date:20170423

Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-23 Thread Hervé Pagès


Nothing strange about this. As I said, all packages are built and
checked daily and the build report is updated every day with the new
results. But there is a lag between your changes in svn and what
you see in the build report. More precisely, yesterday's report
didn't reflect your latest changes yet because you made them on
Apr 21 after the builds started.

The 'Snapshot Date' information on the report tells you when the
builds started. Also the 'Last Changed Rev' and 'Last Changed Date'
information tells you which revision of your package is showing up
in the report.

Hope this helps,
H.


On 04/23/2017 06:29 PM, Maia Smith wrote:

Thanks, Hervé. Very strange, when I checked that link earlier today, it
appeared to still have errors. All good now!

On Sun, Apr 23, 2017 at 4:49 PM, Hervé Pagès > wrote:

Hi Maia,

On 04/23/2017 10:09 AM, Maia Smith wrote:

Just an update - the checked in code is passing R CMD check on
my computer
(no errors, 1 warning), and has a version bump from 0.99.9 to
0.99.10, but
I still haven't seen a build attempt on bioconductor since I
committed the
code a few days ago.


Not sure where you are looking at or what you mean exactly by "build
attempt" but, unless our build system is down, every Bioconductor
software package gets built and checked every day. timescape is no
exception:

  https://bioconductor.org/checkResults/3.5/bioc-LATEST/timescape/



Cheers,
H.

I'm a bit worried because I know the release is
occurring tomorrow...

On Sat, Apr 22, 2017 at 3:34 PM, Maia Smith > wrote:

Thank you, Sean and James! I think this fixed the problem,
Sean - will
know when the build is finished today. MUCH appreciated.

On Fri, Apr 21, 2017 at 4:13 PM, Sean Davis
> wrote:

Sorry I lead you astray, earlier, Maia.

In general, you do not need to install the package in
the vignette. The
first code block in the vignette where you did
"eval=FALSE" is the way to
go.  The second code block where you actually do the
installation is
unnecessary. The package is installed by R in order to
build the vignette.

Sean




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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 




--
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] Vignette update after change in git mirror repo

2017-04-23 Thread Maia Smith

Thanks, Hervé. Very strange, when I checked that link earlier today, it
appeared to still have errors. All good now!

On Sun, Apr 23, 2017 at 4:49 PM, Hervé Pagès  wrote:

> Hi Maia,
>
> On 04/23/2017 10:09 AM, Maia Smith wrote:
>
>> Just an update - the checked in code is passing R CMD check on my computer
>> (no errors, 1 warning), and has a version bump from 0.99.9 to 0.99.10, but
>> I still haven't seen a build attempt on bioconductor since I committed the
>> code a few days ago.
>>
>
> Not sure where you are looking at or what you mean exactly by "build
> attempt" but, unless our build system is down, every Bioconductor
> software package gets built and checked every day. timescape is no
> exception:
>
>   https://bioconductor.org/checkResults/3.5/bioc-LATEST/timescape/
>
> Cheers,
> H.
>
> I'm a bit worried because I know the release is
>> occurring tomorrow...
>>
>> On Sat, Apr 22, 2017 at 3:34 PM, Maia Smith  wrote:
>>
>> Thank you, Sean and James! I think this fixed the problem, Sean - will
>>> know when the build is finished today. MUCH appreciated.
>>>
>>> On Fri, Apr 21, 2017 at 4:13 PM, Sean Davis  wrote:
>>>
>>> Sorry I lead you astray, earlier, Maia.

 In general, you do not need to install the package in the vignette. The
 first code block in the vignette where you did "eval=FALSE" is the way
 to
 go.  The second code block where you actually do the installation is
 unnecessary. The package is installed by R in order to build the
 vignette.

 Sean



>>>
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>>
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>> qBONt6vp_Oq6FB3KMJerSAAggLgiauNhROOSs0EzM=
>> Qc0PP8DM7D6TVI78OCfBh9S_0CfQMWRvo-5yiuKfCkA=
>>
>>
> --
> 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] Vignette update after change in git mirror repo

2017-04-23 Thread Hervé Pagès


Hi Maia,

On 04/23/2017 10:09 AM, Maia Smith wrote:

Just an update - the checked in code is passing R CMD check on my computer
(no errors, 1 warning), and has a version bump from 0.99.9 to 0.99.10, but
I still haven't seen a build attempt on bioconductor since I committed the
code a few days ago.


Not sure where you are looking at or what you mean exactly by "build
attempt" but, unless our build system is down, every Bioconductor
software package gets built and checked every day. timescape is no
exception:

  https://bioconductor.org/checkResults/3.5/bioc-LATEST/timescape/

Cheers,
H.


I'm a bit worried because I know the release is
occurring tomorrow...

On Sat, Apr 22, 2017 at 3:34 PM, Maia Smith  wrote:


Thank you, Sean and James! I think this fixed the problem, Sean - will
know when the build is finished today. MUCH appreciated.

On Fri, Apr 21, 2017 at 4:13 PM, Sean Davis  wrote:


Sorry I lead you astray, earlier, Maia.

In general, you do not need to install the package in the vignette. The
first code block in the vignette where you did "eval=FALSE" is the way to
go.  The second code block where you actually do the installation is
unnecessary. The package is installed by R in order to build the vignette.

Sean






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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

2017-04-23 Thread cstrato

Yes, I know.
I wanted only to mention that this error is hopefully corrected in
today's update.

Christian

On 04/23/17 22:19, Hervé Pagès wrote:

On 04/23/2017 12:15 PM, cstrato wrote:

Dear Herve,

I have just seen that the newest build xps_1.3.3:
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_xps_veracruz2-2Dbuildsrc.html=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=mrLGN0PjKvBtL6gLXpX8Q1TVC5RtZNMk4pZamOjQi2o=ZEHBjBTxOazamSZVumdls85OBYuWJInbBU0MEarY2OE=

still results in an error.

Please understand that the build report is lagging behind your latest
activities on the package.

Today's report says:

Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)

and your rpath fix is from this morning:

hpages@latitude:~/svn/bioconductor/Rpacks/xps$ svn log -r 129056

r129056 | c.stratowa | 2017-04-23 08:07:00 -0700 (Sun, 23 Apr 2017) |
2 lines

update to xps-1.35.4
- update rpath

This is probably due to the fact that it still requires $ROOTSYS.
I hope that my current upload xps_1.3.4 has eliminated this dependency
(see my mail below).

Best regards,
Christian

On 04/23/17 17:31, cstrato wrote:

Dear Herve,

Since some users report problems since many years that the libs are
found in '/usr/local/root/lib/root', I agree that it is a good idea
to set LDFLAGS also to
LDFLAGS = ... -rpath $(shell $(ROOTCONFIG) --prefix)/lib/root

I have just uploaded version xps_1.3.4 to BioC devel.

In this version I have added
- LDFLAGS = ... -rpath $(shell $(ROOTCONFIG) --prefix)/lib/root
- Furthermore, I have removed the dependency on the variable $ROOTSYS
in the case ROOT is installed in fixed location.
(see Makefile.arch line 47 and Makefile line 115)
- I have also added an INSTALL file (which I need to update).

I understand that you have built ROOT using the new build system
with 'cmake'. On Yosemite and earlier machines you can (and probably
should) use the old build system using 'make', which is described in:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_build-2Droot-2Dold-2Dmethod=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=mrLGN0PjKvBtL6gLXpX8Q1TVC5RtZNMk4pZamOjQi2o=jpz0-unZsEzxF9QEqOrMLG7y59pLxuv6K_ZqP0gUbmo=

Interestingly, there is the statement:
Using the fixed location mode, the default "--prefix" path is
`/usr/local',
which will result in the ROOT files to be installed in `/usr/local/bin',
`/usr/local/lib/root', etc.

This means probably, that you could use:
cmake -DCMAKE_INSTALL_PREFIX=/usr/local
but maybe you still end up with libs in /usr/local/root/lib/root.

BTW, on Sierra I have just upgraded to the new version R-3.4.0.pkg.
I must realize that R-3.4.0 requires El Capitan or higher, which means
that people using Yosemite or Mavericks can no longer upgrade to the
newest version of R! Is this correct?

Best regards,
Christian

P.S.:
I am not sure if the following information is of interest to you, but I
was looking at my old mails and I searching the ROOT forum, where users
also report problems since the libraries got installed under
/usr/local/root/lib/root:

1, One series of mails is from/to Dan with cc to you from 03/17/12
regarding installing ROOT on openSUSE 12.1. He mentioned that the libs
were stored in /usr/local/root/lib/root. My response was that he only
need to change prefix to "--prefix=/usr/local". However he reported
that the problem was lack of read and listing permissions on the
/etc/root directory.

2, One user recently (Mar 2016) tried to install ROOT 6 on Ubuntu
14.04.4, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root-2Dforum.cern.ch_t_rootn-2Dexe-2Dstartup-2Dcrashes-2Don-2Dubuntu-2D14-2D04-2D4_20825_11=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=mrLGN0PjKvBtL6gLXpX8Q1TVC5RtZNMk4pZamOjQi2o=82sayza_dHZujyTaKcKBVovo-64NMD7uZbfE2W5gMu4=

and reported, e.g. /usr/local/root/lib/root/libCore.so
He then tried:

cmake -DCMAKE_INSTALL_PREFIX="/usr/local"
/home/johnsont/rootsrc/root-6.06.02
cmake --build .
sudo cmake --build . --target install

It seems that now the libraries did install correctly (but there were
other issues).

3, One user had compilation problems on OS Sierra (Oct 2016), see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root-2Dforum.cern.ch_t_compilation-2Dproblem-2Dwith-2Dos-2Dsierra-2Dxcode-2D8-2Droot-2D6-2D06-2D08_22102_6=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=mrLGN0PjKvBtL6gLXpX8Q1TVC5RtZNMk4pZamOjQi2o=hrIBBK0fqAFQNmW8a8vTIHbmcNOB7IVjsclAMGCjKLY=

There was an interesting reply:

Better don't use -j4 when using cmake, just when using make.

I am not sure whether this is still true, since it seems to work in your
case.

On 04/23/17 02:32, Hervé Pagès wrote:

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

2017-04-23 Thread Hervé Pagès

On 04/23/2017 12:15 PM, cstrato wrote:

Dear Herve,

Please understand that the build report is lagging behind your latest
activities on the package.

Today's report says:

Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)

and your rpath fix is from this morning:

hpages@latitude:~/svn/bioconductor/Rpacks/xps$ svn log -r 129056

r129056 | c.stratowa | 2017-04-23 08:07:00 -0700 (Sun, 23 Apr 2017) |
2 lines

update to xps-1.35.4
- update rpath

This is probably due to the fact that it still requires $ROOTSYS.
I hope that my current upload xps_1.3.4 has eliminated this dependency
(see my mail below).

Best regards,
Christian

On 04/23/17 17:31, cstrato wrote:

Dear Herve,

I have just uploaded version xps_1.3.4 to BioC devel.

This means probably, that you could use:
cmake -DCMAKE_INSTALL_PREFIX=/usr/local
but maybe you still end up with libs in /usr/local/root/lib/root.

Best regards,
Christian

and reported, e.g. /usr/local/root/lib/root/libCore.so
He then tried:

cmake -DCMAKE_INSTALL_PREFIX="/usr/local"
/home/johnsont/rootsrc/root-6.06.02
cmake --build .
sudo cmake --build . --target install

It seems that now the libraries did install correctly (but there were
other issues).

There was an interesting reply:

Better don't use -j4 when using cmake, just when using make.

I am not sure whether this is still true, since it seems to work in your
case.

On 04/23/17 02:32, Hervé Pagès wrote:

On 04/22/2017 02:57 PM, cstrato wrote:

Dear Herve,

Thank you for your efforts to get xps running.

I will make the changes in Makefile.arch, too, and update

Re: [Bioc-devel] citation on landing page does not update

2017-04-23 Thread Obenchain, Valerie

Looking at the build logs we see this error for the data package:

ERROR: extractCitations
  tarball:
/home/biocadmin/PACKAGES/3.5/data/experiment/src/contrib/pathprintGEOData_1.0.0.tar.gz
  error: /tmp/Rtmpo8k7A4/pathprintGEOData/inst/CITATION:18:181:
unexpected symbol
17: pages ="68--81",
18: textVersion = paste("Altschuler, G. M., O. Hofmann, I.
Kalatskaya, R. Payne, S. J. Ho Sui, U. Saxena, A. V. Krivtsov, S. A.
Armstrong, T. Cai, L. Stein and W. A. Hide (2013). "Pathprinting

and the same for software:

ERROR: extractCitations
  tarball:
/home/biocadmin/PACKAGES/3.5/bioc/src/contrib/pathprint_1.2.4.tar.gz
  error: 18:181: unexpected symbol
17: pages ="68--81",
18: textVersion = paste("Altschuler, G. M., O. Hofmann, I.
Kalatskaya, R. Payne, S. J. Ho Sui, U. Saxena, A. V. Krivtsov, S. A.
Armstrong, T. Cai, L. Stein and W. A. Hide (2013). "Pathprinting

Replace the double dash with single and it should be fine.

Valerie

On 04/23/2017 05:29 AM, Sokratis Kariotis wrote:
> Dear all,
>
> I have updated the CITATION file in my packages pathprint and
> pathprintGEOData (to be ready for the release), but in the landing page the
> old citation still shows (even the package version in the citation is
> different than the one in the details). How can I mend this? Thanks in
> advance!
>
> https://bioconductor.org/packages/devel/bioc/html/pathprint.html
> https://www.bioconductor.org/packages/devel/data/experiment/html/pathprintGEOData.html
>
> Regards,
> Sokratis Kariotis
>
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Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

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

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

Re: [Bioc-devel] citation on landing page does not update

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