Re: [Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData

[Obenchain, Valerie]

Yes, changes are in ExperimentHubData 1.1.4 and ExperimentHub 1.1.2 as
stated below.

The change was made after the builds picked up yesterday so the new
version should propagate to the landing page tomorrow (Wed Dec 7) or you
can get them immediately from svn with

svn co
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ExperimentHub
svn co
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ExperimentHubData

Valerie


On 12/06/2016 10:38 AM, Marcin Kosiński wrote:
> Hi Valerie,
>
> Thanks for looking around.
> Have you provided this changes to the vignette?
> In
> https://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html#bug-fixes
> devel there looks to be a code appearance issue in chapter
>
>
> 2.2 Building the software package -> documentation data loading
>
> check release vignette
> https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html
>
>
> 2016-12-05 17:54 GMT+01:00 Obenchain, Valerie
>  >:
>
> Hi,
>
> I downloaded your package from github, removed the dependencies on
> AnnotationHub and utils and was able to reproduce the problem for
> read.csv() but not query().
>
> I've reworked the suggested .onLoad() file in the ExperimentHubData
> vignette. Hopefully this is a more straightforward implementation; the
> helpers in ExperimentHub incorporate the call to query() but not
> read.csv(). If you use the suggested .onLoad() then yes, you will need
> to import utils and importFrom(utils, read.csv) in the NAMESPACE.
> Changes are in ExperimentHub 1.1.2 and ExperimentHubData 1.1.4.
>
> Let me know if you run into problems.
>
> Valerie
>
> On 12/01/2016 07:13 AM, Marcin Kosiński wrote:
> > Hi Valerie,
> >
> > Thanks for the responce. Yes I have ExperimentHub in Depends.
> >
> > In the following code results I present the `query` NOTE that comes
> > out after devtools::check().
> > Then I present the content of my DESCRIPTION file and NAMESPACE.
> > After I added AnnotationHub to Imports and importFrom(AnnotationHub,
> > query) to NAMESPACE, the NOTE disappeared
> >
> >
> >
> > > devtools::check()
> > Updating RTCGA.clinical.20160128 documentation
> > Loading RTCGA.clinical.20160128
> > Setting env vars
> >
> --
> > CFLAGS  : -Wall -pedantic
> > CXXFLAGS: -Wall -pedantic
> > Building RTCGA.clinical.20160128
> > --
> > '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save
> --no-restore
> > --quiet CMD build  \
> >   '/home/mkosinski/RTCGA.clinical.20160128' --no-resave-data
> --no-manual
> >
> > * checking for file
> > ‘/home/mkosinski/RTCGA.clinical.20160128/DESCRIPTION’ ... OK
> > * preparing ‘RTCGA.clinical.20160128’:
> > * checking DESCRIPTION meta-information ... OK
> > * installing the package to build vignettes
> > * creating vignettes ... OK
> > * checking for LF line-endings in source and make files
> > * checking for empty or unneeded directories
> > * looking to see if a ‘data/datalist’ file should be added
> > * building ‘RTCGA.clinical.20160128_0.99.0.tar.gz’
> >
> > Setting env vars
> >
> --
> > _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
> > _R_CHECK_CRAN_INCOMING_   : FALSE
> > _R_CHECK_FORCE_SUGGESTS_  : FALSE
> > Checking RTCGA.clinical.20160128
> > --
> > '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save
> --no-restore
> > --quiet CMD check  \
> >   '/tmp/RtmpWLIOjs/RTCGA.clinical.20160128_0.99.0.tar.gz' --as-cran
> > --timings  \
> >   --no-manual
> >
> > * using log directory
> ‘/tmp/RtmpWLIOjs/RTCGA.clinical.20160128.Rcheck’
> > * using R version 3.3.1 (2016-06-21)
> > * using platform: x86_64-pc-linux-gnu (64-bit)
> > * using session charset: UTF-8
> > * using options ‘--no-manual --as-cran’
> > * checking for file ‘RTCGA.clinical.20160128/DESCRIPTION’ ... OK
> > * checking extension type ... Package
> > * this is package ‘RTCGA.clinical.20160128’ version ‘0.99.0’
> > * checking package namespace information ... OK
> > * checking package dependencies ... OK
> > * checking if this is a source package ... OK
> > * checking if there is a namespace ... OK
> > * checking for executable files ... OK
> > * checking for hidden files and directories ... OK
> > * checking for portable file names ... OK
> > * checking for sufficient/correct file permissions ... OK
> > * checking whether package ‘RTCGA.clinical.20160128’ can 

Re: [Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData

[Marcin Kosiński]

Hi Valerie,

Thanks for looking around.
Have you provided this changes to the vignette?
In
https://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html#bug-fixes
devel there looks to be a code appearance issue in chapter
2.2 Building the software package -> documentation data loading

check release vignette
https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html

2016-12-05 17:54 GMT+01:00 Obenchain, Valerie <
valerie.obench...@roswellpark.org>:

> Hi,
>
> I downloaded your package from github, removed the dependencies on
> AnnotationHub and utils and was able to reproduce the problem for
> read.csv() but not query().
>
> I've reworked the suggested .onLoad() file in the ExperimentHubData
> vignette. Hopefully this is a more straightforward implementation; the
> helpers in ExperimentHub incorporate the call to query() but not
> read.csv(). If you use the suggested .onLoad() then yes, you will need
> to import utils and importFrom(utils, read.csv) in the NAMESPACE.
> Changes are in ExperimentHub 1.1.2 and ExperimentHubData 1.1.4.
>
> Let me know if you run into problems.
>
> Valerie
>
> On 12/01/2016 07:13 AM, Marcin Kosiński wrote:
> > Hi Valerie,
> >
> > Thanks for the responce. Yes I have ExperimentHub in Depends.
> >
> > In the following code results I present the `query` NOTE that comes
> > out after devtools::check().
> > Then I present the content of my DESCRIPTION file and NAMESPACE.
> > After I added AnnotationHub to Imports and importFrom(AnnotationHub,
> > query) to NAMESPACE, the NOTE disappeared
> >
> >
> >
> > > devtools::check()
> > Updating RTCGA.clinical.20160128 documentation
> > Loading RTCGA.clinical.20160128
> > Setting env vars
> > 
> --
> > CFLAGS  : -Wall -pedantic
> > CXXFLAGS: -Wall -pedantic
> > Building RTCGA.clinical.20160128
> > --
> > '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore
> > --quiet CMD build  \
> >   '/home/mkosinski/RTCGA.clinical.20160128' --no-resave-data --no-manual
> >
> > * checking for file
> > ‘/home/mkosinski/RTCGA.clinical.20160128/DESCRIPTION’ ... OK
> > * preparing ‘RTCGA.clinical.20160128’:
> > * checking DESCRIPTION meta-information ... OK
> > * installing the package to build vignettes
> > * creating vignettes ... OK
> > * checking for LF line-endings in source and make files
> > * checking for empty or unneeded directories
> > * looking to see if a ‘data/datalist’ file should be added
> > * building ‘RTCGA.clinical.20160128_0.99.0.tar.gz’
> >
> > Setting env vars
> > 
> --
> > _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
> > _R_CHECK_CRAN_INCOMING_   : FALSE
> > _R_CHECK_FORCE_SUGGESTS_  : FALSE
> > Checking RTCGA.clinical.20160128
> > --
> > '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore
> > --quiet CMD check  \
> >   '/tmp/RtmpWLIOjs/RTCGA.clinical.20160128_0.99.0.tar.gz' --as-cran
> > --timings  \
> >   --no-manual
> >
> > * using log directory ‘/tmp/RtmpWLIOjs/RTCGA.clinical.20160128.Rcheck’
> > * using R version 3.3.1 (2016-06-21)
> > * using platform: x86_64-pc-linux-gnu (64-bit)
> > * using session charset: UTF-8
> > * using options ‘--no-manual --as-cran’
> > * checking for file ‘RTCGA.clinical.20160128/DESCRIPTION’ ... OK
> > * checking extension type ... Package
> > * this is package ‘RTCGA.clinical.20160128’ version ‘0.99.0’
> > * checking package namespace information ... OK
> > * checking package dependencies ... OK
> > * checking if this is a source package ... OK
> > * checking if there is a namespace ... OK
> > * checking for executable files ... OK
> > * checking for hidden files and directories ... OK
> > * checking for portable file names ... OK
> > * checking for sufficient/correct file permissions ... OK
> > * checking whether package ‘RTCGA.clinical.20160128’ can be installed
> > ... OK
> > * checking installed package size ... NOTE
> >   installed size is 18.2Mb
> >   sub-directories of 1Mb or more:
> > data  18.0Mb
> > * checking package directory ... OK
> > * checking ‘build’ directory ... OK
> > * checking DESCRIPTION meta-information ... OK
> > * checking top-level files ... NOTE
> > Non-standard file/directory found at top level:
> >   ‘createTCGA.R’
> > * checking for left-over files ... OK
> > * checking index information ... OK
> > * checking package subdirectories ... OK
> > * checking R files for non-ASCII characters ... OK
> > * checking R files for syntax errors ... OK
> > * checking whether the package can be loaded ... OK
> > * checking whether the package can be loaded with stated dependencies
> > ... OK
> > * checking whether the package can be unloaded cleanly ... OK
> > * checking whether the namespace ca

Re: [Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData

[Obenchain, Valerie]

Hi,

I downloaded your package from github, removed the dependencies on
AnnotationHub and utils and was able to reproduce the problem for
read.csv() but not query().

I've reworked the suggested .onLoad() file in the ExperimentHubData
vignette. Hopefully this is a more straightforward implementation; the
helpers in ExperimentHub incorporate the call to query() but not
read.csv(). If you use the suggested .onLoad() then yes, you will need
to import utils and importFrom(utils, read.csv) in the NAMESPACE.
Changes are in ExperimentHub 1.1.2 and ExperimentHubData 1.1.4.

Let me know if you run into problems.

Valerie

On 12/01/2016 07:13 AM, Marcin Kosiński wrote:
> Hi Valerie,
>
> Thanks for the responce. Yes I have ExperimentHub in Depends.
>
> In the following code results I present the `query` NOTE that comes
> out after devtools::check().
> Then I present the content of my DESCRIPTION file and NAMESPACE.
> After I added AnnotationHub to Imports and importFrom(AnnotationHub,
> query) to NAMESPACE, the NOTE disappeared
>
>
>
> > devtools::check()
> Updating RTCGA.clinical.20160128 documentation
> Loading RTCGA.clinical.20160128
> Setting env vars
> --
> CFLAGS  : -Wall -pedantic
> CXXFLAGS: -Wall -pedantic
> Building RTCGA.clinical.20160128
> --
> '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore
> --quiet CMD build  \
>   '/home/mkosinski/RTCGA.clinical.20160128' --no-resave-data --no-manual
>
> * checking for file
> ‘/home/mkosinski/RTCGA.clinical.20160128/DESCRIPTION’ ... OK
> * preparing ‘RTCGA.clinical.20160128’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * looking to see if a ‘data/datalist’ file should be added
> * building ‘RTCGA.clinical.20160128_0.99.0.tar.gz’
>
> Setting env vars
> --
> _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
> _R_CHECK_CRAN_INCOMING_   : FALSE
> _R_CHECK_FORCE_SUGGESTS_  : FALSE
> Checking RTCGA.clinical.20160128
> --
> '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore
> --quiet CMD check  \
>   '/tmp/RtmpWLIOjs/RTCGA.clinical.20160128_0.99.0.tar.gz' --as-cran
> --timings  \
>   --no-manual
>
> * using log directory ‘/tmp/RtmpWLIOjs/RTCGA.clinical.20160128.Rcheck’
> * using R version 3.3.1 (2016-06-21)
> * using platform: x86_64-pc-linux-gnu (64-bit)
> * using session charset: UTF-8
> * using options ‘--no-manual --as-cran’
> * checking for file ‘RTCGA.clinical.20160128/DESCRIPTION’ ... OK
> * checking extension type ... Package
> * this is package ‘RTCGA.clinical.20160128’ version ‘0.99.0’
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking whether package ‘RTCGA.clinical.20160128’ can be installed
> ... OK
> * checking installed package size ... NOTE
>   installed size is 18.2Mb
>   sub-directories of 1Mb or more:
> data  18.0Mb
> * checking package directory ... OK
> * checking ‘build’ directory ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... NOTE
> Non-standard file/directory found at top level:
>   ‘createTCGA.R’
> * checking for left-over files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated dependencies
> ... OK
> * checking whether the package can be unloaded cleanly ... OK
> * checking whether the namespace can be loaded with stated
> dependencies ... OK
> * checking whether the namespace can be unloaded cleanly ... OK
> * checking loading without being on the library search path ... OK
> * checking dependencies in R code ... OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... NOTE
> .onLoad :  : func: no visible global function definition for
>   ‘query’
> ACC.clinical.20160128: no visible global function definition for
>   ‘query’
> BLCA.clinical.20160128: no visible global function definition for
>   ‘query’
> BRCA.clinical.20160128: no visible global function definition for
>   ‘query’
> CESC.clinical.20160128: no visi

Re: [Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData

[Marcin Kosiński]

Hi Valerie,

Thanks for the responce. Yes I have ExperimentHub in Depends.

In the following code results I present the `query` NOTE that comes out
after devtools::check().
Then I present the content of my DESCRIPTION file and NAMESPACE.
After I added AnnotationHub to Imports and importFrom(AnnotationHub, query)
to NAMESPACE, the NOTE disappeared



> devtools::check()
Updating RTCGA.clinical.20160128 documentation
Loading RTCGA.clinical.20160128
Setting env vars
--
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building RTCGA.clinical.20160128
--
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore
--quiet CMD build  \
  '/home/mkosinski/RTCGA.clinical.20160128' --no-resave-data --no-manual

* checking for file ‘/home/mkosinski/RTCGA.clinical.20160128/DESCRIPTION’
... OK
* preparing ‘RTCGA.clinical.20160128’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘RTCGA.clinical.20160128_0.99.0.tar.gz’

Setting env vars
--
_R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
_R_CHECK_CRAN_INCOMING_   : FALSE
_R_CHECK_FORCE_SUGGESTS_  : FALSE
Checking RTCGA.clinical.20160128
--
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore
--quiet CMD check  \
  '/tmp/RtmpWLIOjs/RTCGA.clinical.20160128_0.99.0.tar.gz' --as-cran
--timings  \
  --no-manual

* using log directory ‘/tmp/RtmpWLIOjs/RTCGA.clinical.20160128.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘RTCGA.clinical.20160128/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCGA.clinical.20160128’ version ‘0.99.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RTCGA.clinical.20160128’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 18.2Mb
  sub-directories of 1Mb or more:
data  18.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘createTCGA.R’
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ...
OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onLoad :  : func: no visible global function definition for
  ‘query’
ACC.clinical.20160128: no visible global function definition for
  ‘query’
BLCA.clinical.20160128: no visible global function definition for
  ‘query’
BRCA.clinical.20160128: no visible global function definition for
  ‘query’
CESC.clinical.20160128: no visible global function definition for
  ‘query’
CHOL.clinical.20160128: no visible global function definition for
  ‘query’
COADREAD.clinical.20160128: no visible global function definition for
  ‘query’
DLBC.clinical.20160128: no visible global function definition for
  ‘query’
ESCA.clinical.20160128: no visible global function definition for
  ‘query’
FPPP.clinical.20160128: no visible global function definition for
  ‘query’
GBMLGG.clinical.20160128: no visible global function definition for
  ‘query’
HNSC.clinical.20160128: no visible global function definition for
  ‘query’
KICH.clinical.20160128: no visible global function definition for
  ‘query’
KIPAN.clinical.20160128: no visible global function definition for
  ‘query’
KIRC.clinical.20160128: no visible global function definition for
  ‘query’
KIRP.clinical.20160128: no visible global function defin

Re: [Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData

[Obenchain, Valerie]

There is a section in the vignette that describes what should be imported:

DESCRIPTION / NAMESPACE

The package should depend on and fully import ExperimentHub.
...

ExperimentHub depends on AnnotationHub. When ExperimentHub is loaded you
can see AnnotationHub attached to the search path with search().
read.csv is imported in AnnotationHub so adding this dependency should
take care of all the warnings you mentioned.

Are you depending on ExpermentHub?

Valerie

On 11/30/2016 09:52 AM, Marcin Kosiński wrote:
> Hi bioc devs!
>
> In this manual about creeating ExperimentHubData package
> http://www.bioconductor.org/packages/3.4/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html
> there is a suggestion to create a zzz.R file where `query` function is used.
>
> This function comes from AnnotationHub package, so there somewhere someone
> should add an information about adding AnnotationHub to Imports in
> DESCRIPTION and about importing query from AnnotationHub in NAMESPACE.
> Without that the CRAN CHECK results in `query is an undocumented object or
> function`. What is more, I even had to add importFrom(utils, read.csv) to
> the NAMESPACE, just from that reason :)
>
> Cheers!
> Marcin
>
>   [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



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