Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-31 Thread Martin Morgan 

On 03/31/2017 05:29 AM, Sokratis Kariotis wrote:

Hey all,

Following your advice, the package now builds successfully! However, I
got this error while checking:

* checking package dependencies ... ERROR
Namespace dependency not required: ‘SummarizedExperiment’

Should I add /Imports ://SummarizedExperiment/ in my DESCRIPTION file?


Your experiment data package doesn't have an R/ directory so no R code 
(this is normal for experiment data packages). There is therefore no 
need to import(SummarizedExperiment) in your NAMESPACE, so remove it 
there. The warning will then go away.


Martin



Regards,

Sokratis


On 30 March 2017 at 12:05, Martin Morgan > wrote:

On 03/30/2017 05:21 AM, Sokratis Kariotis wrote:

Hey all,

Thanks for the input! I followed Marcel's advice and included
the library
in my vignette. Also, I replaced lazyData with a datalist. The
datalist
file includes "compressed_result : result" which is in turn
loaded in the
vignette using "data(compressed_result)". However, I got:

Warning in data(compressed_result) :
  data set ‘compressed_result’ not found

Error: processing vignette 'usingPathprintGEOData.Rnw' failed
with diagnostics:
 chunk 1
Error in assays(result) : object 'result' not found



I Stangle'd the vignette

  cd pathprintGEOData/vignettes
  R CMD Stangle usingPathprintGEOData.Rnw

and then walked through the lines of R code. I got to

> data(compressed_result)
Warning message:
In data(compressed_result) : data set 'compressed_result' not found

The data 'compressed_result' is not found, because it is in the
pathprintGEOData package, and the pathprintGEOData package is not on
the search path.

> search()
 [1] ".GlobalEnv"   "package:SummarizedExperiment"
 [3] "package:DelayedArray" "package:matrixStats"
 [5] "package:Biobase"  "package:GenomicRanges"
 [7] "package:GenomeInfoDb" "package:IRanges"
 [9] "package:S4Vectors""package:BiocGenerics"
[11] "package:parallel" "package:stats4"
[13] "package:pathprint""ESSR"
[15] "package:BiocInstaller""package:stats"
[17] "package:graphics" "package:grDevices"
[19] "package:utils""package:datasets"
[21] "package:methods"  "Autoloads"
[23] "package:base"

It is not on the search path because, originally, pathprint had
Depends: pathprintGEOData, but that was modified, as you know, to
Suggests: pathprintGEOData, to avoid circular dependencies that
thwart our build system. So previously library(pathprint) was enough
to make the data available, but now you must either load the package

  library(pathprintGEOData)
  data(compressed_result)

or tell data() where the data set is

  data(compressed_result, package="pathprintGEOData")

One would still like to use an informative name for the data (first
argument of data) and presumably an identical name for the object
that is loaded.

Martin



So the dataset is still not loaded (again, these errors did not
exist
prior to package acceptance). I have been using devtools to
build/check the package (since the github issue was closed) and
these
warnings/errors dont show up, which imakes it difficult for me
to fix
them. Thanks again for any input!

Regards,

Sokratis


On 27 March 2017 at 19:58, Michael Lawrence
>
wrote:

Actually, I don't see where the package itself is loaded in the
vignette. If it were, this error would not occur.

Unsurprisingly, I get this when trying to run the vignette code:

Warning message:
In data(list = ds) : data set ‘pathprintSummarizedGEOData’
not found

I noticed that pathprintGEOData just provides
compressed_result, not
the "pathprintSummarizedGEOData" so I'm not sure where that
lives now.
You might also consider turning off lazy data and using a
datalist
file for that package since the file is somewhat large.

I also think that the datalist file for pathprint is out of
date.

Michael

On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
> wrote:

Hi Sokratis,

You can resolve this issue by moving
`SummarizedExperiment` to the
Suggests field and

including a

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-31 Thread Sokratis Kariotis 
Hey all,

Following your advice, the package now builds successfully! However, I got
this error while checking:

* checking package dependencies ... ERROR
Namespace dependency not required: ‘SummarizedExperiment’

Should I add *Imports :**SummarizedExperiment* in my DESCRIPTION file?

Regards,

Sokratis


On 30 March 2017 at 12:05, Martin Morgan 
wrote:

> On 03/30/2017 05:21 AM, Sokratis Kariotis wrote:
>
>> Hey all,
>>
>> Thanks for the input! I followed Marcel's advice and included the library
>> in my vignette. Also, I replaced lazyData with a datalist. The datalist
>> file includes "compressed_result : result" which is in turn loaded in the
>> vignette using "data(compressed_result)". However, I got:
>>
>> Warning in data(compressed_result) :
>>   data set ‘compressed_result’ not found
>>
>> Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
>> diagnostics:
>>  chunk 1
>> Error in assays(result) : object 'result' not found
>>
>
>
> I Stangle'd the vignette
>
>   cd pathprintGEOData/vignettes
>   R CMD Stangle usingPathprintGEOData.Rnw
>
> and then walked through the lines of R code. I got to
>
> > data(compressed_result)
> Warning message:
> In data(compressed_result) : data set 'compressed_result' not found
>
> The data 'compressed_result' is not found, because it is in the
> pathprintGEOData package, and the pathprintGEOData package is not on the
> search path.
>
> > search()
>  [1] ".GlobalEnv"   "package:SummarizedExperiment"
>  [3] "package:DelayedArray" "package:matrixStats"
>  [5] "package:Biobase"  "package:GenomicRanges"
>  [7] "package:GenomeInfoDb" "package:IRanges"
>  [9] "package:S4Vectors""package:BiocGenerics"
> [11] "package:parallel" "package:stats4"
> [13] "package:pathprint""ESSR"
> [15] "package:BiocInstaller""package:stats"
> [17] "package:graphics" "package:grDevices"
> [19] "package:utils""package:datasets"
> [21] "package:methods"  "Autoloads"
> [23] "package:base"
>
> It is not on the search path because, originally, pathprint had Depends:
> pathprintGEOData, but that was modified, as you know, to Suggests:
> pathprintGEOData, to avoid circular dependencies that thwart our build
> system. So previously library(pathprint) was enough to make the data
> available, but now you must either load the package
>
>   library(pathprintGEOData)
>   data(compressed_result)
>
> or tell data() where the data set is
>
>   data(compressed_result, package="pathprintGEOData")
>
> One would still like to use an informative name for the data (first
> argument of data) and presumably an identical name for the object that is
> loaded.
>
> Martin
>
>
>
>> So the dataset is still not loaded (again, these errors did not exist
>> prior to package acceptance). I have been using devtools to
>> build/check the package (since the github issue was closed) and these
>> warnings/errors dont show up, which imakes it difficult for me to fix
>> them. Thanks again for any input!
>>
>> Regards,
>>
>> Sokratis
>>
>>
>> On 27 March 2017 at 19:58, Michael Lawrence 
>> wrote:
>>
>> Actually, I don't see where the package itself is loaded in the
>>> vignette. If it were, this error would not occur.
>>>
>>> Unsurprisingly, I get this when trying to run the vignette code:
>>>
>>> Warning message:
>>> In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found
>>>
>>> I noticed that pathprintGEOData just provides compressed_result, not
>>> the "pathprintSummarizedGEOData" so I'm not sure where that lives now.
>>> You might also consider turning off lazy data and using a datalist
>>> file for that package since the file is somewhat large.
>>>
>>> I also think that the datalist file for pathprint is out of date.
>>>
>>> Michael
>>>
>>> On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
>>>  wrote:
>>>
 Hi Sokratis,

 You can resolve this issue by moving `SummarizedExperiment` to the
 Suggests field and

 including a `library(SummarizedExperiment)` call in your vignette.

 Best regards,

 Marcel


 On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis
 > wrote:

 Hey,

 I have submitted the package pathprintGEOData, which got accepted,
 but the
 build/check report is now producing the following error:



 *Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
 diagnostics:  chunk 1 Error in assays(result) : could not find

>>> function
>>>
 "assays"*

 *assays *is a function from the SummarizedExperiment package which I
 have
 added on my Depends in DESCRIPTION. This error was not present
 during
 building/checking before this package was

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-30 Thread Sokratis Kariotis 
Hey all,

Thanks for the input! I followed Marcel's advice and included the library
in my vignette. Also, I replaced lazyData with a datalist. The datalist
file includes "compressed_result : result" which is in turn loaded in the
vignette using "data(compressed_result)". However, I got:

Warning in data(compressed_result) :
  data set ‘compressed_result’ not found

Error: processing vignette 'usingPathprintGEOData.Rnw' failed with diagnostics:
 chunk 1
Error in assays(result) : object 'result' not found

So the dataset is still not loaded (again, these errors did not exist
prior to package acceptance). I have been using devtools to
build/check the package (since the github issue was closed) and these
warnings/errors dont show up, which imakes it difficult for me to fix
them. Thanks again for any input!

Regards,

Sokratis


On 27 March 2017 at 19:58, Michael Lawrence 
wrote:

> Actually, I don't see where the package itself is loaded in the
> vignette. If it were, this error would not occur.
>
> Unsurprisingly, I get this when trying to run the vignette code:
>
> Warning message:
> In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found
>
> I noticed that pathprintGEOData just provides compressed_result, not
> the "pathprintSummarizedGEOData" so I'm not sure where that lives now.
> You might also consider turning off lazy data and using a datalist
> file for that package since the file is somewhat large.
>
> I also think that the datalist file for pathprint is out of date.
>
> Michael
>
> On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
>  wrote:
> > Hi Sokratis,
> >
> > You can resolve this issue by moving `SummarizedExperiment` to the
> > Suggests field and
> >
> > including a `library(SummarizedExperiment)` call in your vignette.
> >
> > Best regards,
> >
> > Marcel
> >
> >
> > On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis
> > > wrote:
> >
> > Hey,
> >
> > I have submitted the package pathprintGEOData, which got accepted,
> > but the
> > build/check report is now producing the following error:
> >
> >
> >
> > *Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
> > diagnostics:  chunk 1 Error in assays(result) : could not find
> function
> > "assays"*
> >
> > *assays *is a function from the SummarizedExperiment package which I
> > have
> > added on my Depends in DESCRIPTION. This error was not present during
> > building/checking before this package was accepted. Besides adding
> > SummarizedExperiment
> > to my Imports what else might be responsible for that error?
> >
> > Thank you for any help on the matter!
> >
> > -Sokratis
> >
> >  [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing
> list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> >
> > --
> > Marcel Ramos
> > Bioconductor Core Team Member
> > Roswell Park Cancer Institute
> >
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:4}}
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-27 Thread Michael Lawrence 
Actually, I don't see where the package itself is loaded in the
vignette. If it were, this error would not occur.

Unsurprisingly, I get this when trying to run the vignette code:

Warning message:
In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found

I noticed that pathprintGEOData just provides compressed_result, not
the "pathprintSummarizedGEOData" so I'm not sure where that lives now.
You might also consider turning off lazy data and using a datalist
file for that package since the file is somewhat large.

I also think that the datalist file for pathprint is out of date.

Michael

On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
 wrote:
> Hi Sokratis,
>
> You can resolve this issue by moving `SummarizedExperiment` to the
> Suggests field and
>
> including a `library(SummarizedExperiment)` call in your vignette.
>
> Best regards,
>
> Marcel
>
>
> On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis
> > wrote:
>
> Hey,
>
> I have submitted the package pathprintGEOData, which got accepted,
> but the
> build/check report is now producing the following error:
>
>
>
> *Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
> diagnostics:  chunk 1 Error in assays(result) : could not find function
> "assays"*
>
> *assays *is a function from the SummarizedExperiment package which I
> have
> added on my Depends in DESCRIPTION. This error was not present during
> building/checking before this package was accepted. Besides adding
> SummarizedExperiment
> to my Imports what else might be responsible for that error?
>
> Thank you for any help on the matter!
>
> -Sokratis
>
>  [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
>
> --
> Marcel Ramos
> Bioconductor Core Team Member
> Roswell Park Cancer Institute
>
>
>
> This email message may contain legally privileged and/or...{{dropped:4}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-27 Thread Marcel Ramos 
Hi Sokratis,

You can resolve this issue by moving `SummarizedExperiment` to the 
Suggests field and

including a `library(SummarizedExperiment)` call in your vignette.

Best regards,

Marcel


On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis 
> wrote:

Hey,

I have submitted the package pathprintGEOData, which got accepted,
but the
build/check report is now producing the following error:



*Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
diagnostics:  chunk 1 Error in assays(result) : could not find function
"assays"*

*assays *is a function from the SummarizedExperiment package which I
have
added on my Depends in DESCRIPTION. This error was not present during
building/checking before this package was accepted. Besides adding
SummarizedExperiment
to my Imports what else might be responsible for that error?

Thank you for any help on the matter!

-Sokratis

 [[alternative HTML version deleted]]

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-- 
Marcel Ramos
Bioconductor Core Team Member
Roswell Park Cancer Institute



This email message may contain legally privileged and/or...{{dropped:4}}

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[Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-27 Thread Sokratis Kariotis 
Hey,

I have submitted the package pathprintGEOData, which got accepted, but the
build/check report is now producing the following error:



*Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
diagnostics:  chunk 1 Error in assays(result) : could not find function
"assays"*

*assays *is a function from the SummarizedExperiment package which I have
added on my Depends in DESCRIPTION. This error was not present during
building/checking before this package was accepted. Besides adding
SummarizedExperiment
to my Imports what else might be responsible for that error?

Thank you for any help on the matter!

-Sokratis

[[alternative HTML version deleted]]

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