[Bioc-devel] [Bioc-degel] AnnotationHub needed in the description of the ExperimentHubData
Marcin Kosiński
m.p.kosinski at gmail.com
Thu Dec 1 16:12:43 CET 2016
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>
Maintainer: Marcin Kosinski <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/.
Clinical
data format is explained on NCI TCGA wiki
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>:
> 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]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
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