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 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.kosin...@gmail.com > > <mailto:m.p.kosin...@gmail.com>> > > Maintainer: Marcin Kosinski <m.p.kosin...@gmail.com > > <mailto:m.p.kosin...@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.obench...@roswellpark.org > > <mailto:valerie.obench...@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]] > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > > mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > > > > > > > > > This email message may contain legally privileged and/or > > confidential information. If you are not the intended > > recipient(s), or the employee or agent responsible for the > > delivery of this message to the intended recipient(s), you are > > hereby notified that any disclosure, copying, distribution, or use > > of this email message is prohibited. If you have received this > > message in error, please notify the sender immediately by e-mail > > and delete this email message from your computer. Thank you. > > > > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
