Re: [Bioc-devel] build cache on bioconductor build system?

[Shepherd, Lori]

The single package builder has not built in the functionality to obey this 
particular BBSoption but should be active on the builder once officially 
accepted into Bioconductor.  Your reviewer will be aware of this and be able to 
proceed with the review.


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 Vivek Bhardwaj 

Sent: Thursday, May 31, 2018 11:13:52 AM
To: Herv� Pag�s; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] build cache on bioconductor build system?

The name of my package is icetea. Here's the link
<https://github.com/Bioconductor/Contributions/issues/719> to the
submission. I checked today and VariantAnnotation build was passing now,
so simply re-pushed with bumped version and it worked! (well not
exactly, I still have the RSubread issue with windows that I mentioned
last week, but at least VariantAnnotation is not throwing errors).

@Herv� Regarding the issue with RSubread, I tried adding the .BBSoptions
file in the package source dir. Although I added this file under
.Rbuildignore as well to avoid R CMD check complaining about
non-standard dir. It didn't work.


Thanks for the input everyone.

Best,

Vivek



On 5/30/18 7:31 PM, Herv� Pag�s wrote:
> Hi Vivek,
>
> Are you submitting a package and bumped its version in order to trigger
> a new build? The build system used for the submission is the "Single
> Package Builder" (SPB) and is not the same as the main builder used
> for the daily builds (BBS). It would help if you could provide the link
> to the build report where you see the error or at least the name of
> your package.
>
> On 05/30/2018 07:30 AM, Vivek Bhardwaj wrote:
>>
>> The package throwing error is*VariantAnnotation *(coming from function:
>> locateVariants). I checked it's build for the dev branch and indeed it's
>> broken. **
>>
>> All right then I would remove version specification from my package and
>> I guess I'll wait for**VariantAnnotation to get fixed.
>
> FWIW the latest version of VariantAnnotation in devel is 1.27.1:
>
> https://bioconductor.org/packages/3.8/bioc/html/VariantAnnotation.html
>
> and it passes BUILD and CHECK today on all platforms today.
>
> The SPB sometimes needs to install dependencies that in some rare
> occasion can get stale a few days later. So in a sense yes it can
> cache packages. Lori, our SPB expert, will be able to help you with
> this if you provide the name of your package. Thanks!
>
> H.
>
>>
>> Best,
>> Vivek
>>
>>
>>
>> On 05/30/2018 04:04 PM, Martin Morgan wrote:
>>> There is no cache; like users you get the 'current' version of the
>>> package from the relevant repository. If your package used
>>> concatenateObjects, then it needs to be updated. If your package is
>>> broken through a third package, it needs to be fixed (perhaps it has
>>> been but did not propagate, see the build reports for packages in the
>>> devel branch
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=XilqVN5SNnjEa4_siRsVQPa3EsNEK53OKM7n156DDnc=nghjJ8CDqIvM9dcgTCxhGrxP3XlnGhurWc5aREDAIyk=
>>> , and look for the
>>> stoplight at the right).
>>>
>>> Martin
>>>
>>> On 05/30/2018 09:56 AM, Vivek Bhardwaj wrote:
>>>> Hi All
>>>>
>>>> Is there any build cache on bioc build system? I updated S4Vector and
>>>> IRanges in my dependencies and triggered a new build of my package,
>>>> only
>>>> to find that this broke other dependencies due to renaming of function
>>>> `concatenateObjects ` to `bindRows` in S4Vector. Now I removed the
>>>> mentioned versions in my DESCRIPTION, but the build is still broken.
>>>> Also tried specifying a particular version of these packages and I get
>>>> the error :
>>>>
>>>> ** byte-compile and prepare package for lazy loading Error in
>>>> loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
>>>> vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but ==
>>>> 2.14.10
>>>> is required
>>>>
>>>> How do I refresh the cache?
>>>>
>>>
>>>
>>> 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
>>&g

Re: [Bioc-devel] build cache on bioconductor build system?

[Vivek Bhardwaj]

The name of my package is icetea. Here's the link 
 to the 
submission. I checked today and VariantAnnotation build was passing now, 
so simply re-pushed with bumped version and it worked! (well not 
exactly, I still have the RSubread issue with windows that I mentioned 
last week, but at least VariantAnnotation is not throwing errors).

@Hervé Regarding the issue with RSubread, I tried adding the .BBSoptions 
file in the package source dir. Although I added this file under 
.Rbuildignore as well to avoid R CMD check complaining about 
non-standard dir. It didn't work.


Thanks for the input everyone.

Best,

Vivek



On 5/30/18 7:31 PM, Hervé Pagès wrote:
> Hi Vivek,
>
> Are you submitting a package and bumped its version in order to trigger
> a new build? The build system used for the submission is the "Single
> Package Builder" (SPB) and is not the same as the main builder used
> for the daily builds (BBS). It would help if you could provide the link
> to the build report where you see the error or at least the name of
> your package.
>
> On 05/30/2018 07:30 AM, Vivek Bhardwaj wrote:
>>
>> The package throwing error is*VariantAnnotation *(coming from function:
>> locateVariants). I checked it's build for the dev branch and indeed it's
>> broken. **
>>
>> All right then I would remove version specification from my package and
>> I guess I'll wait for**VariantAnnotation to get fixed.
>
> FWIW the latest version of VariantAnnotation in devel is 1.27.1:
>
> https://bioconductor.org/packages/3.8/bioc/html/VariantAnnotation.html
>
> and it passes BUILD and CHECK today on all platforms today.
>
> The SPB sometimes needs to install dependencies that in some rare
> occasion can get stale a few days later. So in a sense yes it can
> cache packages. Lori, our SPB expert, will be able to help you with
> this if you provide the name of your package. Thanks!
>
> H.
>
>>
>> Best,
>> Vivek
>>
>>
>>
>> On 05/30/2018 04:04 PM, Martin Morgan wrote:
>>> There is no cache; like users you get the 'current' version of the
>>> package from the relevant repository. If your package used
>>> concatenateObjects, then it needs to be updated. If your package is
>>> broken through a third package, it needs to be fixed (perhaps it has
>>> been but did not propagate, see the build reports for packages in the
>>> devel branch 
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=XilqVN5SNnjEa4_siRsVQPa3EsNEK53OKM7n156DDnc=nghjJ8CDqIvM9dcgTCxhGrxP3XlnGhurWc5aREDAIyk=
>>>  
>>> , and look for the
>>> stoplight at the right).
>>>
>>> Martin
>>>
>>> On 05/30/2018 09:56 AM, Vivek Bhardwaj wrote:
 Hi All

 Is there any build cache on bioc build system? I updated S4Vector and
 IRanges in my dependencies and triggered a new build of my package, 
 only
 to find that this broke other dependencies due to renaming of function
 `concatenateObjects ` to `bindRows` in S4Vector. Now I removed the
 mentioned versions in my DESCRIPTION, but the build is still broken.
 Also tried specifying a particular version of these packages and I get
 the error :

 ** byte-compile and prepare package for lazy loading Error in
 loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
 vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but == 
 2.14.10
 is required

 How do I refresh the cache?

>>>
>>>
>>> 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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Re: [Bioc-devel] build cache on bioconductor build system?

[Hervé Pagès]

Hi Vivek,

Are you submitting a package and bumped its version in order to trigger
a new build? The build system used for the submission is the "Single
Package Builder" (SPB) and is not the same as the main builder used
for the daily builds (BBS). It would help if you could provide the link
to the build report where you see the error or at least the name of
your package.

On 05/30/2018 07:30 AM, Vivek Bhardwaj wrote:


The package throwing error is*VariantAnnotation *(coming from function:
locateVariants). I checked it's build for the dev branch and indeed it's
broken. **

All right then I would remove version specification from my package and
I guess I'll wait for**VariantAnnotation to get fixed.


FWIW the latest version of VariantAnnotation in devel is 1.27.1:

  https://bioconductor.org/packages/3.8/bioc/html/VariantAnnotation.html

and it passes BUILD and CHECK today on all platforms today.

The SPB sometimes needs to install dependencies that in some rare
occasion can get stale a few days later. So in a sense yes it can
cache packages. Lori, our SPB expert, will be able to help you with
this if you provide the name of your package. Thanks!

H.



Best,
Vivek



On 05/30/2018 04:04 PM, Martin Morgan wrote:

There is no cache; like users you get the 'current' version of the
package from the relevant repository. If your package used
concatenateObjects, then it needs to be updated. If your package is
broken through a third package, it needs to be fixed (perhaps it has
been but did not propagate, see the build reports for packages in the
devel branch 
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=XilqVN5SNnjEa4_siRsVQPa3EsNEK53OKM7n156DDnc=nghjJ8CDqIvM9dcgTCxhGrxP3XlnGhurWc5aREDAIyk=
 , and look for the
stoplight at the right).

Martin

On 05/30/2018 09:56 AM, Vivek Bhardwaj wrote:

Hi All

Is there any build cache on bioc build system? I updated S4Vector and
IRanges in my dependencies and triggered a new build of my package, only
to find that this broke other dependencies due to renaming of function
`concatenateObjects ` to `bindRows` in S4Vector. Now I removed the
mentioned versions in my DESCRIPTION, but the build is still broken.
Also tried specifying a particular version of these packages and I get
the error :

** byte-compile and prepare package for lazy loading Error in
loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but == 2.14.10
is required

How do I refresh the cache?




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.





--
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] build cache on bioconductor build system?

[Vivek Bhardwaj]

The package throwing error is*VariantAnnotation *(coming from function: 
locateVariants). I checked it's build for the dev branch and indeed it's 
broken. **

All right then I would remove version specification from my package and 
I guess I'll wait for**VariantAnnotation to get fixed.

Best,
Vivek



On 05/30/2018 04:04 PM, Martin Morgan wrote:
> There is no cache; like users you get the 'current' version of the 
> package from the relevant repository. If your package used 
> concatenateObjects, then it needs to be updated. If your package is 
> broken through a third package, it needs to be fixed (perhaps it has 
> been but did not propagate, see the build reports for packages in the 
> devel branch http://bioconductor.org/checkResults/ , and look for the 
> stoplight at the right).
>
> Martin
>
> On 05/30/2018 09:56 AM, Vivek Bhardwaj wrote:
>> Hi All
>>
>> Is there any build cache on bioc build system? I updated S4Vector and
>> IRanges in my dependencies and triggered a new build of my package, only
>> to find that this broke other dependencies due to renaming of function
>> `concatenateObjects ` to `bindRows` in S4Vector. Now I removed the
>> mentioned versions in my DESCRIPTION, but the build is still broken.
>> Also tried specifying a particular version of these packages and I get
>> the error :
>>
>> ** byte-compile and prepare package for lazy loading Error in
>> loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
>> vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but == 2.14.10
>> is required
>>
>> How do I refresh the cache?
>>
>
>
> 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.


-- 

Best Wishes
Vivek



*Vivek Bhardwaj*
PhD Candidate | International Max Planck Research School
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51, Freiburg
E-mail: bhard...@ie-freiburg.mpg.de
Tel: +49-761-5108-472
Website: https://vivekbhr.github.io

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Re: [Bioc-devel] build cache on bioconductor build system?

[Martin Morgan]

There is no cache; like users you get the 'current' version of the 
package from the relevant repository. If your package used 
concatenateObjects, then it needs to be updated. If your package is 
broken through a third package, it needs to be fixed (perhaps it has 
been but did not propagate, see the build reports for packages in the 
devel branch http://bioconductor.org/checkResults/ , and look for the 
stoplight at the right).


Martin

On 05/30/2018 09:56 AM, Vivek Bhardwaj wrote:

Hi All

Is there any build cache on bioc build system? I updated S4Vector and
IRanges in my dependencies and triggered a new build of my package, only
to find that this broke other dependencies due to renaming of function
`concatenateObjects ` to `bindRows` in S4Vector. Now I removed the
mentioned versions in my DESCRIPTION, but the build is still broken.
Also tried specifying a particular version of these packages and I get
the error :

** byte-compile and prepare package for lazy loading Error in
loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but == 2.14.10
is required

How do I refresh the cache?




This email message may contain legally privileged and/or...{{dropped:2}}

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[Bioc-devel] build cache on bioconductor build system?

[Vivek Bhardwaj]

Hi All

Is there any build cache on bioc build system? I updated S4Vector and 
IRanges in my dependencies and triggered a new build of my package, only 
to find that this broke other dependencies due to renaming of function 
`concatenateObjects ` to `bindRows` in S4Vector. Now I removed the 
mentioned versions in my DESCRIPTION, but the build is still broken. 
Also tried specifying a particular version of these packages and I get 
the error :

** byte-compile and prepare package for lazy loading Error in 
loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = 
vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but == 2.14.10 
is required

How do I refresh the cache?

-- 

Best Wishes
Vivek



*Vivek Bhardwaj*
PhD Candidate | International Max Planck Research School
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51, Freiburg
E-mail: bhard...@ie-freiburg.mpg.de
Tel: +49-761-5108-472
Website: https://vivekbhr.github.io

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