Re: [Bioc-devel] Logolas package broken for R (3.4) users

2018-08-30 Thread kushal kumar dey 
Thanks so much Valerie and Kasper for the helpful comments...I will look
into the issue as you suggested.

Best

Kushal

On Wednesday, 29 August 2018, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Kasper is right, you can only update code in the current release (Bioc
> 3.7) or devel (Bioc 3.8). Sorry I didn't read your question carefully
> enough. You could, however, use the AMI suggested below to attempt to
> reproduce the reported error.
>
> This is the last build report for Bioc 3.6 and Logolas is not broken:
>
>   https://www.bioconductor.org/checkResults/3.6/bioc-20180412/
>
> If you can reproduce the error (with the AMI) you probably did not have a
> comprehensive set of tests which is why the build report is green. If you
> can't reproduce the error, the people reporting problems may be using
> mismatched R/Bioconductor package versions. The output of their
> sessionInfo() should be informative.
>
> Valerie
>
>
>
> On 08/29/2018 09:45 AM, Kasper Daniel Hansen wrote:
>
> I think the "correct" answer to this, is that it is impossible. Old
> releases are locked.
>
> The way to discover such things is to have appropriate test functions
> which will signal an error if things break.
>
> Best,
> Kasper
>
> On Tue, Aug 28, 2018 at 2:17 PM Obenchain, Valerie  roswellpark.org> wrote:
>
>> You could use an AMI with R 3.4 installed. See the 'AMI IDs' section:
>>
>> https://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids
>>
>> Valerie
>>
>>
>> On 08/27/2018 11:48 AM, kushal kumar dey wrote:
>>
>> Hi,
>>
>> I just found based on user reports that the old version of my package
>> Logolas for R 3.4 and Bioc 3.6 is broken. It does install fine but the
>> main
>> function does not run. Everything seems to be fine however for R 3.5 and
>> Bioc 3.7. I would like to produce either an error message if someone < R
>> 3.5 tries to install Logolas, or to mend the old version. Can you please
>> let me know what is the procedure for either of these cases?
>>
>> Thanks so much.
>>
>> Kushal
>>
>>
>>
>>
>>
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>> agent responsible for the delivery of this message to the intended
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>>
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>
>
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-- 
Kushal K. Dey
Graduate Student
5 th Year, Department of Statistics
University of Chicago
Contact: +1 312-709-0680 | kk...@uchicago.edu

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Re: [Bioc-devel] Logolas package broken for R (3.4) users

2018-08-29 Thread Obenchain, Valerie 
Kasper is right, you can only update code in the current release (Bioc  3.7) or 
devel (Bioc 3.8). Sorry I didn't read your question carefully enough. You 
could, however, use the AMI suggested below to attempt to reproduce the 
reported error.

This is the last build report for Bioc 3.6 and Logolas is not broken:

  https://www.bioconductor.org/checkResults/3.6/bioc-20180412/

If you can reproduce the error (with the AMI) you probably did not have a 
comprehensive set of tests which is why the build report is green. If you can't 
reproduce the error, the people reporting problems may be using mismatched 
R/Bioconductor package versions. The output of their sessionInfo() should be 
informative.

Valerie



On 08/29/2018 09:45 AM, Kasper Daniel Hansen wrote:
I think the "correct" answer to this, is that it is impossible. Old releases 
are locked.

The way to discover such things is to have appropriate test functions which 
will signal an error if things break.

Best,
Kasper

On Tue, Aug 28, 2018 at 2:17 PM Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>> 
wrote:
You could use an AMI with R 3.4 installed. See the 'AMI IDs' section:

https://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids

Valerie


On 08/27/2018 11:48 AM, kushal kumar dey wrote:

Hi,

I just found based on user reports that the old version of my package
Logolas for R 3.4 and Bioc 3.6 is broken. It does install fine but the main
function does not run. Everything seems to be fine however for R 3.5 and
Bioc 3.7. I would like to produce either an error message if someone < R
3.5 tries to install Logolas, or to mend the old version. Can you please
let me know what is the procedure for either of these cases?

Thanks so much.

Kushal





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information.  If you are not the intended recipient(s), or the employee or 
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distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] Logolas package broken for R (3.4) users

2018-08-28 Thread Obenchain, Valerie 
You could use an AMI with R 3.4 installed. See the 'AMI IDs' section:

https://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids

Valerie


On 08/27/2018 11:48 AM, kushal kumar dey wrote:

Hi,

I just found based on user reports that the old version of my package
Logolas for R 3.4 and Bioc 3.6 is broken. It does install fine but the main
function does not run. Everything seems to be fine however for R 3.5 and
Bioc 3.7. I would like to produce either an error message if someone < R
3.5 tries to install Logolas, or to mend the old version. Can you please
let me know what is the procedure for either of these cases?

Thanks so much.

Kushal





This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] Logolas package broken for R (3.4) users

2018-08-27 Thread kushal kumar dey 
Hi,

I just found based on user reports that the old version of my package
Logolas for R 3.4 and Bioc 3.6 is broken. It does install fine but the main
function does not run. Everything seems to be fine however for R 3.5 and
Bioc 3.7. I would like to produce either an error message if someone < R
3.5 tries to install Logolas, or to mend the old version. Can you please
let me know what is the procedure for either of these cases?

Thanks so much.

Kushal

-- 
Kushal K. Dey
Graduate Student
5 th Year, Department of Statistics
University of Chicago
Contact: +1 312-709-0680  | kk...@uchicago.edu

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