[Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData
Obenchain, Valerie
Valerie.Obenchain at roswellpark.org
Tue Dec 6 20:40:50 CET 2016
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
> <Valerie.Obenchain at roswellpark.org
> <mailto:Valerie.Obenchain at 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 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 : <anonymous> : 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 definition for
> > ‘query’
> > LAML.clinical.20160128: no visible global function definition for
> > ‘query’
> > LIHC.clinical.20160128: no visible global function definition for
> > ‘query’
> > LUAD.clinical.20160128: no visible global function definition for
> > ‘query’
> > LUSC.clinical.20160128: no visible global function definition for
> > ‘query’
> > MESO.clinical.20160128: no visible global function definition for
> > ‘query’
> > OV.clinical.20160128: no visible global function definition for
> ‘query’
> > PAAD.clinical.20160128: no visible global function definition for
> > ‘query’
> > PCPG.clinical.20160128: no visible global function definition for
> > ‘query’
> > PRAD.clinical.20160128: no visible global function definition for
> > ‘query’
> > SARC.clinical.20160128: no visible global function definition for
> > ‘query’
> > SKCM.clinical.20160128: no visible global function definition for
> > ‘query’
> > STAD.clinical.20160128: no visible global function definition for
> > ‘query’
> > STES.clinical.20160128: no visible global function definition for
> > ‘query’
> > TGCT.clinical.20160128: no visible global function definition for
> > ‘query’
> > THCA.clinical.20160128: no visible global function definition for
> > ‘query’
> > THYM.clinical.20160128: no visible global function definition for
> > ‘query’
> > UCEC.clinical.20160128: no visible global function definition for
> > ‘query’
> > UCS.clinical.20160128: no visible global function definition for
> > ‘query’
> > UVM.clinical.20160128: no visible global function definition for
> > ‘query’
> > Undefined global functions or variables:
> > query
> > * checking Rd files ... OK
> > * checking Rd metadata ... OK
> > * checking Rd line widths ... OK
> > * checking Rd cross-references ... OK
> > * checking for missing documentation entries ... OK
> > * checking for code/documentation mismatches ... OK
> > * checking Rd \usage sections ... OK
> > * checking Rd contents ... OK
> > * checking for unstated dependencies in examples ... OK
> > * checking contents of ‘data’ directory ... OK
> > * checking data for non-ASCII characters ... OK
> > * checking data for ASCII and uncompressed saves ... OK
> > * checking installed files from ‘inst/doc’ ... OK
> > * checking files in ‘vignettes’ ... OK
> > * checking examples ... OK
> > * checking for unstated dependencies in vignettes ... OK
> > * checking package vignettes in ‘inst/doc’ ... OK
> > * checking re-building of vignette outputs ... OK
> > * DONE
> >
> > Status: 3 NOTEs
> > See
> > ‘/tmp/RtmpWLIOjs/RTCGA.clinical.20160128.Rcheck/00check.log’
> > for details.
> >
> >
> > R CMD check results
> > 0 errors | 0 warnings | 3 notes
> > checking installed package size ... NOTE
> > installed size is 18.2Mb
> > sub-directories of 1Mb or more:
> > data 18.0Mb
> >
> > checking top-level files ... NOTE
> > Non-standard file/directory found at top level:
> > ‘createTCGA.R’
> >
> > checking R code for possible problems ... NOTE
> > .onLoad : <anonymous> : 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
> > ... 52 lines ...
> > ‘query’
> > THYM.clinical.20160128: no visible global function definition for
> > ‘query’
> > UCEC.clinical.20160128: no visible global function definition for
> > ‘query’
> > UCS.clinical.20160128: no visible global function definition for
> > ‘query’
> > UVM.clinical.20160128: no visible global function definition for
> > ‘query’
> > Undefined global functions or variables:
> > query
> > > cat(readLines('NAMESPACE'), sep="\n")
> > # Generated by roxygen2: do not edit by hand
> >
> > import(ExperimentHub)
> > import(RTCGA)
> > importFrom(utils,read.csv)
> > > cat(readLines('DESCRIPTION'), sep="\n")
> > Package: RTCGA.clinical.20160128
> > Type: Package
> > Title: Clinical datasets from The Cancer Genome Atlas Project from
> > 2016-01-28
> > Version: 0.99.0
> > Date: 2016-11-29
> > Author: Marcin Kosinski <m.p.kosinski at gmail.com
> <mailto:m.p.kosinski at gmail.com>
> > <mailto:m.p.kosinski at gmail.com <mailto:m.p.kosinski at gmail.com>>>
> > Maintainer: Marcin Kosinski <m.p.kosinski at gmail.com
> <mailto:m.p.kosinski at gmail.com>
> > <mailto:m.p.kosinski at gmail.com <mailto:m.p.kosinski at gmail.com>>>
> > Description: Package provides clinical datasets from The Cancer Genome
> > Atlas
> > Project for all cohorts types from
> http://gdac.broadinstitute.org/ <http://gdac.broadinstitute.org/>
> > <http://gdac.broadinstitute.org/
> <http://gdac.broadinstitute.org/>>. Clinical
> > data format is explained on NCI TCGA wiki
> > https://wiki.nci.nih.gov/display/TCGA/
> <https://wiki.nci.nih.gov/display/TCGA/>
> > <https://wiki.nci.nih.gov/display/TCGA/
> <https://wiki.nci.nih.gov/display/TCGA/>>
> > Clinical+Data+Overview. Data taken from 2016-01-28 release. All
> > release dates are
> > available here http://gdac.broadinstitute.org/runs/
> <http://gdac.broadinstitute.org/runs/> .
> > License: GPL-2
> > LazyData: TRUE
> > Repository: Bioconductor
> > BugReports: https://github.com/RTCGA/RTCGA/issues
> <https://github.com/RTCGA/RTCGA/issues>
> > Depends: R (>= 3.2.0), RTCGA, ExperimentHub
> > Suggests: knitr
> > biocViews: Annotation Data
> > VignetteBuilder: knitr
> > NeedsCompilation: no
> > RoxygenNote: 5.0.1
> > TCGAdataSet: Merge_Clinical.Level_1
> > TCGAreleaseDate: 2016-01-28
> > TCGAdataType: clinical
> >
> > 2016-11-30 20:27 GMT+01:00 Obenchain, Valerie
> > <Valerie.Obenchain at roswellpark.org
> <mailto:Valerie.Obenchain at roswellpark.org>
> > <mailto:Valerie.Obenchain at roswellpark.org
> <mailto:Valerie.Obenchain at roswellpark.org>>>:
> >
> > 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
> <http://www.bioconductor.org/packages/3.4/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html>
> >
> <http://www.bioconductor.org/packages/3.4/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html
> <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]]
> > >
> > > _______________________________________________
> > > Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
> <mailto:Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>>
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> > >
> >
> >
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