Re: [Bioc-devel] release schedule

[Tyler Smith]

Ok, thanks.  

I  nearly  missed  the last one, and had a sudden panic this afternoon
when I realised it was almost time for the next :-)


Best,

Tyler
-- 
plantarum.ca

On Thu, Mar 16, 2017, at 06:55 PM, Obenchain, Valerie wrote:
> Hi Tyler,
> 
> Yes, there is another release coming up. We usually release a day or two
> after R does so we don't set a date until R has announced theirs. As
> soon as we know the R schedule we'll make an announcement on bioc-devel
> and the support site. I'll also post the new release schedule.
> 
> Valerie
> 
> On 03/16/2017 02:53 PM, Tyler Smith wrote:
> > Hi,
> >
> > Is there a deadline for for updates to packages for the next release
> > yet? The webpage hasn't been updated since October
> > (http://bioconductor.org/developers/release-schedule/), but I think
> > there is another release in April?
> >
> > Best,
> >
> > Tyler
> >
> 
> 
> 
> This email message may contain legally privileged and/or confidential
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Re: [Bioc-devel] release schedule

[Obenchain, Valerie]

Hi Tyler,

Yes, there is another release coming up. We usually release a day or two
after R does so we don't set a date until R has announced theirs. As
soon as we know the R schedule we'll make an announcement on bioc-devel
and the support site. I'll also post the new release schedule.

Valerie

On 03/16/2017 02:53 PM, Tyler Smith wrote:
> Hi,
>
> Is there a deadline for for updates to packages for the next release
> yet? The webpage hasn't been updated since October
> (http://bioconductor.org/developers/release-schedule/), but I think
> there is another release in April?
>
> Best,
>
> Tyler
>



This email message may contain legally privileged and/or confidential 
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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 
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[Bioc-devel] release schedule

[Tyler Smith]

Hi,

Is there a deadline for for updates to packages for the next release
yet? The webpage hasn't been updated since October
(http://bioconductor.org/developers/release-schedule/), but I think
there is another release in April?

Best,

Tyler

-- 
plantarum.ca

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Re: [Bioc-devel] Question on the build and biocheck of the package

[Martin Morgan]

On 03/16/2017 01:56 PM, Aayush Raman wrote:

Hello Hervé

Thanks for a quick reply. I have some more questions:

1. This the report of the build of package from Bioconductor:
http://bioconductor.org/spb_reports/DASC_buildreport_20170306051600.html.
Here, you will see *dependencies error* in the tokay2 BUILD SRC output.
Should I include these packages under Depends or Imports is fine ? Just to
make sure, my package uses NMF function from NMF package and another
function from cvxclustr package.

2. I have made some changes in my code (https://github.com/aayushraman/DASC)
and have changed the version to 0.1.1. I would like to know if I have to do
anything else to inform the Single Package Builder to rebuild and check my
package again.


note that versions of packages added to Contributions/issues should be 
0.99.0, 0.99.1, 0.99.2, 


Also, it is appropriate to ask questions specific to your package under 
the github issue associated with your package,


  https://github.com/Bioconductor/Contributions/issues/305

Martin



Thanks,
-Ar


On Thu, Mar 16, 2017 at 11:57 AM, Hervé Pagès  wrote:


Hi Ar,

On 03/15/2017 12:57 AM, Aayush Raman wrote:


Hello Everyone,

I have developed a Bioconductor package and submit the issue to build and
check. I have some questions regarding on the build and BioCheck of the
package. Here are the questions:

1. It has passed the build and check on Mac OS and Windows. However, when
I
am checking it on linux, I am getting the following error:

"ERROR: dependencies ‘NMF’, ‘cvxclustr’ are not available for package
‘DASC’"

Although, I know the NMF and cvxclustr are not present in the linux
machine, I would like to know if it possible to build the package by
installing other packages that my package depends on ? I am already
mentioned it on DESCRIPTION file. Do I need to do anything else before
submitting my package ?



You have these packages listed in your Imports field so they will be
automatically installed by the Single Package Builder on the 3 build
machines if they are not already present.



2. After successfully building (using R CMD build) and checking (R CMD
check), I did a BiocCheck on my package. I got 2 warnings:

a. WARNING: Use FALSE instead of F (found in 1 files)

I am using a function called norm (from base package) where I need to
specify the type. The type I would like to use is Frobenius norm which is
specified by "F/f". How can I remove this warning ? or infom bioconductor
about this warning prior to their checks ?



I don't see this when I run Rbiocdev CMD BiocCheck DASC_0.1.1.tar.gz.
Have you addressed this already? Please note that the way to specify
the type in base::norm() is with a 1-letter *string* ("O", "I", "F",
"M", or "2"). This has nothing to do with the use of F (unquoted) for
specifying the single logical value FALSE.



b. WARNING: Add non-empty \value sections to the following man pages:
data.Rd:

data.Rd is a dataset that I will be uploading with our package. I would
like to know how can I remove this error ?



Man pages for data sets need a \format section instead of a \value
section. If you have one, and R CMD BiocCheck still complains about
the lack of a \value section, please ignore the warning.

Hope this helps,

H.



Any help or advice would be much appreciated.

Thanks,
-Ar

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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] Question on the build and biocheck of the package

[Shepherd, Lori]

Hello,



1. Please ignore the dependency ERROR on tokay2 for now.  Some of this is on 
our end and we are in the process of correcting.


2. You have to make sure the webhook is set up for your package to 
automatically build on version bumps.  If you have not set up the webhook, 
please do so and then make another version bump in the DESCRIPTION file. See 
the instructions here:

https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Aayush Raman 

Sent: Thursday, March 16, 2017 1:56:15 PM
To: Herv� Pag�s
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Question on the build and biocheck of the package

Hello Herv�

Thanks for a quick reply. I have some more questions:

1. This the report of the build of package from Bioconductor:
http://bioconductor.org/spb_reports/DASC_buildreport_20170306051600.html.
Here, you will see *dependencies error* in the tokay2 BUILD SRC output.
Should I include these packages under Depends or Imports is fine ? Just to
make sure, my package uses NMF function from NMF package and another
function from cvxclustr package.

2. I have made some changes in my code (https://github.com/aayushraman/DASC)
and have changed the version to 0.1.1. I would like to know if I have to do
anything else to inform the Single Package Builder to rebuild and check my
package again.

Thanks,
-Ar


On Thu, Mar 16, 2017 at 11:57 AM, Herv� Pag�s  wrote:

> Hi Ar,
>
> On 03/15/2017 12:57 AM, Aayush Raman wrote:
>
>> Hello Everyone,
>>
>> I have developed a Bioconductor package and submit the issue to build and
>> check. I have some questions regarding on the build and BioCheck of the
>> package. Here are the questions:
>>
>> 1. It has passed the build and check on Mac OS and Windows. However, when
>> I
>> am checking it on linux, I am getting the following error:
>>
>> "ERROR: dependencies �NMF�, �cvxclustr� are not available for package
>> �DASC�"
>>
>> Although, I know the NMF and cvxclustr are not present in the linux
>> machine, I would like to know if it possible to build the package by
>> installing other packages that my package depends on ? I am already
>> mentioned it on DESCRIPTION file. Do I need to do anything else before
>> submitting my package ?
>>
>
> You have these packages listed in your Imports field so they will be
> automatically installed by the Single Package Builder on the 3 build
> machines if they are not already present.
>
>
>> 2. After successfully building (using R CMD build) and checking (R CMD
>> check), I did a BiocCheck on my package. I got 2 warnings:
>>
>> a. WARNING: Use FALSE instead of F (found in 1 files)
>>
>> I am using a function called norm (from base package) where I need to
>> specify the type. The type I would like to use is Frobenius norm which is
>> specified by "F/f". How can I remove this warning ? or infom bioconductor
>> about this warning prior to their checks ?
>>
>
> I don't see this when I run Rbiocdev CMD BiocCheck DASC_0.1.1.tar.gz.
> Have you addressed this already? Please note that the way to specify
> the type in base::norm() is with a 1-letter *string* ("O", "I", "F",
> "M", or "2"). This has nothing to do with the use of F (unquoted) for
> specifying the single logical value FALSE.
>
>
>> b. WARNING: Add non-empty \value sections to the following man pages:
>> data.Rd:
>>
>> data.Rd is a dataset that I will be uploading with our package. I would
>> like to know how can I remove this error ?
>>
>
> Man pages for data sets need a \format section instead of a \value
> section. If you have one, and R CMD BiocCheck still complains about
> the lack of a \value section, please ignore the warning.
>
> Hope this helps,
>
> H.
>
>
>> Any help or advice would be much appreciated.
>>
>> Thanks,
>> -Ar
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt
>> 84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Yi
>> ZGNUYd-khI-yvgitdzYaCkX0YYV4RafW040QHUJRo=-ddB-ch5A6i-pe7Q
>> zHb6mH7ARR6Rap0LnufSyE_Qjvg=
>>
>>
> --
> 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
>

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This email 

Re: [Bioc-devel] Question on the build and biocheck of the package

[Aayush Raman]

Hello Hervé

Thanks for a quick reply. I have some more questions:

1. This the report of the build of package from Bioconductor:
http://bioconductor.org/spb_reports/DASC_buildreport_20170306051600.html.
Here, you will see *dependencies error* in the tokay2 BUILD SRC output.
Should I include these packages under Depends or Imports is fine ? Just to
make sure, my package uses NMF function from NMF package and another
function from cvxclustr package.

2. I have made some changes in my code (https://github.com/aayushraman/DASC)
and have changed the version to 0.1.1. I would like to know if I have to do
anything else to inform the Single Package Builder to rebuild and check my
package again.

Thanks,
-Ar


On Thu, Mar 16, 2017 at 11:57 AM, Hervé Pagès  wrote:

> Hi Ar,
>
> On 03/15/2017 12:57 AM, Aayush Raman wrote:
>
>> Hello Everyone,
>>
>> I have developed a Bioconductor package and submit the issue to build and
>> check. I have some questions regarding on the build and BioCheck of the
>> package. Here are the questions:
>>
>> 1. It has passed the build and check on Mac OS and Windows. However, when
>> I
>> am checking it on linux, I am getting the following error:
>>
>> "ERROR: dependencies ‘NMF’, ‘cvxclustr’ are not available for package
>> ‘DASC’"
>>
>> Although, I know the NMF and cvxclustr are not present in the linux
>> machine, I would like to know if it possible to build the package by
>> installing other packages that my package depends on ? I am already
>> mentioned it on DESCRIPTION file. Do I need to do anything else before
>> submitting my package ?
>>
>
> You have these packages listed in your Imports field so they will be
> automatically installed by the Single Package Builder on the 3 build
> machines if they are not already present.
>
>
>> 2. After successfully building (using R CMD build) and checking (R CMD
>> check), I did a BiocCheck on my package. I got 2 warnings:
>>
>> a. WARNING: Use FALSE instead of F (found in 1 files)
>>
>> I am using a function called norm (from base package) where I need to
>> specify the type. The type I would like to use is Frobenius norm which is
>> specified by "F/f". How can I remove this warning ? or infom bioconductor
>> about this warning prior to their checks ?
>>
>
> I don't see this when I run Rbiocdev CMD BiocCheck DASC_0.1.1.tar.gz.
> Have you addressed this already? Please note that the way to specify
> the type in base::norm() is with a 1-letter *string* ("O", "I", "F",
> "M", or "2"). This has nothing to do with the use of F (unquoted) for
> specifying the single logical value FALSE.
>
>
>> b. WARNING: Add non-empty \value sections to the following man pages:
>> data.Rd:
>>
>> data.Rd is a dataset that I will be uploading with our package. I would
>> like to know how can I remove this error ?
>>
>
> Man pages for data sets need a \format section instead of a \value
> section. If you have one, and R CMD BiocCheck still complains about
> the lack of a \value section, please ignore the warning.
>
> Hope this helps,
>
> H.
>
>
>> Any help or advice would be much appreciated.
>>
>> Thanks,
>> -Ar
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt
>> 84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Yi
>> ZGNUYd-khI-yvgitdzYaCkX0YYV4RafW040QHUJRo=-ddB-ch5A6i-pe7Q
>> zHb6mH7ARR6Rap0LnufSyE_Qjvg=
>>
>>
> --
> 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] Question on the build and biocheck of the package

[Hervé Pagès]

Hi Ar,

On 03/15/2017 12:57 AM, Aayush Raman wrote:

Hello Everyone,

I have developed a Bioconductor package and submit the issue to build and
check. I have some questions regarding on the build and BioCheck of the
package. Here are the questions:

1. It has passed the build and check on Mac OS and Windows. However, when I
am checking it on linux, I am getting the following error:

"ERROR: dependencies ‘NMF’, ‘cvxclustr’ are not available for package
‘DASC’"

Although, I know the NMF and cvxclustr are not present in the linux
machine, I would like to know if it possible to build the package by
installing other packages that my package depends on ? I am already
mentioned it on DESCRIPTION file. Do I need to do anything else before
submitting my package ?


You have these packages listed in your Imports field so they will be
automatically installed by the Single Package Builder on the 3 build
machines if they are not already present.



2. After successfully building (using R CMD build) and checking (R CMD
check), I did a BiocCheck on my package. I got 2 warnings:

a. WARNING: Use FALSE instead of F (found in 1 files)

I am using a function called norm (from base package) where I need to
specify the type. The type I would like to use is Frobenius norm which is
specified by "F/f". How can I remove this warning ? or infom bioconductor
about this warning prior to their checks ?


I don't see this when I run Rbiocdev CMD BiocCheck DASC_0.1.1.tar.gz.
Have you addressed this already? Please note that the way to specify
the type in base::norm() is with a 1-letter *string* ("O", "I", "F",
"M", or "2"). This has nothing to do with the use of F (unquoted) for
specifying the single logical value FALSE.



b. WARNING: Add non-empty \value sections to the following man pages:
data.Rd:

data.Rd is a dataset that I will be uploading with our package. I would
like to know how can I remove this error ?


Man pages for data sets need a \format section instead of a \value
section. If you have one, and R CMD BiocCheck still complains about
the lack of a \value section, please ignore the warning.

Hope this helps,

H.



Any help or advice would be much appreciated.

Thanks,
-Ar

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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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[Bioc-devel] Conference: BioC 2017: Where Software and Biology Connect, July 26 - 28, Boston MA

[Martin Morgan]

Developers!

Please join us at our annual conference

  https://bioconductor.org/BioC2017

Consider contributing by proposing a user-oriented workshop or 
community-building birds-of-a-feather session; applications are on the 
conference web site.


See you in Boston!

Martin Morgan
Bioconductor


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[Bioc-devel] Question on the build and biocheck of the package

[Aayush Raman]

Hello Everyone,

I have developed a Bioconductor package and submit the issue to build and
check. I have some questions regarding on the build and BioCheck of the
package. Here are the questions:

1. It has passed the build and check on Mac OS and Windows. However, when I
am checking it on linux, I am getting the following error:

"ERROR: dependencies ‘NMF’, ‘cvxclustr’ are not available for package
‘DASC’"

Although, I know the NMF and cvxclustr are not present in the linux
machine, I would like to know if it possible to build the package by
installing other packages that my package depends on ? I am already
mentioned it on DESCRIPTION file. Do I need to do anything else before
submitting my package ?

2. After successfully building (using R CMD build) and checking (R CMD
check), I did a BiocCheck on my package. I got 2 warnings:

a. WARNING: Use FALSE instead of F (found in 1 files)

I am using a function called norm (from base package) where I need to
specify the type. The type I would like to use is Frobenius norm which is
specified by "F/f". How can I remove this warning ? or infom bioconductor
about this warning prior to their checks ?

b. WARNING: Add non-empty \value sections to the following man pages:
data.Rd:

data.Rd is a dataset that I will be uploading with our package. I would
like to know how can I remove this error ?

Any help or advice would be much appreciated.

Thanks,
-Ar

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