compiled ROOT 5 from source on veracruz2.



With the help of my README file people could compile ROOT from source
for XCode 8.x.


However, you have mentioned that the CRAN people are using clang 4.0.0
for producing the Mac binaries of R and CRAN packages and thus you are
using the same on veracruz2.


Yes.



Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0,
which
is not officially supported by Apple?


With clang 4.0.0.



The question is whether xps built with this version of ROOT will work
with the ROOT binaries which people can download from ROOT?


I guess someone will need to figure this out.

Note that if people need to compile their own ROOT anyway in order to
be able to use the xps binary we distribute, then they should also be
able to install xps from source. So that defeats the purpose of
providing a binary in the first place.

Cheers,
H.



Best regards,
Christian



On 04/20/17 20:00, Hervé Pagès wrote:

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that

  ^^
oops, no double negative intended here. I meant, doing 'csrutil
disable'
might help... etc

H.


won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.


On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear
that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-20 Thread Dan Tenenbaum

Disabling SIP should not be done anywhere. Every page I've read on this topic 
strongly discourages doing this.


- Original Message -
> From: "Hervé Pagès" <hpa...@fredhutch.org>
> To: "cstrato" <cstr...@aon.at>, "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Thursday, April 20, 2017 3:17:23 PM
> Subject: Re: [Bioc-devel] xps build problem on veracruz2

> On 04/20/2017 03:01 PM, cstrato wrote:
>> Dear Herve,
>>
>> Doing 'csrutil disable' does indeed solve the problem, since:
>>
>> 1, in this way I was able to build xps on Mac OS Sierra
>>
>> 2, in this way I could already help one user of xps, see:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=
>>
>> This means, that users of xps seem to be willing to disable csrutil.
> 
> I'm not a statistician but I wouldn't draw conclusions from a sample
> of size 1. Mac users who cannot install xps on their machine will
> use something else, or, if they desperately need xps, they will
> grab a Linux box.
> 
> Sorry but disabling SIP on our Mac builders is not an option.
> 
>>
>>
>>
>> However, I just realized that there may be an even greater problem,
>> namely, which version of ROOT should a user install?
>>
>> People can download ROOT binaries built with XCode 7.x from:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=
>> for OS X 10.10 and 10.11.
>>
>> Thus for El Capitan they can download the following binaries:
>> - root_v5.34.36.macosx64-10.11-clang70.dmg
>> - root_v5.34.36.macosx64-10.11-clang70.tar.gz
>>
>> Did you install one of those binaries or did you compile ROOT from source?
> 
> As I said earlier, I compiled ROOT 5 from source on veracruz2.
> 
>>
>> With the help of my README file people could compile ROOT from source
>> for XCode 8.x.
>>
>>
>> However, you have mentioned that the CRAN people are using clang 4.0.0
>> for producing the Mac binaries of R and CRAN packages and thus you are
>> using the same on veracruz2.
> 
> Yes.
> 
>>
>> Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which
>> is not officially supported by Apple?
> 
> With clang 4.0.0.
> 
>>
>> The question is whether xps built with this version of ROOT will work
>> with the ROOT binaries which people can download from ROOT?
> 
> I guess someone will need to figure this out.
> 
> Note that if people need to compile their own ROOT anyway in order to
> be able to use the xps binary we distribute, then they should also be
> able to install xps from source. So that defeats the purpose of
> providing a binary in the first place.
> 
> Cheers,
> H.
> 
>>
>> Best regards,
>> Christian
>>
>>
>>
>> On 04/20/17 20:00, Hervé Pagès wrote:
>>> On 04/20/2017 10:59 AM, Hervé Pagès wrote:
>>>> Hi Christian,
>>>>
>>>> Disabling 'csrutil disable' might help xps on veracruz2 but that
>>>   ^^
>>> oops, no double negative intended here. I meant, doing 'csrutil disable'
>>> might help... etc
>>>
>>> H.
>>>
>>>> won't help your end users.
>>>>
>>>> I'm no expert in developing a package on Mac but other people on
>>>> this list are. Also R-SIG-Mac might be a good place to seek help
>>>> for this.
>>>>
>>>> Cheers,
>>>> H.
>>>>
>>>>
>>>> On 04/20/2017 10:53 AM, cstrato wrote:
>>>>> Dear Herve,
>>>>>
>>>>> Thank you for your efforts to try to install xps. I am glad to hear
>>>>> that
>>>>> you could build ROOT 5 from source.
>>>>>
>>>>> It's a pity that Apple does no longer allow the use of
>>>>> DYLD_LIBRARY_PATH. This seems to break the code of a lot of people
>>>>> (when
>>>>> googling around).
>>>>>
>>>>> I will try to change the build process and will see if I succeed.
>>>>> However, at the moment I have a couple of questions:
&

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-20 Thread Hervé Pagès


Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and
has been discouraged for years. xps is the only Bioconductor package
that relies on these variables for its configure/build process.

H.

On 04/20/2017 03:24 PM, Dan Tenenbaum wrote:

Disabling SIP should not be done anywhere. Every page I've read on this topic 
strongly discourages doing this.


- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "Dan Tenenbaum" <dtene...@fredhutch.org>
Cc: "bioc-devel" <bioc-devel@r-project.org>
Sent: Thursday, April 20, 2017 3:17:23 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 04/20/2017 03:01 PM, cstrato wrote:

Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=

This means, that users of xps seem to be willing to disable csrutil.


I'm not a statistician but I wouldn't draw conclusions from a sample
of size 1. Mac users who cannot install xps on their machine will
use something else, or, if they desperately need xps, they will
grab a Linux box.

Sorry but disabling SIP on our Mac builders is not an option.





However, I just realized that there may be an even greater problem,
namely, which version of ROOT should a user install?

People can download ROOT binaries built with XCode 7.x from:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=
for OS X 10.10 and 10.11.

Thus for El Capitan they can download the following binaries:
- root_v5.34.36.macosx64-10.11-clang70.dmg
- root_v5.34.36.macosx64-10.11-clang70.tar.gz

Did you install one of those binaries or did you compile ROOT from source?


As I said earlier, I compiled ROOT 5 from source on veracruz2.



With the help of my README file people could compile ROOT from source
for XCode 8.x.


However, you have mentioned that the CRAN people are using clang 4.0.0
for producing the Mac binaries of R and CRAN packages and thus you are
using the same on veracruz2.


Yes.



Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which
is not officially supported by Apple?


With clang 4.0.0.



The question is whether xps built with this version of ROOT will work
with the ROOT binaries which people can download from ROOT?


I guess someone will need to figure this out.

Note that if people need to compile their own ROOT anyway in order to
be able to use the xps binary we distribute, then they should also be
able to install xps from source. So that defeats the purpose of
providing a binary in the first place.

Cheers,
H.



Best regards,
Christian



On 04/20/17 20:00, Hervé Pagès wrote:

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that

  ^^
oops, no double negative intended here. I meant, doing 'csrutil disable'
might help... etc

H.


won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.


On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear
that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people
(when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:


1, Is there any reason that you do not want to 'csrutil disable'?


2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since you say that the problem can be solved by adding the -rpath flag
when linking, I assume that I have to change  the following line in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint how to
change
it?


3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=




Interestingly, there is the following line:

'Instead

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-20 Thread Hervé Pagès

On 04/20/2017 03:01 PM, cstrato wrote:

Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=

This means, that users of xps seem to be willing to disable csrutil.

I'm not a statistician but I wouldn't draw conclusions from a sample
of size 1. Mac users who cannot install xps on their machine will
use something else, or, if they desperately need xps, they will
grab a Linux box.

Sorry but disabling SIP on our Mac builders is not an option.

However, I just realized that there may be an even greater problem,
namely, which version of ROOT should a user install?

People can download ROOT binaries built with XCode 7.x from:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=
for OS X 10.10 and 10.11.

Thus for El Capitan they can download the following binaries:
- root_v5.34.36.macosx64-10.11-clang70.dmg
- root_v5.34.36.macosx64-10.11-clang70.tar.gz

Did you install one of those binaries or did you compile ROOT from source?

As I said earlier, I compiled ROOT 5 from source on veracruz2.

With the help of my README file people could compile ROOT from source
for XCode 8.x.

However, you have mentioned that the CRAN people are using clang 4.0.0
for producing the Mac binaries of R and CRAN packages and thus you are
using the same on veracruz2.

Yes.

Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which
is not officially supported by Apple?

With clang 4.0.0.

The question is whether xps built with this version of ROOT will work
with the ROOT binaries which people can download from ROOT?

I guess someone will need to figure this out.

Note that if people need to compile their own ROOT anyway in order to
be able to use the xps binary we distribute, then they should also be
able to install xps from source. So that defeats the purpose of
providing a binary in the first place.

Cheers,
H.

Best regards,
Christian

On 04/20/17 20:00, Hervé Pagès wrote:

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that

^^
oops, no double negative intended here. I meant, doing 'csrutil disable'
might help... etc

won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.

On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear
that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people
(when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:

1, Is there any reason that you do not want to 'csrutil disable'?

2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since you say that the problem can be solved by adding the -rpath flag
when linking, I assume that I have to change the following line in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
$(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint how to
change
it?

3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=

Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?

4, Googling for the DYLD_LIBRARY_PATH problem I have also found the
following discussion:
https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk=

There, one answer mentioned:
'Also, rpath is a good idea. Also

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-20 Thread cstrato


Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://support.bioconductor.org/p/90056/#90247

This means, that users of xps seem to be willing to disable csrutil.



However, I just realized that there may be an even greater problem, 
namely, which version of ROOT should a user install?


People can download ROOT binaries built with XCode 7.x from:
https://root.cern.ch/content/release-53436
for OS X 10.10 and 10.11.

Thus for El Capitan they can download the following binaries:
- root_v5.34.36.macosx64-10.11-clang70.dmg
- root_v5.34.36.macosx64-10.11-clang70.tar.gz

Did you install one of those binaries or did you compile ROOT from source?

With the help of my README file people could compile ROOT from source 
for XCode 8.x.



However, you have mentioned that the CRAN people are using clang 4.0.0 
for producing the Mac binaries of R and CRAN packages and thus you are

using the same on veracruz2.

Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which 
is not officially supported by Apple?


The question is whether xps built with this version of ROOT will work 
with the ROOT binaries which people can download from ROOT?


Best regards,
Christian



On 04/20/17 20:00, Hervé Pagès wrote:

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that

  ^^
oops, no double negative intended here. I meant, doing 'csrutil disable'
might help... etc

H.


won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.


On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:


1, Is there any reason that you do not want to 'csrutil disable'?


2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since you say that the problem can be solved by adding the -rpath flag
when linking, I assume that I have to change  the following line in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint how to change
it?


3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=



Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?


4, Googling for the DYLD_LIBRARY_PATH problem I have also found the
following discussion:
https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk=



There, one answer mentioned:
'Also, rpath is a good idea. Also see install_name_tool, which can
change the load paths of libraries.'

Doing a search for 'install_name_tool' I found:
https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_2985315_using-2Dinstall-2Dname-2Dtool-2Dwhats-2Dgoing-2Dwrong=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=r5LiHlxkGAeJAcciwteD2XD6ffNtWLiknvcIj9EJL8E=



There, one answer mentioned (see also $man install_name_tool):
'Having experimented more: install_name_tool -id newname file will do
the trick.'

See also:
https://urldefense.proofpoint.com/v2/url?u=http-3A__qin.laya.com_tech-5Fcoding-5Fhelp_dylib-5Flinking.html=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=FL17xv1uuzR6UF59mgJstMQ-1seE1UeKDQVVXQgXnUo=




Do you think that either using the environment variable LD_RUN_PATH or
using 'install_name_tool' could solve the problem without having to use
'-rpath'?


Thank you in advance.
Best regards,
Christian



On 04/19/17 22:51, Hervé Pagès wrote:

Hi Christian,

So I installed ROOT 5

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-20 Thread Hervé Pagès

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that

^^
oops, no double negative intended here. I meant, doing 'csrutil disable'
might help... etc

won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.

On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:

1, Is there any reason that you do not want to 'csrutil disable'?

2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since I am not familiar with -rpath can you give me a hint how to change
it?

Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?

There, one answer mentioned:
'Also, rpath is a good idea. Also see install_name_tool, which can
change the load paths of libraries.'

Doing a search for 'install_name_tool' I found:
https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_2985315_using-2Dinstall-2Dname-2Dtool-2Dwhats-2Dgoing-2Dwrong=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=r5LiHlxkGAeJAcciwteD2XD6ffNtWLiknvcIj9EJL8E=

There, one answer mentioned (see also $man install_name_tool):
'Having experimented more: install_name_tool -id newname file will do
the trick.'

See also:
https://urldefense.proofpoint.com/v2/url?u=http-3A__qin.laya.com_tech-5Fcoding-5Fhelp_dylib-5Flinking.html=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=FL17xv1uuzR6UF59mgJstMQ-1seE1UeKDQVVXQgXnUo=

Do you think that either using the environment variable LD_RUN_PATH or
using 'install_name_tool' could solve the problem without having to use
'-rpath'?

Thank you in advance.
Best regards,
Christian

On 04/19/17 22:51, Hervé Pagès wrote:

Hi Christian,

So I installed ROOT 5 from source on veracruz2. It's in
/usr/local/root.

However, Apple's SIP (System Integrity Protection, new and
enabled by default on El Capitan) is getting in the way when
trying to install xps. That's because xps configure and build
process relies on DYLD_LIBRARY_PATH. Problem is that this
environment variable (and any other variables that control
dynamic loading) is not inherited by child processes when SIP
is on:

veracruz2:~ biocbuild$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!';
else echo 'nope!'; fi
yep!

veracruz2:~ biocbuild$ sh
sh-3.2$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo
'nope!'; fi
nope!

That breaks xps configure script:

veracruz2:~ biocbuild$ export LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH

veracruz2:~ biocbuild$ echo $LD_LIBRARY_PATH
/usr/local/mysql/lib:/usr/local/root/lib/root:/ImageMagick-7.0.5/lib:/usr/local/ensembl-vep/htslib

veracruz2:~ biocbuild$ R CMD INSTALL xps
* installing to library
‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘xps’ ...
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-20 Thread Hervé Pagès

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that
won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.

On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:

1, Is there any reason that you do not want to 'csrutil disable'?

2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since I am not familiar with -rpath can you give me a hint how to change
it?

Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?

There, one answer mentioned:
'Also, rpath is a good idea. Also see install_name_tool, which can
change the load paths of libraries.'

There, one answer mentioned (see also $man install_name_tool):
'Having experimented more: install_name_tool -id newname file will do
the trick.'

Do you think that either using the environment variable LD_RUN_PATH or
using 'install_name_tool' could solve the problem without having to use
'-rpath'?

Thank you in advance.
Best regards,
Christian

On 04/19/17 22:51, Hervé Pagès wrote:

Hi Christian,

So I installed ROOT 5 from source on veracruz2. It's in
/usr/local/root.

veracruz2:~ biocbuild$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!';
else echo 'nope!'; fi
yep!

veracruz2:~ biocbuild$ sh
sh-3.2$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo
'nope!'; fi
nope!

That breaks xps configure script:

veracruz2:~ biocbuild$ export LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH

veracruz2:~ biocbuild$ echo $LD_LIBRARY_PATH
/usr/local/mysql/lib:/usr/local/root/lib/root:/ImageMagick-7.0.5/lib:/usr/local/ensembl-vep/htslib

Re: [Bioc-devel] xps build problem on veracruz2

2017-04-19 Thread Hervé Pagès

 revisit xps configure and build process? Make sure
you test it on a machine where SIP is enabled.

Thanks,
H.


On 03/24/2017 12:14 PM, cstrato wrote:



On 03/24/17 19:55, Hervé Pagès wrote:

On 03/24/2017 11:37 AM, cstrato wrote:



On 03/24/17 19:23, Hervé Pagès wrote:

On 03/24/2017 11:10 AM, cstrato wrote:



On 03/24/17 18:02, Hervé Pagès wrote:

On 03/24/2017 06:52 AM, cstrato wrote:

R/Bioc is still building on Mavericks,


Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:



You are right, I did not check R devel.



https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA=






and before was built on Snow
Leopard (which many people are sill using).

Personally I think that it does not make much difference whether
Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.


How much experience you have with setting a Mavericks or El Capitan
build machine to build and distribute thousands of package binaries
for
hundreds ot thousands of users?



You probably misunderstood what I wanted to say.

It is clear to me that you are doing a great job distributing
thousands
of package binaries. No one does know it better than me with the
special
problems you have to build binaries for xps. I really appreciate that
during all these years you and Dan (and others) managed to support xps
like all other BioC packages.

I meant that from the user standpoint it probably does not matter much
which of these three systems are used to build BioC, in contrast to
Sierra.


Of course it matters. If you use an older OS than the one we use to
produce the binaries then some binaries won't work for you. You keep
missing the whole point.

H.



Sorry, but I do understand this point. Users who are still using e.g.
Snow Leopard (because they think this was the best system) will have
problems. For that reason I thought that maybe it is best to use the
system which is currently used by most users.


That would be the thing to do if we didn't have neither forward- nor
backward- compatibility. But we *do* have forward-compatibility. So
there is no reason to use the system which is currently used by most
users. It's enough to make sure that we use a system that is
*compatible* with what most users have. And also not too old because
it's hard to find powerful hardware that runs old OS X versions and
because many software components needed for the builds are not
available or not maintained anymore for old OS X versions.

Like Dan said, it's a tradeoff.

H.



You are right, using a system which is compatible with what most users
have, is the best choice.

Christian





Christian




But as you said below backward-compatibility is always lost, so the
question which system to use to build R/BioC is always tricky. Maybe,
the best (?) decision would be to use the system which most Mac users
are currently using, but I don't know.

Best regards,
Christian



However, Sierra is different, and when the CRAN people are
experimenting
with clang 4.0.0 for producing the Mac binaries, as Herve has
mentioned,
then backwards-compatibility would probably be lost anyhow.


I think you misunderstood what Dan said. Backward-compatibility is
always lost i.e. binaries built on a given OS X versions are not
guaranteed to be backward compatible with older OS X versions. That's
why building them on the latest OS X version is a bad idea.



But I understand that this is a decision the CRAN people have to
make.


You're welcome to discuss this choice on the R-SIG-Mac mailing list.

Cheers,
H.



Best regards,
Christian


On 03/24/17 01:10, Dan Tenenbaum wrote:



- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "bioc-devel"
<bioc-devel@r-project.org>
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 03/23/2017 11:09 AM, cstrato wrote:

Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have
tried it
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and
ROOT 5
was still supported, I have decided to stay with ROOT 5.


OK



BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of
using
the newest OS Sierra? (I have the impression that most Mac users
are
either happy to stay with their old OS or they upgrade to the
newest
one.)


Same reason as for the choice of compilers: that's what the R
folks
decided to use for producing the Mac binaries of R and CRAN
packages.
We're just following their lead on that.



Also, it's always good not to require users to upgrade if they
don't
have to. Building on El Capitan means users will not have to
u

Re: [Bioc-devel] xps build problem on veracruz2

2017-03-24 Thread cstrato




On 03/24/17 19:55, Hervé Pagès wrote:

On 03/24/2017 11:37 AM, cstrato wrote:



On 03/24/17 19:23, Hervé Pagès wrote:

On 03/24/2017 11:10 AM, cstrato wrote:



On 03/24/17 18:02, Hervé Pagès wrote:

On 03/24/2017 06:52 AM, cstrato wrote:

R/Bioc is still building on Mavericks,


Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:



You are right, I did not check R devel.



https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA=





and before was built on Snow
Leopard (which many people are sill using).

Personally I think that it does not make much difference whether
Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.


How much experience you have with setting a Mavericks or El Capitan
build machine to build and distribute thousands of package binaries
for
hundreds ot thousands of users?



You probably misunderstood what I wanted to say.

It is clear to me that you are doing a great job distributing thousands
of package binaries. No one does know it better than me with the
special
problems you have to build binaries for xps. I really appreciate that
during all these years you and Dan (and others) managed to support xps
like all other BioC packages.

I meant that from the user standpoint it probably does not matter much
which of these three systems are used to build BioC, in contrast to
Sierra.


Of course it matters. If you use an older OS than the one we use to
produce the binaries then some binaries won't work for you. You keep
missing the whole point.

H.



Sorry, but I do understand this point. Users who are still using e.g.
Snow Leopard (because they think this was the best system) will have
problems. For that reason I thought that maybe it is best to use the
system which is currently used by most users.


That would be the thing to do if we didn't have neither forward- nor
backward- compatibility. But we *do* have forward-compatibility. So
there is no reason to use the system which is currently used by most
users. It's enough to make sure that we use a system that is
*compatible* with what most users have. And also not too old because
it's hard to find powerful hardware that runs old OS X versions and
because many software components needed for the builds are not
available or not maintained anymore for old OS X versions.

Like Dan said, it's a tradeoff.

H.



You are right, using a system which is compatible with what most users 
have, is the best choice.


Christian





Christian




But as you said below backward-compatibility is always lost, so the
question which system to use to build R/BioC is always tricky. Maybe,
the best (?) decision would be to use the system which most Mac users
are currently using, but I don't know.

Best regards,
Christian



However, Sierra is different, and when the CRAN people are
experimenting
with clang 4.0.0 for producing the Mac binaries, as Herve has
mentioned,
then backwards-compatibility would probably be lost anyhow.


I think you misunderstood what Dan said. Backward-compatibility is
always lost i.e. binaries built on a given OS X versions are not
guaranteed to be backward compatible with older OS X versions. That's
why building them on the latest OS X version is a bad idea.



But I understand that this is a decision the CRAN people have to
make.


You're welcome to discuss this choice on the R-SIG-Mac mailing list.

Cheers,
H.



Best regards,
Christian


On 03/24/17 01:10, Dan Tenenbaum wrote:



- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "bioc-devel"
<bioc-devel@r-project.org>
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 03/23/2017 11:09 AM, cstrato wrote:

Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have
tried it
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and
ROOT 5
was still supported, I have decided to stay with ROOT 5.


OK



BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of
using
the newest OS Sierra? (I have the impression that most Mac users
are
either happy to stay with their old OS or they upgrade to the
newest
one.)


Same reason as for the choice of compilers: that's what the R folks
decided to use for producing the Mac binaries of R and CRAN
packages.
We're just following their lead on that.



Also, it's always good not to require users to upgrade if they don't
have to. Building on El Capitan means users will not have to upgrade
to macOS Sierra if they don't want to. Building on Sierra would
mean R
and packages would not be backwards-compatible with El

Re: [Bioc-devel] xps build problem on veracruz2

2017-03-24 Thread Hervé Pagès


On 03/24/2017 11:37 AM, cstrato wrote:



On 03/24/17 19:23, Hervé Pagès wrote:

On 03/24/2017 11:10 AM, cstrato wrote:



On 03/24/17 18:02, Hervé Pagès wrote:

On 03/24/2017 06:52 AM, cstrato wrote:

R/Bioc is still building on Mavericks,


Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:



You are right, I did not check R devel.



https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA=




and before was built on Snow
Leopard (which many people are sill using).

Personally I think that it does not make much difference whether
Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.


How much experience you have with setting a Mavericks or El Capitan
build machine to build and distribute thousands of package binaries for
hundreds ot thousands of users?



You probably misunderstood what I wanted to say.

It is clear to me that you are doing a great job distributing thousands
of package binaries. No one does know it better than me with the special
problems you have to build binaries for xps. I really appreciate that
during all these years you and Dan (and others) managed to support xps
like all other BioC packages.

I meant that from the user standpoint it probably does not matter much
which of these three systems are used to build BioC, in contrast to
Sierra.


Of course it matters. If you use an older OS than the one we use to
produce the binaries then some binaries won't work for you. You keep
missing the whole point.

H.



Sorry, but I do understand this point. Users who are still using e.g.
Snow Leopard (because they think this was the best system) will have
problems. For that reason I thought that maybe it is best to use the
system which is currently used by most users.


That would be the thing to do if we didn't have neither forward- nor
backward- compatibility. But we *do* have forward-compatibility. So
there is no reason to use the system which is currently used by most
users. It's enough to make sure that we use a system that is
*compatible* with what most users have. And also not too old because
it's hard to find powerful hardware that runs old OS X versions and
because many software components needed for the builds are not
available or not maintained anymore for old OS X versions.

Like Dan said, it's a tradeoff.

H.




Christian




But as you said below backward-compatibility is always lost, so the
question which system to use to build R/BioC is always tricky. Maybe,
the best (?) decision would be to use the system which most Mac users
are currently using, but I don't know.

Best regards,
Christian



However, Sierra is different, and when the CRAN people are
experimenting
with clang 4.0.0 for producing the Mac binaries, as Herve has
mentioned,
then backwards-compatibility would probably be lost anyhow.


I think you misunderstood what Dan said. Backward-compatibility is
always lost i.e. binaries built on a given OS X versions are not
guaranteed to be backward compatible with older OS X versions. That's
why building them on the latest OS X version is a bad idea.



But I understand that this is a decision the CRAN people have to make.


You're welcome to discuss this choice on the R-SIG-Mac mailing list.

Cheers,
H.



Best regards,
Christian


On 03/24/17 01:10, Dan Tenenbaum wrote:



- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "bioc-devel"
<bioc-devel@r-project.org>
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 03/23/2017 11:09 AM, cstrato wrote:

Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have
tried it
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and
ROOT 5
was still supported, I have decided to stay with ROOT 5.


OK



BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of
using
the newest OS Sierra? (I have the impression that most Mac users
are
either happy to stay with their old OS or they upgrade to the
newest
one.)


Same reason as for the choice of compilers: that's what the R folks
decided to use for producing the Mac binaries of R and CRAN
packages.
We're just following their lead on that.



Also, it's always good not to require users to upgrade if they don't
have to. Building on El Capitan means users will not have to upgrade
to macOS Sierra if they don't want to. Building on Sierra would
mean R
and packages would not be backwards-compatible with El Capitan.

But it's a tradeoff that also involves the difficulty of maintaining
build machines with old OSes, and wanting to take advantage of newer
compiler tech

Re: [Bioc-devel] xps build problem on veracruz2

2017-03-24 Thread cstrato




On 03/24/17 19:23, Hervé Pagès wrote:

On 03/24/2017 11:10 AM, cstrato wrote:



On 03/24/17 18:02, Hervé Pagès wrote:

On 03/24/2017 06:52 AM, cstrato wrote:

R/Bioc is still building on Mavericks,


Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:



You are right, I did not check R devel.



https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA=



and before was built on Snow
Leopard (which many people are sill using).

Personally I think that it does not make much difference whether
Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.


How much experience you have with setting a Mavericks or El Capitan
build machine to build and distribute thousands of package binaries for
hundreds ot thousands of users?



You probably misunderstood what I wanted to say.

It is clear to me that you are doing a great job distributing thousands
of package binaries. No one does know it better than me with the special
problems you have to build binaries for xps. I really appreciate that
during all these years you and Dan (and others) managed to support xps
like all other BioC packages.

I meant that from the user standpoint it probably does not matter much
which of these three systems are used to build BioC, in contrast to
Sierra.


Of course it matters. If you use an older OS than the one we use to
produce the binaries then some binaries won't work for you. You keep
missing the whole point.

H.



Sorry, but I do understand this point. Users who are still using e.g. 
Snow Leopard (because they think this was the best system) will have 
problems. For that reason I thought that maybe it is best to use the 
system which is currently used by most users.


Christian




But as you said below backward-compatibility is always lost, so the
question which system to use to build R/BioC is always tricky. Maybe,
the best (?) decision would be to use the system which most Mac users
are currently using, but I don't know.

Best regards,
Christian



However, Sierra is different, and when the CRAN people are
experimenting
with clang 4.0.0 for producing the Mac binaries, as Herve has
mentioned,
then backwards-compatibility would probably be lost anyhow.


I think you misunderstood what Dan said. Backward-compatibility is
always lost i.e. binaries built on a given OS X versions are not
guaranteed to be backward compatible with older OS X versions. That's
why building them on the latest OS X version is a bad idea.



But I understand that this is a decision the CRAN people have to make.


You're welcome to discuss this choice on the R-SIG-Mac mailing list.

Cheers,
H.



Best regards,
Christian


On 03/24/17 01:10, Dan Tenenbaum wrote:



- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "bioc-devel"
<bioc-devel@r-project.org>
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 03/23/2017 11:09 AM, cstrato wrote:

Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have
tried it
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and
ROOT 5
was still supported, I have decided to stay with ROOT 5.


OK



BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of
using
the newest OS Sierra? (I have the impression that most Mac users are
either happy to stay with their old OS or they upgrade to the newest
one.)


Same reason as for the choice of compilers: that's what the R folks
decided to use for producing the Mac binaries of R and CRAN packages.
We're just following their lead on that.



Also, it's always good not to require users to upgrade if they don't
have to. Building on El Capitan means users will not have to upgrade
to macOS Sierra if they don't want to. Building on Sierra would mean R
and packages would not be backwards-compatible with El Capitan.

But it's a tradeoff that also involves the difficulty of maintaining
build machines with old OSes, and wanting to take advantage of newer
compiler technology. Otherwise R/Bioc would still be building on
Mavericks, or Snow Leopard...

Dan



Cheers,
H.



Best regards,
Christian


On 03/23/17 17:47, Hervé Pagès wrote:

Hi Christian,

The CRAN folks are currently experimenting with clang 4.0.0 for
producing the Mac binaries of R and CRAN packages so we are using
the same on veracruz2. This is a version of clang that is ahead of
what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
to compile ROOT from source on veracruz2.

BTW any reason not to make xps work with ROOT 6?

Cheers,
H.

On 03/23/2017 07:28 AM, cstrato wrote:

Dear Valerie,

I

Re: [Bioc-devel] xps build problem on veracruz2

2017-03-24 Thread Hervé Pagès


On 03/24/2017 11:10 AM, cstrato wrote:



On 03/24/17 18:02, Hervé Pagès wrote:

On 03/24/2017 06:52 AM, cstrato wrote:

R/Bioc is still building on Mavericks,


Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:



You are right, I did not check R devel.



https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA=


and before was built on Snow
Leopard (which many people are sill using).

Personally I think that it does not make much difference whether
Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.


How much experience you have with setting a Mavericks or El Capitan
build machine to build and distribute thousands of package binaries for
hundreds ot thousands of users?



You probably misunderstood what I wanted to say.

It is clear to me that you are doing a great job distributing thousands
of package binaries. No one does know it better than me with the special
problems you have to build binaries for xps. I really appreciate that
during all these years you and Dan (and others) managed to support xps
like all other BioC packages.

I meant that from the user standpoint it probably does not matter much
which of these three systems are used to build BioC, in contrast to Sierra.


Of course it matters. If you use an older OS than the one we use to
produce the binaries then some binaries won't work for you. You keep
missing the whole point.

H.



But as you said below backward-compatibility is always lost, so the
question which system to use to build R/BioC is always tricky. Maybe,
the best (?) decision would be to use the system which most Mac users
are currently using, but I don't know.

Best regards,
Christian



However, Sierra is different, and when the CRAN people are experimenting
with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned,
then backwards-compatibility would probably be lost anyhow.


I think you misunderstood what Dan said. Backward-compatibility is
always lost i.e. binaries built on a given OS X versions are not
guaranteed to be backward compatible with older OS X versions. That's
why building them on the latest OS X version is a bad idea.



But I understand that this is a decision the CRAN people have to make.


You're welcome to discuss this choice on the R-SIG-Mac mailing list.

Cheers,
H.



Best regards,
Christian


On 03/24/17 01:10, Dan Tenenbaum wrote:



- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "bioc-devel"
<bioc-devel@r-project.org>
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 03/23/2017 11:09 AM, cstrato wrote:

Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have tried it
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and
ROOT 5
was still supported, I have decided to stay with ROOT 5.


OK



BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of
using
the newest OS Sierra? (I have the impression that most Mac users are
either happy to stay with their old OS or they upgrade to the newest
one.)


Same reason as for the choice of compilers: that's what the R folks
decided to use for producing the Mac binaries of R and CRAN packages.
We're just following their lead on that.



Also, it's always good not to require users to upgrade if they don't
have to. Building on El Capitan means users will not have to upgrade
to macOS Sierra if they don't want to. Building on Sierra would mean R
and packages would not be backwards-compatible with El Capitan.

But it's a tradeoff that also involves the difficulty of maintaining
build machines with old OSes, and wanting to take advantage of newer
compiler technology. Otherwise R/Bioc would still be building on
Mavericks, or Snow Leopard...

Dan



Cheers,
H.



Best regards,
Christian


On 03/23/17 17:47, Hervé Pagès wrote:

Hi Christian,

The CRAN folks are currently experimenting with clang 4.0.0 for
producing the Mac binaries of R and CRAN packages so we are using
the same on veracruz2. This is a version of clang that is ahead of
what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
to compile ROOT from source on veracruz2.

BTW any reason not to make xps work with ROOT 6?

Cheers,
H.

On 03/23/2017 07:28 AM, cstrato wrote:

Dear Valerie,

I have seen that you have set up a new Mac server, veracruz2,
running El
Capitan.

Although the development version of xps does even run on Mac OS
Sierra,
one issue still remains the same:

You need to install the latest ROOT version 5, since xps does not
run
with ROOT 6!

So you need to install on veracruz2 the same

Re: [Bioc-devel] xps build problem on veracruz2

2017-03-24 Thread cstrato




On 03/24/17 18:02, Hervé Pagès wrote:

On 03/24/2017 06:52 AM, cstrato wrote:

R/Bioc is still building on Mavericks,


Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:



You are right, I did not check R devel.


  https://r.research.att.com/


and before was built on Snow
Leopard (which many people are sill using).

Personally I think that it does not make much difference whether
Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.


How much experience you have with setting a Mavericks or El Capitan
build machine to build and distribute thousands of package binaries for
hundreds ot thousands of users?



You probably misunderstood what I wanted to say.

It is clear to me that you are doing a great job distributing thousands 
of package binaries. No one does know it better than me with the special 
problems you have to build binaries for xps. I really appreciate that 
during all these years you and Dan (and others) managed to support xps 
like all other BioC packages.


I meant that from the user standpoint it probably does not matter much 
which of these three systems are used to build BioC, in contrast to Sierra.


But as you said below backward-compatibility is always lost, so the 
question which system to use to build R/BioC is always tricky. Maybe, 
the best (?) decision would be to use the system which most Mac users 
are currently using, but I don't know.


Best regards,
Christian



However, Sierra is different, and when the CRAN people are experimenting
with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned,
then backwards-compatibility would probably be lost anyhow.


I think you misunderstood what Dan said. Backward-compatibility is
always lost i.e. binaries built on a given OS X versions are not
guaranteed to be backward compatible with older OS X versions. That's
why building them on the latest OS X version is a bad idea.



But I understand that this is a decision the CRAN people have to make.


You're welcome to discuss this choice on the R-SIG-Mac mailing list.

Cheers,
H.



Best regards,
Christian


On 03/24/17 01:10, Dan Tenenbaum wrote:



- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "bioc-devel" <bioc-devel@r-project.org>
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 03/23/2017 11:09 AM, cstrato wrote:

Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have tried it
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5
was still supported, I have decided to stay with ROOT 5.


OK



BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of
using
the newest OS Sierra? (I have the impression that most Mac users are
either happy to stay with their old OS or they upgrade to the newest
one.)


Same reason as for the choice of compilers: that's what the R folks
decided to use for producing the Mac binaries of R and CRAN packages.
We're just following their lead on that.



Also, it's always good not to require users to upgrade if they don't
have to. Building on El Capitan means users will not have to upgrade
to macOS Sierra if they don't want to. Building on Sierra would mean R
and packages would not be backwards-compatible with El Capitan.

But it's a tradeoff that also involves the difficulty of maintaining
build machines with old OSes, and wanting to take advantage of newer
compiler technology. Otherwise R/Bioc would still be building on
Mavericks, or Snow Leopard...

Dan



Cheers,
H.



Best regards,
Christian


On 03/23/17 17:47, Hervé Pagès wrote:

Hi Christian,

The CRAN folks are currently experimenting with clang 4.0.0 for
producing the Mac binaries of R and CRAN packages so we are using
the same on veracruz2. This is a version of clang that is ahead of
what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
to compile ROOT from source on veracruz2.

BTW any reason not to make xps work with ROOT 6?

Cheers,
H.

On 03/23/2017 07:28 AM, cstrato wrote:

Dear Valerie,

I have seen that you have set up a new Mac server, veracruz2,
running El
Capitan.

Although the development version of xps does even run on Mac OS
Sierra,
one issue still remains the same:

You need to install the latest ROOT version 5, since xps does not
run
with ROOT 6!

So you need to install on veracruz2 the same root version that you
have
installed on toluca2 running Maverics, i.e.
root_v5.34.36.macosx64-10.11-clang70.dmg

However, if you have installed on El Capitan XCode 8.x instead of
XCode
7.x, then you need to compile ROOT from source, i.e.:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz=DwICAg=eRAMFD45gAfqt84VtB

Re: [Bioc-devel] xps build problem on veracruz2

2017-03-24 Thread Hervé Pagès


On 03/24/2017 06:52 AM, cstrato wrote:

R/Bioc is still building on Mavericks,


Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:

  https://r.research.att.com/


and before was built on Snow
Leopard (which many people are sill using).

Personally I think that it does not make much difference whether
Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.


How much experience you have with setting a Mavericks or El Capitan
build machine to build and distribute thousands of package binaries for
hundreds ot thousands of users?



However, Sierra is different, and when the CRAN people are experimenting
with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned,
then backwards-compatibility would probably be lost anyhow.


I think you misunderstood what Dan said. Backward-compatibility is
always lost i.e. binaries built on a given OS X versions are not
guaranteed to be backward compatible with older OS X versions. That's
why building them on the latest OS X version is a bad idea.



But I understand that this is a decision the CRAN people have to make.


You're welcome to discuss this choice on the R-SIG-Mac mailing list.

Cheers,
H.



Best regards,
Christian


On 03/24/17 01:10, Dan Tenenbaum wrote:



- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "bioc-devel" <bioc-devel@r-project.org>
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 03/23/2017 11:09 AM, cstrato wrote:

Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have tried it
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5
was still supported, I have decided to stay with ROOT 5.


OK



BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of using
the newest OS Sierra? (I have the impression that most Mac users are
either happy to stay with their old OS or they upgrade to the newest
one.)


Same reason as for the choice of compilers: that's what the R folks
decided to use for producing the Mac binaries of R and CRAN packages.
We're just following their lead on that.



Also, it's always good not to require users to upgrade if they don't
have to. Building on El Capitan means users will not have to upgrade
to macOS Sierra if they don't want to. Building on Sierra would mean R
and packages would not be backwards-compatible with El Capitan.

But it's a tradeoff that also involves the difficulty of maintaining
build machines with old OSes, and wanting to take advantage of newer
compiler technology. Otherwise R/Bioc would still be building on
Mavericks, or Snow Leopard...

Dan



Cheers,
H.



Best regards,
Christian


On 03/23/17 17:47, Hervé Pagès wrote:

Hi Christian,

The CRAN folks are currently experimenting with clang 4.0.0 for
producing the Mac binaries of R and CRAN packages so we are using
the same on veracruz2. This is a version of clang that is ahead of
what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
to compile ROOT from source on veracruz2.

BTW any reason not to make xps work with ROOT 6?

Cheers,
H.

On 03/23/2017 07:28 AM, cstrato wrote:

Dear Valerie,

I have seen that you have set up a new Mac server, veracruz2,
running El
Capitan.

Although the development version of xps does even run on Mac OS
Sierra,
one issue still remains the same:

You need to install the latest ROOT version 5, since xps does not run
with ROOT 6!

So you need to install on veracruz2 the same root version that you
have
installed on toluca2 running Maverics, i.e.
root_v5.34.36.macosx64-10.11-clang70.dmg

However, if you have installed on El Capitan XCode 8.x instead of
XCode
7.x, then you need to compile ROOT from source, i.e.:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw=




The README file of xps does explain how to compile ROOT for
Sierra. This
should also be valid for El Capitan running XCode 8.x.

Thank you in advance.
Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a   A.u.s.t.r.i.a
e.m.a.i.l:cstrato at aon.at
_._._._._._._._._._._._._._._._._._

___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU=








--
Hervé Pagès

Program in Computational Biology
Division of Public

Re: [Bioc-devel] xps build problem on veracruz2

2017-03-24 Thread cstrato

R/Bioc is still building on Mavericks, and before was built on Snow 
Leopard (which many people are sill using).


Personally I think that it does not make much difference whether 
Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.


However, Sierra is different, and when the CRAN people are experimenting 
with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned, 
then backwards-compatibility would probably be lost anyhow.


But I understand that this is a decision the CRAN people have to make.

Best regards,
Christian


On 03/24/17 01:10, Dan Tenenbaum wrote:



- Original Message -

From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "cstrato" <cstr...@aon.at>, "bioc-devel" <bioc-devel@r-project.org>
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 03/23/2017 11:09 AM, cstrato wrote:

Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have tried it
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5
was still supported, I have decided to stay with ROOT 5.


OK



BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of using
the newest OS Sierra? (I have the impression that most Mac users are
either happy to stay with their old OS or they upgrade to the newest one.)


Same reason as for the choice of compilers: that's what the R folks
decided to use for producing the Mac binaries of R and CRAN packages.
We're just following their lead on that.



Also, it's always good not to require users to upgrade if they don't have to. 
Building on El Capitan means users will not have to upgrade to macOS Sierra if 
they don't want to. Building on Sierra would mean R and packages would not be 
backwards-compatible with El Capitan.

But it's a tradeoff that also involves the difficulty of maintaining build 
machines with old OSes, and wanting to take advantage of newer compiler 
technology. Otherwise R/Bioc would still be building on Mavericks, or Snow 
Leopard...

Dan



Cheers,
H.



Best regards,
Christian


On 03/23/17 17:47, Hervé Pagès wrote:

Hi Christian,

The CRAN folks are currently experimenting with clang 4.0.0 for
producing the Mac binaries of R and CRAN packages so we are using
the same on veracruz2. This is a version of clang that is ahead of
what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
to compile ROOT from source on veracruz2.

BTW any reason not to make xps work with ROOT 6?

Cheers,
H.

On 03/23/2017 07:28 AM, cstrato wrote:

Dear Valerie,

I have seen that you have set up a new Mac server, veracruz2, running El
Capitan.

Although the development version of xps does even run on Mac OS Sierra,
one issue still remains the same:

You need to install the latest ROOT version 5, since xps does not run
with ROOT 6!

So you need to install on veracruz2 the same root version that you have
installed on toluca2 running Maverics, i.e.
root_v5.34.36.macosx64-10.11-clang70.dmg

However, if you have installed on El Capitan XCode 8.x instead of XCode
7.x, then you need to compile ROOT from source, i.e.:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw=



The README file of xps does explain how to compile ROOT for Sierra. This
should also be valid for El Capitan running XCode 8.x.

Thank you in advance.
Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a   A.u.s.t.r.i.a
e.m.a.i.l:cstrato at aon.at
_._._._._._._._._._._._._._._._._._

___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU=







--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
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Re: [Bioc-devel] xps build problem on veracruz2

2017-03-23 Thread Dan Tenenbaum



- Original Message -
> From: "Hervé Pagès" <hpa...@fredhutch.org>
> To: "cstrato" <cstr...@aon.at>, "bioc-devel" <bioc-devel@r-project.org>
> Sent: Thursday, March 23, 2017 12:14:38 PM
> Subject: Re: [Bioc-devel] xps build problem on veracruz2

> On 03/23/2017 11:09 AM, cstrato wrote:
>> Dear Herve,
>>
>> Thank you for your explanation.
>>
>> The reason that xps does not work with ROOT 6 is that I have tried it
>> but there seem to be so many changes, that I did not succeed.
>> Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5
>> was still supported, I have decided to stay with ROOT 5.
> 
> OK
> 
>>
>> BTW, I have also one question:
>> Why did you decide to set up a new Mac with El Capitan instead of using
>> the newest OS Sierra? (I have the impression that most Mac users are
>> either happy to stay with their old OS or they upgrade to the newest one.)
> 
> Same reason as for the choice of compilers: that's what the R folks
> decided to use for producing the Mac binaries of R and CRAN packages.
> We're just following their lead on that.
> 

Also, it's always good not to require users to upgrade if they don't have to. 
Building on El Capitan means users will not have to upgrade to macOS Sierra if 
they don't want to. Building on Sierra would mean R and packages would not be 
backwards-compatible with El Capitan.

But it's a tradeoff that also involves the difficulty of maintaining build 
machines with old OSes, and wanting to take advantage of newer compiler 
technology. Otherwise R/Bioc would still be building on Mavericks, or Snow 
Leopard...

Dan


> Cheers,
> H.
> 
>>
>> Best regards,
>> Christian
>>
>>
>> On 03/23/17 17:47, Hervé Pagès wrote:
>>> Hi Christian,
>>>
>>> The CRAN folks are currently experimenting with clang 4.0.0 for
>>> producing the Mac binaries of R and CRAN packages so we are using
>>> the same on veracruz2. This is a version of clang that is ahead of
>>> what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
>>> to compile ROOT from source on veracruz2.
>>>
>>> BTW any reason not to make xps work with ROOT 6?
>>>
>>> Cheers,
>>> H.
>>>
>>> On 03/23/2017 07:28 AM, cstrato wrote:
>>>> Dear Valerie,
>>>>
>>>> I have seen that you have set up a new Mac server, veracruz2, running El
>>>> Capitan.
>>>>
>>>> Although the development version of xps does even run on Mac OS Sierra,
>>>> one issue still remains the same:
>>>>
>>>> You need to install the latest ROOT version 5, since xps does not run
>>>> with ROOT 6!
>>>>
>>>> So you need to install on veracruz2 the same root version that you have
>>>> installed on toluca2 running Maverics, i.e.
>>>> root_v5.34.36.macosx64-10.11-clang70.dmg
>>>>
>>>> However, if you have installed on El Capitan XCode 8.x instead of XCode
>>>> 7.x, then you need to compile ROOT from source, i.e.:
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw=
>>>>
>>>>
>>>>
>>>> The README file of xps does explain how to compile ROOT for Sierra. This
>>>> should also be valid for El Capitan running XCode 8.x.
>>>>
>>>> Thank you in advance.
>>>> Best regards,
>>>> Christian
>>>> _._._._._._._._._._._._._._._._._._
>>>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>>>> V.i.e.n.n.a   A.u.s.t.r.i.a
>>>> e.m.a.i.l:cstrato at aon.at
>>>> _._._._._._._._._._._._._._._._._._
>>>>
>>>> ___
>>>> Bioc-devel@r-project.org mailing list
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU=
>>>>
>>>>
>>>>
>>>
> 
> --
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo=

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Re: [Bioc-devel] xps build problem on veracruz2

2017-03-23 Thread Hervé Pagès

On 03/23/2017 11:09 AM, cstrato wrote:

Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have tried it
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5
was still supported, I have decided to stay with ROOT 5.

BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of using
the newest OS Sierra? (I have the impression that most Mac users are
either happy to stay with their old OS or they upgrade to the newest one.)

Same reason as for the choice of compilers: that's what the R folks
decided to use for producing the Mac binaries of R and CRAN packages.
We're just following their lead on that.

Cheers,
H.

Best regards,
Christian

On 03/23/17 17:47, Hervé Pagès wrote:

Hi Christian,

The CRAN folks are currently experimenting with clang 4.0.0 for
producing the Mac binaries of R and CRAN packages so we are using
the same on veracruz2. This is a version of clang that is ahead of
what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
to compile ROOT from source on veracruz2.

BTW any reason not to make xps work with ROOT 6?

Cheers,
H.

On 03/23/2017 07:28 AM, cstrato wrote:

Dear Valerie,

I have seen that you have set up a new Mac server, veracruz2, running El
Capitan.

Although the development version of xps does even run on Mac OS Sierra,
one issue still remains the same:

You need to install the latest ROOT version 5, since xps does not run
with ROOT 6!

So you need to install on veracruz2 the same root version that you have
installed on toluca2 running Maverics, i.e.
root_v5.34.36.macosx64-10.11-clang70.dmg

However, if you have installed on El Capitan XCode 8.x instead of XCode
7.x, then you need to compile ROOT from source, i.e.:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw=

The README file of xps does explain how to compile ROOT for Sierra. This
should also be valid for El Capitan running XCode 8.x.

Thank you in advance.
Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a A.u.s.t.r.i.a
e.m.a.i.l:cstrato at aon.at
_._._._._._._._._._._._._._._._._._

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] xps build problem on veracruz2

2017-03-23 Thread cstrato


Dear Herve,

Thank you for your explanation.

The reason that xps does not work with ROOT 6 is that I have tried it 
but there seem to be so many changes, that I did not succeed.
Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 
was still supported, I have decided to stay with ROOT 5.


BTW, I have also one question:
Why did you decide to set up a new Mac with El Capitan instead of using 
the newest OS Sierra? (I have the impression that most Mac users are 
either happy to stay with their old OS or they upgrade to the newest one.)


Best regards,
Christian


On 03/23/17 17:47, Hervé Pagès wrote:

Hi Christian,

The CRAN folks are currently experimenting with clang 4.0.0 for
producing the Mac binaries of R and CRAN packages so we are using
the same on veracruz2. This is a version of clang that is ahead of
what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
to compile ROOT from source on veracruz2.

BTW any reason not to make xps work with ROOT 6?

Cheers,
H.

On 03/23/2017 07:28 AM, cstrato wrote:

Dear Valerie,

I have seen that you have set up a new Mac server, veracruz2, running El
Capitan.

Although the development version of xps does even run on Mac OS Sierra,
one issue still remains the same:

You need to install the latest ROOT version 5, since xps does not run
with ROOT 6!

So you need to install on veracruz2 the same root version that you have
installed on toluca2 running Maverics, i.e.
root_v5.34.36.macosx64-10.11-clang70.dmg

However, if you have installed on El Capitan XCode 8.x instead of XCode
7.x, then you need to compile ROOT from source, i.e.:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw=


The README file of xps does explain how to compile ROOT for Sierra. This
should also be valid for El Capitan running XCode 8.x.

Thank you in advance.
Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a   A.u.s.t.r.i.a
e.m.a.i.l:cstrato at aon.at
_._._._._._._._._._._._._._._._._._

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Re: [Bioc-devel] xps build problem on veracruz2

2017-03-23 Thread Hervé Pagès


Hi Christian,

The CRAN folks are currently experimenting with clang 4.0.0 for
producing the Mac binaries of R and CRAN packages so we are using
the same on veracruz2. This is a version of clang that is ahead of
what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
to compile ROOT from source on veracruz2.

BTW any reason not to make xps work with ROOT 6?

Cheers,
H.

On 03/23/2017 07:28 AM, cstrato wrote:

Dear Valerie,

I have seen that you have set up a new Mac server, veracruz2, running El
Capitan.

Although the development version of xps does even run on Mac OS Sierra,
one issue still remains the same:

You need to install the latest ROOT version 5, since xps does not run
with ROOT 6!

So you need to install on veracruz2 the same root version that you have
installed on toluca2 running Maverics, i.e.
root_v5.34.36.macosx64-10.11-clang70.dmg

However, if you have installed on El Capitan XCode 8.x instead of XCode
7.x, then you need to compile ROOT from source, i.e.:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw=

The README file of xps does explain how to compile ROOT for Sierra. This
should also be valid for El Capitan running XCode 8.x.

Thank you in advance.
Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a   A.u.s.t.r.i.a
e.m.a.i.l:cstrato at aon.at
_._._._._._._._._._._._._._._._._._

___
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
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Re: [Bioc-devel] xps build problem on veracruz2

2017-03-23 Thread Obenchain, Valerie

Hi,

veracruz2 is in testing / setup stage and is not the official Mac devel
builder. See my post here:

  https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010629.html

Currently there are more pressing issues than the ROOT system
dependency. Rest assured that ROOT will be correctly installed on
veracruz2 when it becomes the official builder, as it was on toluca2
when that machine replaced oaxaca.

Valerie

On 03/23/2017 07:28 AM, cstrato wrote:
> Dear Valerie,
>
> I have seen that you have set up a new Mac server, veracruz2, running El 
> Capitan.
>
> Although the development version of xps does even run on Mac OS Sierra, 
> one issue still remains the same:
>
> You need to install the latest ROOT version 5, since xps does not run 
> with ROOT 6!
>
> So you need to install on veracruz2 the same root version that you have 
> installed on toluca2 running Maverics, i.e. 
> root_v5.34.36.macosx64-10.11-clang70.dmg
>
> However, if you have installed on El Capitan XCode 8.x instead of XCode 
> 7.x, then you need to compile ROOT from source, i.e.:
> https://root.cern.ch/download/root_v5.34.36.source.tar.gz
>
> The README file of xps does explain how to compile ROOT for Sierra. This 
> should also be valid for El Capitan running XCode 8.x.
>
> Thank you in advance.
> Best regards,
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a   A.u.s.t.r.i.a
> e.m.a.i.l:cstrato at aon.at
> _._._._._._._._._._._._._._._._._._
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

Re: [Bioc-devel] xps build problem on veracruz2

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