Re: [Bioc-devel] "TissueEnrich" is missing in the BioC 3.7 build report

[Ashish Jain]

Hi Martin,

Thank you for the reply. I think I accidently updated the DESCRIPTION file.
I will fix it now.

Regards,
Ashish Jain

On Sun, Apr 15, 2018 at 4:35 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> I made a clean 'read only' clone of your git repository
>
> git$ git clone https://git.bioconductor.org/packages/TissueEnrich
>
> then tried to build it
>
> git$ Rdev CMD build TissueEnrich
> Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help
> * checking for file 'TissueEnrich/DESCRIPTION' ... OK
> * preparing 'TissueEnrich':
> * checking DESCRIPTION meta-information ... ERROR
> Authors@R field gives more than one person with maintainer role:
>   Ashish Jain  [aut, cre]
>   Geetu Tuteja  [aut, cre]
>
> See section 'The DESCRIPTION file' in the 'Writing R Extensions'
> manual.
>
> Have you tried to correct this?
>
> Martin
>
> On 04/15/2018 05:30 PM, Ashish Jain wrote:
>
>> Hi All,
>>
>> I am the developer of the "TissueEnrich" package which got accepted 6 days
>> back. After the acceptance, the package was included in the Bioc 3.7 build
>> and I was able to see it in the build report. But suddenly for last two
>> days, it is not there in the Bioc 3.7 build report. Can somebody help me
>> with this?
>>
>>
>
> This email message may contain legally privileged and/or confidential
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>



-- 
Regards,
Ashish Jain
BCB-Graduate Student
Iowa State University
Ph +1-317-529-7973
Website: *https://ashishjain1988.github.io/
*
Github: https://github.com/ashishjain1988/

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Re: [Bioc-devel] Need some help to submit a R package.

[Ruqian Lyu]

Hi Pijush,

Did you open the build report which is a link to an HTML page with details
of the warning?


Regards,
Ruqian



On Fri, Apr 13, 2018 at 4:54 PM, Pijush Das  wrote:

> Dear Sir,
>
>
> I have submitted an R package named "sigFeature" in Github and also
> Bioconductor 9 days before.
> The reviewers only said that there is some WARNING problem in the package
> in different platform.
>
> But after that they are not communicating any thing regarding the package.
> I have checked the package
> windows and Ubuntu it is working fine.
>
> I unable to understand what actually the problem is ?
> And the reviewers are not communicating about the problem. Though I am
> getting lots of email from bioc-devel dealing with others package
> problem .
>
> Please suggest me what should I do now ?
>
>
>
>
> Thank you
>
>
>
> Regards
> Pijush
>
>
>
>
> On Mon, Apr 2, 2018 at 4:26 PM, Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
>
> > Hi,
> >
> > Please read through this documentation.
> >
> > http://bioconductor.org/developers/package-submission/
> >
> >
> > Nitesh
> >
> > > On Apr 2, 2018, at 2:00 AM, Pijush Das  wrote:
> > >
> > > Dear Sir,
> > >
> > >
> > >
> > > I have developed an R package. I want to submit this package in
> > > Bioconductor.
> > > Please help me to submit the R package.
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > regards
> > > Pijush Das
> > >
> > >   [[alternative HTML version deleted]]
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
> > 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.
> >
>
> [[alternative HTML version deleted]]
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Re: [Bioc-devel] "TissueEnrich" is missing in the BioC 3.7 build report

[Martin Morgan]

I made a clean 'read only' clone of your git repository

git$ git clone https://git.bioconductor.org/packages/TissueEnrich

then tried to build it

git$ Rdev CMD build TissueEnrich
Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help
* checking for file 'TissueEnrich/DESCRIPTION' ... OK
* preparing 'TissueEnrich':
* checking DESCRIPTION meta-information ... ERROR
Authors@R field gives more than one person with maintainer role:
  Ashish Jain  [aut, cre]
  Geetu Tuteja  [aut, cre]

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

Have you tried to correct this?

Martin

On 04/15/2018 05:30 PM, Ashish Jain wrote:

Hi All,

I am the developer of the "TissueEnrich" package which got accepted 6 days
back. After the acceptance, the package was included in the Bioc 3.7 build
and I was able to see it in the build report. But suddenly for last two
days, it is not there in the Bioc 3.7 build report. Can somebody help me
with this?




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

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[Bioc-devel] "TissueEnrich" is missing in the BioC 3.7 build report

[Ashish Jain]

Hi All,

I am the developer of the "TissueEnrich" package which got accepted 6 days
back. After the acceptance, the package was included in the Bioc 3.7 build
and I was able to see it in the build report. But suddenly for last two
days, it is not there in the Bioc 3.7 build report. Can somebody help me
with this?

-- 
Regards,
Ashish Jain
BCB-Graduate Student
Iowa State University
Ph +1-317-529-7973
Website: *https://ashishjain1988.github.io/
*
Github: https://github.com/ashishjain1988/

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Re: [Bioc-devel] tokay2 error with httr

[Martin Morgan]

Hi Klara --

You have code structured like

  out <- tryCatch({
  response = httr::GET(url)
  ...
   }, error = function(cond) {
  ...
  ... htr::http_status(response)$message
   })

so if GET() fails, response is undefined; I guess this is what happened, 
the "why" is a mystery but could be as simple as transient internet 
connectivity.


It seems like you could instead report conditionMessage(cond) in the 
error function (catching the GET() error), and use 
httr::stop_for_status() to check for invalid status response from the 
server.


FWIW your code in utils.R is not consistently indented (sometimes tabs, 
sometimes spaces); I'd strongly suggest 4 spaces and no tabs. Also 
message(paste(...)) can usually be represented simply as message(..., 
including multiline messages.


Martin

On 04/15/2018 12:25 PM, Klara Kaleb wrote:

Hi Bioc team,

I am one of the maintainers the roma package in the devel version.  The package 
is building fine on mac and linux, however I am experience an error on tokay2 
that I have been so far unable to solve. The problem seems to be in receiving 
the responses from the API. which fails in the first vignette with the 
following error message:


"

Error: processing vignette 'exploring_hogs.Rmd' failed with diagnostics:
object 'response' not found
"

I have checked the relevant end point and it works as it is suppose to do. 
Furthermore, the same error does not show up in mac and linux servers. Would 
you happen to have any pointers to what might be causing this error?


Thank you in advance,

Klara

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Re: [Bioc-devel] RareVariantVis failed

[Tomasz Stokowy]

Dear Robert,

Thank you for clarification. I updated package following your instructions  
and committed changes to

https://github.com/tstokowy/RareVariantVis.

I will verify if the R CMD check goes through this time.

Kind regards,

--
Tomasz


On Tue, 03 Apr 2018 15:16:55 +0200, Robert Castelo  
 wrote:



hi Tomasz,

regarding the warning caused by GenomicScores:

 > Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,
 > GRanges(seqnames = paste0("chr",  :
 >The 'scores()' method has been deprecated and will become defunct  
in
 > the next release version of Biocondcutor 3.8. Please use its  
replacement functions 'gscores()' and 'score()'.


for this one just replace, the call:

scores(phastCons100way.UCSC.hg19, scores.only = TRUE, etc...

by

score(phastCons100way.UCSC.hg19, etc...

i.e., 'scores()' by 'score()' and remove 'scores.only=TRUE'.

 > Warning in gscores(object, ranges, ...) :
 >assuming query ranges genome build is the one of the GScores object
 > (Genome Reference Consortium GRCh37).

here the 'genome' column in the sequence information ('seqinfo()') from  
the input ranges ranges is probably something like "hg19" or NA, while  
the one in the GScores object is "Genome Reference Consortium GRCh37".  
if you know both objects have positions over the same reference genome,  
you can forget about this warning. however, probably a warning is not  
necessary here, i'll replace it by a message and the warning will  
dissappear in a couple of days.


btw, i'm assuming we're talking here about the current 'development'  
branch of Bioconductor, i.e., GenomicScores version 1.3.21.


cheers,

robert.


On 04/03/2018 12:43 PM, Tomasz Stokowy wrote:

Dear bioc-devel,
 My package RareVariantVis currently failed check because of examples  
warnings/error. I am not able to reproduce this on my system, despite  
updating R and Bioconductor.
It seems that recent changes in dependencies are causing this trouble.  
Should I go for useDevel() to solve this issues?
  
http://bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html  
 https://github.com/tstokowy/RareVariantVis

 Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
   GRanges object contains 2 out-of-bound ranges located on sequence
   68559. Note that ranges located on a sequence whose length is unknown
   (NA) or on a circular sequence are not considered out-of-bound (use
   seqlengths() and isCircular() to get the lengths and circularity  
flags
   of the underlying sequences). You can use trim() to trim these  
ranges.

   See ?`trim,GenomicRanges-method` for more information.
Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,  
GRanges(seqnames = paste0("chr",  :
   The 'scores()' method has been deprecated and will become defunct in  
the next release version of Biocondcutor 3.8. Please use its  
replacement functions 'gscores()' and 'score()'.

Warning in gscores(object, ranges, ...) :
   assuming query ranges genome build is the one of the GScores object  
(Genome Reference Consortium GRCh37).

Error in match.names(clabs, nmi) : names do not match previous names
Calls: chromosomeVis ... eval -> eval -> eval -> rbind -> rbind ->  
match.names

 I will be thankful for any suggestions.
 Kind regards,






--
Tomasz Stokowy
Department of Clinical Science
University of Bergen

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Re: [Bioc-devel] WARNING regarding imporing SummarizedExperiment

[Martin Morgan]

The solution is, in the NAMESPACE, to import only those functions used

  importFrom(SummarizedExperiment, "start", "end")
  importFrom(stats, "mean")

or to import everything but

   importFrom(stats, except = c(start, end))

or to explicitly resolve symbols in the code and not mention them in the 
NAMESPACE file.


SummarizedExperiment::start(...)

Each of these styles is supported by roxygen2.

Martin


On 04/14/2018 08:37 PM, Ruqian Lyu wrote:

Hi guys,

I have identified the problem.
It's the packages I imported have same function name, so the previous
functions get overwritten.


Thanks


Ruqian

On Sun, Apr 15, 2018 at 10:18 AM, Ruqian Lyu 

Re: [Bioc-devel] WARNING regarding imporing SummarizedExperiment

[Ruqian Lyu]

Thanks, Martin!

Cheers,
Ruqian

On Sun, Apr 15, 2018 at 9:06 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> The solution is, in the NAMESPACE, to import only those functions used
>
>   importFrom(SummarizedExperiment, "start", "end")
>   importFrom(stats, "mean")
>
> or to import everything but
>
>importFrom(stats, except = c(start, end))
>
> or to explicitly resolve symbols in the code and not mention them in the
> NAMESPACE file.
>
> SummarizedExperiment::start(...)
>
> Each of these styles is supported by roxygen2.
>
> Martin
>
>
>
> On 04/14/2018 08:37 PM, Ruqian Lyu wrote:
>
>> Hi guys,
>>
>> I have identified the problem.
>> It's the packages I imported have same function name, so the previous
>> functions get overwritten.
>>
>>
>> Thanks
>>
>>
>> Ruqian
>>
>> On Sun, Apr 15, 2018 at 10:18 AM, Ruqian Lyu <
>> ruqi...@student.unimelb.edu.au
>>
>>> wrote:
>>>
>>
>> Hi guys,
>>>
>>> I'm wondering if any of you have met this warning message :
>>>
>>> Warning: replacing previous import 'SummarizedExperiment::start' by
>>> 'stats::start' when loading 'singscore'
>>> Warning: replacing previous import 'SummarizedExperiment::end' by
>>> 'stats::end' when loading 'singscore'
>>>
>>> I have import SummarizedExperiment in my DESCRIPTION and NAMESPACE.
>>> The package passed R CMD Check and BiocCheck without warnings. But the
>>> build report returned the warnings above.
>>>
>>> Link to the report:
>>>
>>> http://bioconductor.org/spb_reports/singscore_buildreport_
>>> 20180414041637.html
>>>
>>>
>>> I'm not sure why this is happening.
>>> Any help will be appreciated.
>>>
>>> Thanks!
>>>
>>> Regards,
>>> Ruqian
>>>
>>>
>>>
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>>
>
> 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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