[Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData
Marcin Kosiński
m.p.kosinski at gmail.com
Tue Dec 6 19:38:29 CET 2016
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>:
> 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>>
> > Maintainer: Marcin Kosinski <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/>. Clinical
> > data format is explained on NCI TCGA wiki
> > 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/ .
> > License: GPL-2
> > LazyData: TRUE
> > Repository: Bioconductor
> > BugReports: 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>>:
> >
> > 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>
> > > 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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> > >
> >
> >
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