Re: [Bioc-devel] Version numbers incremented?

[Dan Tenenbaum]

For the record, here is the log message:

Version bump to trigger package rebuilding now that purl()'ing issue
has been correctly identified. knitr does not create purl()'ed
(Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which
the build system was setting. Now it's not set, so these .R files are
now created. See https://github.com/yihui/knitr/issues/1212 for more.

Dan


- Original Message -
> From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>
> To: "Ulrich Bodenhofer" <bodenho...@bioinf.jku.at>
> Cc: "bioc-devel" <bioc-devel@r-project.org>, "msa" <m...@bioinf.jku.at>, 
> keb...@bioinf.jku.at
> Sent: Tuesday, May 17, 2016 7:15:35 AM
> Subject: Re: [Bioc-devel] Version numbers incremented?

> Ulrich, "svn log" does not help you here?
> 
> On Tue, May 17, 2016 at 9:12 AM, Ulrich Bodenhofer <bodenho...@bioinf.jku.at
>> wrote:
> 
>> Thanks, Leonardo! Yes, all my four packages use knitr, while the other
>> eight packages I mentioned use Sweave. So my question is answered and the
>> issue is closed, thanks again! I just wanted to know what happened, since I
>> could not find an explaination why the version numbers have been bumped.
>>
>> Best regards,
>> Ulrich
>>
>>
>> On 05/17/2016 02:17 PM, Leonardo Collado Torres wrote:
>>
>>> Hi,
>>>
>>> Does your package use knitr for creating the vignettes? If so, it must
>>> be because of
>>> https://github.com/lcolladotor/derfinder/commit/c70ede92fb14e83a0fe0032353f7f897ff55b5d5
>>> (the equivalent commit for your package).
>>>
>>> Best,
>>> Leonardo
>>>
>>> On Tue, May 17, 2016 at 4:18 AM, Ulrich Bodenhofer
>>> <bodenho...@bioinf.jku.at> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I just noticed that the version numbers of many (yet not all) packages
>>>> have
>>>> recently been incremented from x.y.0 to x.y.2 both in the devel and in
>>>> the
>>>> release branch. Actually, this affected all four packages I am
>>>> maintaining,
>>>> but strangely none of the other eight packages that are maintained by
>>>> other
>>>> members of my group. As it seems to me, the only change was the version
>>>> number in the DESCRIPTION file itself. What is the reason for that? I'm
>>>> sorry if this subject has been covered already and if I should know
>>>> that. At
>>>> least I could not find any information on the bioc-devel list.
>>>>
>>>> Thanks in advance and best regards,
>>>> Ulrich
>>>>
>>>
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>>
> 
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Re: [Bioc-devel] Version numbers incremented?

[Ulrich Bodenhofer]

Thanks, Kasper and Dan, I already found it. Next time something like 
that happens, I will first check out the logs.


Best regards,
Ulrich


On 05/17/2016 05:09 PM, Dan Tenenbaum wrote:

For the record, here is the log message:

Version bump to trigger package rebuilding now that purl()'ing issue
has been correctly identified. knitr does not create purl()'ed
(Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which
the build system was setting. Now it's not set, so these .R files are
now created. See https://github.com/yihui/knitr/issues/1212 for more.

Dan


- Original Message -

From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>
To: "Ulrich Bodenhofer" <bodenho...@bioinf.jku.at>
Cc: "bioc-devel" <bioc-devel@r-project.org>, "msa" <m...@bioinf.jku.at>, 
keb...@bioinf.jku.at
Sent: Tuesday, May 17, 2016 7:15:35 AM
Subject: Re: [Bioc-devel] Version numbers incremented?
Ulrich, "svn log" does not help you here?

On Tue, May 17, 2016 at 9:12 AM, Ulrich Bodenhofer <bodenho...@bioinf.jku.at

wrote:
Thanks, Leonardo! Yes, all my four packages use knitr, while the other
eight packages I mentioned use Sweave. So my question is answered and the
issue is closed, thanks again! I just wanted to know what happened, since I
could not find an explaination why the version numbers have been bumped.

Best regards,
Ulrich


On 05/17/2016 02:17 PM, Leonardo Collado Torres wrote:


Hi,

Does your package use knitr for creating the vignettes? If so, it must
be because of
https://github.com/lcolladotor/derfinder/commit/c70ede92fb14e83a0fe0032353f7f897ff55b5d5
(the equivalent commit for your package).

Best,
Leonardo

On Tue, May 17, 2016 at 4:18 AM, Ulrich Bodenhofer
<bodenho...@bioinf.jku.at> wrote:


Hi all,

I just noticed that the version numbers of many (yet not all) packages
have
recently been incremented from x.y.0 to x.y.2 both in the devel and in
the
release branch. Actually, this affected all four packages I am
maintaining,
but strangely none of the other eight packages that are maintained by
other
members of my group. As it seems to me, the only change was the version
number in the DESCRIPTION file itself. What is the reason for that? I'm
sorry if this subject has been covered already and if I should know
that. At
least I could not find any information on the bioc-devel list.

Thanks in advance and best regards,
Ulrich



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Re: [Bioc-devel] Version numbers incremented?

[Kasper Daniel Hansen]

Ulrich, "svn log" does not help you here?

On Tue, May 17, 2016 at 9:12 AM, Ulrich Bodenhofer  wrote:

> Thanks, Leonardo! Yes, all my four packages use knitr, while the other
> eight packages I mentioned use Sweave. So my question is answered and the
> issue is closed, thanks again! I just wanted to know what happened, since I
> could not find an explaination why the version numbers have been bumped.
>
> Best regards,
> Ulrich
>
>
> On 05/17/2016 02:17 PM, Leonardo Collado Torres wrote:
>
>> Hi,
>>
>> Does your package use knitr for creating the vignettes? If so, it must
>> be because of
>> https://github.com/lcolladotor/derfinder/commit/c70ede92fb14e83a0fe0032353f7f897ff55b5d5
>> (the equivalent commit for your package).
>>
>> Best,
>> Leonardo
>>
>> On Tue, May 17, 2016 at 4:18 AM, Ulrich Bodenhofer
>>  wrote:
>>
>>> Hi all,
>>>
>>> I just noticed that the version numbers of many (yet not all) packages
>>> have
>>> recently been incremented from x.y.0 to x.y.2 both in the devel and in
>>> the
>>> release branch. Actually, this affected all four packages I am
>>> maintaining,
>>> but strangely none of the other eight packages that are maintained by
>>> other
>>> members of my group. As it seems to me, the only change was the version
>>> number in the DESCRIPTION file itself. What is the reason for that? I'm
>>> sorry if this subject has been covered already and if I should know
>>> that. At
>>> least I could not find any information on the bioc-devel list.
>>>
>>> Thanks in advance and best regards,
>>> Ulrich
>>>
>>
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>

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Re: [Bioc-devel] Version numbers incremented?

[Ulrich Bodenhofer]

Thanks, Leonardo! Yes, all my four packages use knitr, while the other 
eight packages I mentioned use Sweave. So my question is answered and 
the issue is closed, thanks again! I just wanted to know what happened, 
since I could not find an explaination why the version numbers have been 
bumped.


Best regards,
Ulrich


On 05/17/2016 02:17 PM, Leonardo Collado Torres wrote:

Hi,

Does your package use knitr for creating the vignettes? If so, it must
be because of 
https://github.com/lcolladotor/derfinder/commit/c70ede92fb14e83a0fe0032353f7f897ff55b5d5
(the equivalent commit for your package).

Best,
Leonardo

On Tue, May 17, 2016 at 4:18 AM, Ulrich Bodenhofer
 wrote:

Hi all,

I just noticed that the version numbers of many (yet not all) packages have
recently been incremented from x.y.0 to x.y.2 both in the devel and in the
release branch. Actually, this affected all four packages I am maintaining,
but strangely none of the other eight packages that are maintained by other
members of my group. As it seems to me, the only change was the version
number in the DESCRIPTION file itself. What is the reason for that? I'm
sorry if this subject has been covered already and if I should know that. At
least I could not find any information on the bioc-devel list.

Thanks in advance and best regards,
Ulrich


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Re: [Bioc-devel] Version numbers incremented?

[Leonardo Collado Torres]

Hi,

Does your package use knitr for creating the vignettes? If so, it must
be because of 
https://github.com/lcolladotor/derfinder/commit/c70ede92fb14e83a0fe0032353f7f897ff55b5d5
(the equivalent commit for your package).

Best,
Leonardo

On Tue, May 17, 2016 at 4:18 AM, Ulrich Bodenhofer
 wrote:
> Hi all,
>
> I just noticed that the version numbers of many (yet not all) packages have
> recently been incremented from x.y.0 to x.y.2 both in the devel and in the
> release branch. Actually, this affected all four packages I am maintaining,
> but strangely none of the other eight packages that are maintained by other
> members of my group. As it seems to me, the only change was the version
> number in the DESCRIPTION file itself. What is the reason for that? I'm
> sorry if this subject has been covered already and if I should know that. At
> least I could not find any information on the bioc-devel list.
>
> Thanks in advance and best regards,
> Ulrich
>
>
> 
> *Dr. Ulrich Bodenhofer*
> Associate Professor / Institute of Bioinformatics
>
> *JOHANNES KEPLER
> UNIVERSITY LINZ*
> Altenberger Str. 69
> 4040 Linz, Austria
>
> P +43 732 2468 4526
> F +43 732 2468 4539
> bodenho...@bioinf.jku.at 
> www.bioinf.jku.at 
>
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[Bioc-devel] Version numbers incremented?

[Ulrich Bodenhofer]

Hi all,

I just noticed that the version numbers of many (yet not all) packages 
have recently been incremented from x.y.0 to x.y.2 both in the devel and 
in the release branch. Actually, this affected all four packages I am 
maintaining, but strangely none of the other eight packages that are 
maintained by other members of my group. As it seems to me, the only 
change was the version number in the DESCRIPTION file itself. What is 
the reason for that? I'm sorry if this subject has been covered already 
and if I should know that. At least I could not find any information on 
the bioc-devel list.


Thanks in advance and best regards,
Ulrich



*Dr. Ulrich Bodenhofer*
Associate Professor / Institute of Bioinformatics

*JOHANNES KEPLER
UNIVERSITY LINZ*
Altenberger Str. 69
4040 Linz, Austria

P +43 732 2468 4526
F +43 732 2468 4539
bodenho...@bioinf.jku.at 
www.bioinf.jku.at 

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