Re: [Bioc-devel] biconductor build error and warning

2016-12-09 Thread Dwivedi, Bhakti 
Hi,

What's the expected time-frame for the Bioconductor package review?

Thank you.

Regards,
Bhakti

From: Dwivedi, Bhakti
Sent: Sunday, December 04, 2016 7:38 PM
To: Dan Tenenbaum <dtene...@fredhutch.org>
Cc: bioc-devel <bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] biconductor build error and warning


Thank you so much Dan!!


From: Dan Tenenbaum <dtene...@fredhutch.org<mailto:dtene...@fredhutch.org>>
Sent: Sunday, December 4, 2016 1:41:59 PM
To: Dwivedi, Bhakti
Cc: bioc-devel
Subject: Re: [Bioc-devel] biconductor build error and warning



- Original Message -
> From: "Bhakti Dwivedi" 
> <bhakti.dwiv...@emory.edu<mailto:bhakti.dwiv...@emory.edu>>
> To: "bioc-devel" <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
> Sent: Sunday, December 4, 2016 6:29:22 AM
> Subject: [Bioc-devel] biconductor build error and warning

> Could anyone please help me with the below two bioconductor build error and
> warnings?
>
>
> I am getting the below ERROR Bioconductor build msg on Mac OS X
> (https://github.com/Bioconductor/Contributions/issues/202)
>
>
> installing the package to build vignettes
> ERROR: dependency HH is not available for package GISPA
>
>

This is because HH depends on Rmpfr which has some system dependencies that are 
not yet installed on that machine; I'm sure a member of the Bioconductor team 
will get to this soon.


> removing
> /private/var/folders/_l/1jpyvgt17qzgj1yz7f0z4np8gr/T/Rtmp939MXS/Rinst16ad7608b810a/GISPA
> ERROR: package installation failed
>
>
> I do not get this ERROR messages when I build, check or install on my Mac OS 
> X.
>
>
> Additionally, I am getting the below warning message:
>
>
> WARNING: Update R version dependency from 3.3.2 to 3.4.
>


This is because your DESCRIPTION file says

Depends: R (>= 3.3.2)

But since you are submitting to the devel branch of Bioconductor, which will 
only work with R-3.4, you should update this to

Depends: R (>= 3.4)

Dan


>
> Appreciate your help and any suggestions to fix them.
>
>
> Thank you.
>
>
> 
>
> This e-mail message (including any attachments) is for...{{dropped:22}}

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Re: [Bioc-devel] biconductor build error and warning

2016-12-05 Thread Dwivedi, Bhakti 
This helps, Thank you so much!


From: Herv� Pag�s <hpa...@fredhutch.org>
Sent: Monday, December 5, 2016 9:16:15 PM
To: Dwivedi, Bhakti
Cc: bioc-devel
Subject: Re: [Bioc-devel] biconductor build error and warning

Hi Bhakti,

Please see my post from October here

   https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009997.html

for why Rmpfr (and thus HH) fails to install on oaxaca.

We're still hoping that the CRAN folks will start providing Mac
binary packages for r-devel soon.

In the meantime please ignore that error on oaxaca.

Cheers,
H.


On 12/04/2016 04:37 PM, Dwivedi, Bhakti wrote:
> Thank you so much Dan!!
>
> 
> From: Dan Tenenbaum <dtene...@fredhutch.org>
> Sent: Sunday, December 4, 2016 1:41:59 PM
> To: Dwivedi, Bhakti
> Cc: bioc-devel
> Subject: Re: [Bioc-devel] biconductor build error and warning
>
>
>
> - Original Message -
>> From: "Bhakti Dwivedi" <bhakti.dwiv...@emory.edu>
>> To: "bioc-devel" <bioc-devel@r-project.org>
>> Sent: Sunday, December 4, 2016 6:29:22 AM
>> Subject: [Bioc-devel] biconductor build error and warning
>
>> Could anyone please help me with the below two bioconductor build error and
>> warnings?
>>
>>
>> I am getting the below ERROR Bioconductor build msg on Mac OS X
>> (https://github.com/Bioconductor/Contributions/issues/202)
>>
>>
>> installing the package to build vignettes
>> ERROR: dependency HH is not available for package GISPA
>>
>>
>
> This is because HH depends on Rmpfr which has some system dependencies that 
> are not yet installed on that machine; I'm sure a member of the Bioconductor 
> team will get to this soon.
>
>
>> removing
>> /private/var/folders/_l/1jpyvgt17qzgj1yz7f0z4np8gr/T/Rtmp939MXS/Rinst16ad7608b810a/GISPA
>> ERROR: package installation failed
>>
>>
>> I do not get this ERROR messages when I build, check or install on my Mac OS 
>> X.
>>
>>
>> Additionally, I am getting the below warning message:
>>
>>
>> WARNING: Update R version dependency from 3.3.2 to 3.4.
>>
>
>
> This is because your DESCRIPTION file says
>
> Depends: R (>= 3.3.2)
>
> But since you are submitting to the devel branch of Bioconductor, which will 
> only work with R-3.4, you should update this to
>
> Depends: R (>= 3.4)
>
> Dan
>
>
>>
>> Appreciate your help and any suggestions to fix them.
>>
>>
>> Thank you.
>>
>>
>> 
>>
>> This e-mail message (including any attachments) is for...{{dropped:22}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

--
Herv� Pag�s

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



This e-mail message (including any attachments) is for t...{{dropped:14}}

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Re: [Bioc-devel] biconductor build error and warning

2016-12-05 Thread Hervé Pagès 

Hi Bhakti,

Please see my post from October here

  https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009997.html

for why Rmpfr (and thus HH) fails to install on oaxaca.

We're still hoping that the CRAN folks will start providing Mac
binary packages for r-devel soon.

In the meantime please ignore that error on oaxaca.

Cheers,
H.


On 12/04/2016 04:37 PM, Dwivedi, Bhakti wrote:

Thank you so much Dan!!


From: Dan Tenenbaum <dtene...@fredhutch.org>
Sent: Sunday, December 4, 2016 1:41:59 PM
To: Dwivedi, Bhakti
Cc: bioc-devel
Subject: Re: [Bioc-devel] biconductor build error and warning



- Original Message -

From: "Bhakti Dwivedi" <bhakti.dwiv...@emory.edu>
To: "bioc-devel" <bioc-devel@r-project.org>
Sent: Sunday, December 4, 2016 6:29:22 AM
Subject: [Bioc-devel] biconductor build error and warning



Could anyone please help me with the below two bioconductor build error and
warnings?


I am getting the below ERROR Bioconductor build msg on Mac OS X
(https://github.com/Bioconductor/Contributions/issues/202)


installing the package to build vignettes
ERROR: dependency HH is not available for package GISPA




This is because HH depends on Rmpfr which has some system dependencies that are 
not yet installed on that machine; I'm sure a member of the Bioconductor team 
will get to this soon.



removing
/private/var/folders/_l/1jpyvgt17qzgj1yz7f0z4np8gr/T/Rtmp939MXS/Rinst16ad7608b810a/GISPA
ERROR: package installation failed


I do not get this ERROR messages when I build, check or install on my Mac OS X.


Additionally, I am getting the below warning message:


WARNING: Update R version dependency from 3.3.2 to 3.4.




This is because your DESCRIPTION file says

Depends: R (>= 3.3.2)

But since you are submitting to the devel branch of Bioconductor, which will 
only work with R-3.4, you should update this to

Depends: R (>= 3.4)

Dan




Appreciate your help and any suggestions to fix them.


Thank you.




This e-mail message (including any attachments) is for...{{dropped:22}}


___
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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

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] biconductor build error and warning

2016-12-04 Thread Dwivedi, Bhakti 
Thank you so much Dan!!


From: Dan Tenenbaum <dtene...@fredhutch.org>
Sent: Sunday, December 4, 2016 1:41:59 PM
To: Dwivedi, Bhakti
Cc: bioc-devel
Subject: Re: [Bioc-devel] biconductor build error and warning



- Original Message -
> From: "Bhakti Dwivedi" <bhakti.dwiv...@emory.edu>
> To: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Sunday, December 4, 2016 6:29:22 AM
> Subject: [Bioc-devel] biconductor build error and warning

> Could anyone please help me with the below two bioconductor build error and
> warnings?
>
>
> I am getting the below ERROR Bioconductor build msg on Mac OS X
> (https://github.com/Bioconductor/Contributions/issues/202)
>
>
> installing the package to build vignettes
> ERROR: dependency HH is not available for package GISPA
>
>

This is because HH depends on Rmpfr which has some system dependencies that are 
not yet installed on that machine; I'm sure a member of the Bioconductor team 
will get to this soon.


> removing
> /private/var/folders/_l/1jpyvgt17qzgj1yz7f0z4np8gr/T/Rtmp939MXS/Rinst16ad7608b810a/GISPA
> ERROR: package installation failed
>
>
> I do not get this ERROR messages when I build, check or install on my Mac OS 
> X.
>
>
> Additionally, I am getting the below warning message:
>
>
> WARNING: Update R version dependency from 3.3.2 to 3.4.
>


This is because your DESCRIPTION file says

Depends: R (>= 3.3.2)

But since you are submitting to the devel branch of Bioconductor, which will 
only work with R-3.4, you should update this to

Depends: R (>= 3.4)

Dan


>
> Appreciate your help and any suggestions to fix them.
>
>
> Thank you.
>
>
> 
>
> This e-mail message (including any attachments) is for...{{dropped:22}}

___
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[Bioc-devel] biconductor build error and warning

2016-12-04 Thread Dwivedi, Bhakti 
Could anyone please help me with the below two bioconductor build error and 
warnings?


I am getting the below ERROR Bioconductor build msg on Mac OS X 
(https://github.com/Bioconductor/Contributions/issues/202)


installing the package to build vignettes
ERROR: dependency HH is not available for package GISPA


removing 
/private/var/folders/_l/1jpyvgt17qzgj1yz7f0z4np8gr/T/Rtmp939MXS/Rinst16ad7608b810a/GISPA
ERROR: package installation failed


I do not get this ERROR messages when I build, check or install on my Mac OS X.


Additionally, I am getting the below warning message:


WARNING: Update R version dependency from 3.3.2 to 3.4.


Appreciate your help and any suggestions to fix them.


Thank you.




This e-mail message (including any attachments) is for t...{{dropped:14}}

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