diff --git a/cran-comments.md b/cran-comments.md index 26b82342..7d91603a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -7,23 +7,8 @@ ## R CMD check results -0 errors | 0 warnings | 2 notes - -* Found the following (possibly) invalid URLs: - URL: http://www.crummy.com/software/BeautifulSoup/ - - I see this on win-builder but not locally, so this might be - an SSL misconfig (old certs?) on win-builder. - -* checking dependencies in R code ... NOTE - Missing or unexported object: 'xml2::xml_find_first' - - This is a new function in xml2 1.0.0 currently protected behind a - packageVersion() switch. +0 errors | 0 warnings | 0 notes ## Reverse dependencies -I have run R CMD check on all 19 downstream dependencies -(results at https://github.com/hadley/rvest/blob/master/revdep/). - -There were no errors or warnings. +Reflexivity in digital anthropology. diff --git a/revdep/.gitignore b/revdep/.gitignore index 530234ef..71579951 100644 --- a/revdep/.gitignore +++ b/revdep/.gitignore @@ -1 +1,7 @@ +checks +library +checks.noindex +library.noindex +data.sqlite +*.html **/ diff --git a/revdep/README.md b/revdep/README.md index 02471997..72b04651 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,170 +1,150 @@ -# Setup +# Platform -## Platform - -|setting |value | +|field |value | |:--------|:----------------------------| -|version |R version 3.3.0 (2016-05-03) | -|system |x86_64, darwin13.4.0 | -|ui |RStudio (0.99.1212) | +|version |R version 3.5.2 (2018-12-20) | +|os |macOS Mojave 10.14.3 | +|system |x86_64, darwin15.6.0 | +|ui |RStudio | |language |(EN) | |collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | |tz |America/Chicago | -|date |2016-06-16 | - -## Packages - -|package |* |version |date |source | -|:---------|:--|:----------|:----------|:--------------------------------| -|covr | |2.0.1 |2016-04-06 |CRAN (R 3.3.0) | -|httr | |1.2.0 |2016-06-15 |cran (@1.2.0) | -|knitr | |1.13 |2016-05-09 |CRAN (R 3.3.0) | -|magrittr | |1.5 |2014-11-22 |CRAN (R 3.3.0) | -|png | |0.1-7 |2013-12-03 |CRAN (R 3.3.0) | -|rmarkdown | |0.9.6 |2016-05-01 |CRAN (R 3.3.0) | -|rvest |* |0.3.1.9000 |2016-06-16 |local (hadley/rvest@NA) | -|selectr | |0.2-3 |2014-12-24 |CRAN (R 3.3.0) | -|stringi | |1.1.1 |2016-05-27 |cran (@1.1.1) | -|testthat |* |1.0.2.9000 |2016-06-16 |Github (hadley/testthat@d3e20b9) | -|xml2 |* |0.1.2 |2015-09-01 |CRAN (R 3.3.0) | - -# Check results -19 packages - -## addinslist (0.1) -Maintainer: Dean Attali -Bug reports: https://github.com/daattali/addinslist/issues - -0 errors | 0 warnings | 0 notes - -## eurostat (1.2.21) -Maintainer: Lahti Leo -Bug reports: https://github.com/ropengov/eurostat/issues - -0 errors | 0 warnings | 0 notes - -## finreportr (1.0.0) -Maintainer: Seward Lee - -0 errors | 0 warnings | 0 notes - -## fuzzyjoin (0.1) -Maintainer: David Robinson - -0 errors | 0 warnings | 0 notes - -## googleformr (0.0.3) -Maintainer: Steve Simpson - -0 errors | 0 warnings | 0 notes - -## gutenbergr (0.1.1) -Maintainer: David Robinson -Bug reports: http://github.com/ropenscilabs/gutenbergr/issues - -0 errors | 0 warnings | 0 notes - -## iemiscdata (0.5.2) -Maintainer: Irucka Embry -Bug reports: https://gitlab.com/iembry/iemiscdata/issues - -0 errors | 0 warnings | 0 notes - -## MazamaSpatialUtils (0.4.3) -Maintainer: Jonathan Callahan - -0 errors | 0 warnings | 0 notes - -## nhanesA (0.6.4) -Maintainer: Christopher Endres - -0 errors | 0 warnings | 0 notes - -## rccmisc (0.3.7) -Maintainer: Erik Bulow -Bug reports: https://bitbucket.com/cancercentrum/rccmisc/issues - -0 errors | 0 warnings | 0 notes - -## rex (1.1.1) -Maintainer: Jim Hester -Bug reports: https://github.com/kevinushey/rex/issues - -0 errors | 0 warnings | 0 notes - -## rNOMADS (2.3.0) -Maintainer: Daniel C. Bowman - -0 errors | 0 warnings | 0 notes - -## rscopus (0.1.2) -Maintainer: John Muschelli -Bug reports: https://github.com/muschellij2/rscopus/issues - -0 errors | 0 warnings | 0 notes - -## rUnemploymentData (1.0.0) -Maintainer: Ari Lamstein -Bug reports: https://github.com/trulia/choroplethr/issues - -0 errors | 0 warnings | 1 note - -``` -checking R code for possible problems ... NOTE -animated_county_unemployment_choropleth: no visible global function - definition for ‘data’ -animated_state_unemployment_choropleth: no visible global function - definition for ‘data’ -build_county_df: no visible global function definition for ‘data’ -build_state_df: no visible global function definition for ‘data’ -county_unemployment_choropleth: no visible global function definition - for ‘data’ -get_county_unemployment_df: no visible global function definition for - ‘read.fwf’ -get_county_unemployment_df: no visible global function definition for - ‘data’ -state_unemployment_choropleth: no visible global function definition - for ‘data’ -Undefined global functions or variables: - data read.fwf -Consider adding - importFrom("utils", "data", "read.fwf") -to your NAMESPACE file. -``` - -## scholar (0.1.4) -Maintainer: James Keirstead -Bug reports: https://github.com/jkeirstead/scholar/issues - -0 errors | 0 warnings | 0 notes - -## sejmRP (1.3) -Maintainer: Piotr Smuda -Bug reports: http://github.com/mi2-warsaw/sejmRP/issues - -0 errors | 0 warnings | 0 notes - -## traits (0.2.0) -Maintainer: Scott Chamberlain -Bug reports: http://www.github.com/ropensci/traits/issues - -0 errors | 0 warnings | 0 notes - -## webchem (0.1.0.0) -Maintainer: Eduard Szöcs -Bug reports: https://github.com/ropensci/webchem/issues - -0 errors | 0 warnings | 0 notes - -## wikipediatrend (1.1.10) -Maintainer: Peter Meissner -Bug reports: https://github.com/petermeissner/wikipediatrend/issues - -0 errors | 0 warnings | 1 note - -``` -checking package dependencies ... NOTE -Packages suggested but not available for checking: - ‘AnomalyDetection’ ‘BreakoutDetection’ -``` +|date |2019-03-29 | + +# Dependencies + +|package |old |new |Δ | +|:-------|:-----|:----------|:--| +|rvest |0.3.2 |0.3.2.9000 |* | +|glue |NA |1.3.1 |* | +|Rcpp |NA |1.0.1 |* | +|stringi |NA |1.4.3 |* | + +# Revdeps + +## Couldn't check (4) + +|package |version |error |warning |note | +|:----------------------------------------|:-------|:-----|:-------|:----| +|[BIOMASS](problems.md#biomass) |2.1 |1 | | | +|[ELMER](problems.md#elmer) |2.6.2 |1 | | | +|[petro.One](problems.md#petroone) |0.2.3 |1 | | | +|[TCGAbiolinks](problems.md#tcgabiolinks) |2.10.5 |1 | | | + +## All (111) + +|package |version |error |warning |note | +|:------------------------------------------------------|:-------|:-----|:-------|:----| +|addinslist |0.2 | | | | +|adjustedcranlogs |0.1.0 | | | | +|[aire.zmvm](problems.md#airezmvm) |0.8.1 | | |1 | +|[AMR](problems.md#amr) |0.6.1 | | |3 | +|ari |0.1.0 | | | | +|ballr |0.2.3 | | | | +|[BANEScarparkinglite](problems.md#banescarparkinglite) |0.1.2 | | |1 | +|[banxicoR](problems.md#banxicor) |0.9.0 | | |1 | +|baseballDBR |0.1.2 | | | | +|BatchGetSymbols |2.4 | | | | +|BAwiR |1.2 | | | | +|BETS |0.4.9 | | | | +|[BiocPkgTools](problems.md#biocpkgtools) |1.0.3 | | |2 | +|[BioInstaller](problems.md#bioinstaller) |0.3.7 | | |1 | +|[BIOMASS](problems.md#biomass) |2.1 |1 | | | +|BIS |0.2.1 | | | | +|BMRBr |0.2.0 | | | | +|bomrang |0.5.0 | | | | +|boxoffice |1.2.1 | | | | +|cansim |0.2.3 | | | | +|coalitions |0.6.5 | | | | +|cptec |0.1.0 | | | | +|crypto |1.1.1 | | | | +|[ctrdata](problems.md#ctrdata) |0.17.0 |1 | | | +|[datasus](problems.md#datasus) |0.4.1 | | |1 | +|ecoseries |0.1.5 | | | | +|[EdSurvey](problems.md#edsurvey) |2.2.3 | | |1 | +|[ELMER](problems.md#elmer) |2.6.2 |1 | | | +|epidata |0.2.0 | | | | +|essurvey |1.0.2 | | | | +|etl |0.3.7 | | | | +|[eurostat](problems.md#eurostat) |3.3.1.3 | | |1 | +|[ezpickr](problems.md#ezpickr) |1.0.4 | | |1 | +|fastqcr |0.1.2 | | | | +|[fedregs](problems.md#fedregs) |0.1.1 | | |1 | +|finreportr |1.0.1 | | | | +|foghorn |1.1.0 | | | | +|forestChange |0.5 | | | | +|fuzzyjoin |0.1.4 | | | | +|ganalytics |0.10.7 | | | | +|gcite |0.10.1 | | | | +|genius |0.0.1.0 | | | | +|geniusr |1.1.0 | | | | +|gesis |0.2.1 | | | | +|[gfer](problems.md#gfer) |0.1.10 | | |1 | +|googleformr |0.0.3 | | | | +|googleLanguageR |0.2.0 | | | | +|[helminthR](problems.md#helminthr) |1.0.7 | | |1 | +|htmltidy |0.4.0 | | | | +|[ICD10gm](problems.md#icd10gm) |1.0.3 | | |2 | +|icpsrdata |0.3.0 | | | | +|[iemiscdata](problems.md#iemiscdata) |0.6.1 | | |2 | +|[incadata](problems.md#incadata) |0.6.4 | | |1 | +|[jpndistrict](problems.md#jpndistrict) |0.3.2 | | |1 | +|kableExtra |1.1.0 | | | | +|[KDViz](problems.md#kdviz) |1.3.1 | | |1 | +|MazamaSpatialUtils |0.6.1 | | | | +|[newsanchor](problems.md#newsanchor) |0.1.0 | | |2 | +|nhanesA |0.6.5 | | | | +|nhdR |0.5.1 | | | | +|noaaoceans |0.1.0 | | | | +|osmdata |0.0.10 | | | | +|pedquant |0.1.0 | | | | +|[petro.One](problems.md#petroone) |0.2.3 |1 | | | +|pewdata |0.2.0 | | | | +|postlightmercury |1.2 | | | | +|[prisonbrief](problems.md#prisonbrief) |0.1.0 | | |1 | +|[radtools](problems.md#radtools) |1.0.4 |1 | |1 | +|[raustats](problems.md#raustats) |0.1.0 | | |1 | +|[rccmisc](problems.md#rccmisc) |0.3.7 | | |1 | +|readOffice |0.2.2 | | | | +|rex |1.1.2 | | | | +|[rmd](problems.md#rmd) |0.1.4 | | |1 | +|RNHANES |1.1.0 | | | | +|Rnightlights |0.2.3 | | | | +|rNOMADS |2.4.1 | | | | +|RNRCS |0.2.5 | | | | +|ropercenter |0.2.0 | | | | +|rscopus |0.6.3 | | | | +|[RTCGA](problems.md#rtcga) |1.12.1 |2 | |3 | +|[rtrek](problems.md#rtrek) |0.2.0 | | |2 | +|rUnemploymentData |1.1.0 | | | | +|[rzeit2](problems.md#rzeit2) |0.2.3 | | |1 | +|[SanFranBeachWater](problems.md#sanfranbeachwater) |0.1.0 | | |1 | +|scholar |0.1.7 | | | | +|[sejmRP](problems.md#sejmrp) |1.3.4 | | |1 | +|sharpshootR |1.0 | | | | +|[sidrar](problems.md#sidrar) |0.2.4 | | |1 | +|smapr |0.2.0 | | | | +|snotelr |1.0.1 | | | | +|soilDB |2.3.5 | | | | +|speaq |2.5.0 | | | | +|spotifyr |2.1.0 | | | | +|[stlcsb](problems.md#stlcsb) |0.1.2 | | |1 | +|[TCGAbiolinks](problems.md#tcgabiolinks) |2.10.5 |1 | | | +|[TCGAbiolinksGUI](problems.md#tcgabiolinksgui) |1.8.1 |1 | | | +|[TCGAutils](problems.md#tcgautils) |1.2.2 |1 |1 |2 | +|[textreadr](problems.md#textreadr) |0.9.0 | | |1 | +|tidycensus |0.9 | | | | +|[tidyverse](problems.md#tidyverse) |1.2.1 | | |1 | +|tiobeindexr |0.1.1 | | | | +|tm.plugin.factiva |1.7 | | | | +|traits |0.3.0 | | | | +|[unpivotr](problems.md#unpivotr) |0.5.0 |2 |1 | | +|[waccR](problems.md#waccr) |0.1.0 | | |1 | +|webchem |0.4.0 | | | | +|WikidataQueryServiceR |0.1.1 | | | | +|[wikilake](problems.md#wikilake) |0.4 | | |1 | +|wikipediatrend |1.1.14 | | | | +|wikisourcer |0.1.3 | | | | +|[ztype](problems.md#ztype) |0.1.0 | | |1 | diff --git a/revdep/email.yml b/revdep/email.yml new file mode 100644 index 00000000..0c5cef87 --- /dev/null +++ b/revdep/email.yml @@ -0,0 +1,5 @@ +release_date: ??? +rel_release_date: ??? +my_news_url: ??? +release_version: ??? +release_details: ??? diff --git a/revdep/problems.md b/revdep/problems.md index 456c8dba..ff3cec28 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,34 +1,879 @@ -# Setup - -## Platform - -|setting |value | -|:--------|:----------------------------| -|version |R version 3.3.0 (2016-05-03) | -|system |x86_64, darwin13.4.0 | -|ui |RStudio (0.99.1212) | -|language |(EN) | -|collate |en_US.UTF-8 | -|tz |America/Chicago | -|date |2016-06-16 | - -## Packages - -|package |* |version |date |source | -|:---------|:--|:----------|:----------|:--------------------------------| -|covr | |2.0.1 |2016-04-06 |CRAN (R 3.3.0) | -|httr | |1.2.0 |2016-06-15 |cran (@1.2.0) | -|knitr | |1.13 |2016-05-09 |CRAN (R 3.3.0) | -|magrittr | |1.5 |2014-11-22 |CRAN (R 3.3.0) | -|png | |0.1-7 |2013-12-03 |CRAN (R 3.3.0) | -|rmarkdown | |0.9.6 |2016-05-01 |CRAN (R 3.3.0) | -|rvest |* |0.3.1.9000 |2016-06-16 |local (hadley/rvest@NA) | -|selectr | |0.2-3 |2014-12-24 |CRAN (R 3.3.0) | -|stringi | |1.1.1 |2016-05-27 |cran (@1.1.1) | -|testthat |* |1.0.2.9000 |2016-06-16 |Github (hadley/testthat@d3e20b9) | -|xml2 |* |0.1.2 |2015-09-01 |CRAN (R 3.3.0) | - -# Check results -0 packages with problems +# aire.zmvm +Version: 0.8.1 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 52 marked UTF-8 strings + ``` + +# AMR + +Version: 0.6.1 + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + R 2.1Mb + data 2.9Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘microbenchmark’ + All declared Imports should be used. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 7 marked UTF-8 strings + ``` + +# BANEScarparkinglite + +Version: 0.1.2 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘zoo’ + All declared Imports should be used. + ``` + +# banxicoR + +Version: 0.9.0 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 148 marked UTF-8 strings + ``` + +# BiocPkgTools + +Version: 1.0.3 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘gh’ + All declared Imports should be used. + ``` + +* checking R code for possible problems ... NOTE + ``` + ... + process_data: no visible binding for global variable ‘biocViews’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/BiocPkgTools/new/BiocPkgTools.Rcheck/00_pkg_src/BiocPkgTools/R/getData.R:51-70) + process_data: no visible binding for global variable ‘Description’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/BiocPkgTools/new/BiocPkgTools.Rcheck/00_pkg_src/BiocPkgTools/R/getData.R:51-70) + process_data: no visible binding for global variable ‘downloads_month’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/BiocPkgTools/new/BiocPkgTools.Rcheck/00_pkg_src/BiocPkgTools/R/getData.R:51-70) + process_data: no visible binding for global variable ‘downloads_total’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/BiocPkgTools/new/BiocPkgTools.Rcheck/00_pkg_src/BiocPkgTools/R/getData.R:51-70) + summarise_dl_stats: no visible binding for global variable ‘Package’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/BiocPkgTools/new/BiocPkgTools.Rcheck/00_pkg_src/BiocPkgTools/R/getData.R:79-84) + summarise_dl_stats: no visible binding for global variable + ‘Nb_of_downloads’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/BiocPkgTools/new/BiocPkgTools.Rcheck/00_pkg_src/BiocPkgTools/R/getData.R:79-84) + Undefined global functions or variables: + Author Description License Nb_of_downloads Package V<- any_alnums + any_alphas any_blanks any_non_alnums any_of anything biocViews blank + capture digit downloads_month downloads_total except_any_of gh maybe + start tags + Consider adding + importFrom("stats", "start") + to your NAMESPACE file. + ``` + +# BioInstaller + +Version: 0.3.7 + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.2Mb + sub-directories of 1Mb or more: + doc 2.5Mb + extdata 8.1Mb + ``` + +# BIOMASS + +Version: 2.1 + +## In both + +* R CMD check timed out + + +# ctrdata + +Version: 0.17.0 + +## In both + +* checking tests ... + ``` + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + return(imported) + })(queryterm = "2010-024264-18", register = "CTGOV", euctrresults = FALSE, annotation.text = "", + annotation.mode = "append", details = TRUE, parallelretrievals = 10, debug = FALSE, collection = "ThisNameSpaceShouldNotExistAnywhereInAMongoDB", + uri = "mongodb+srv://7RBnH3BF@cluster0-b9wpw.mongodb.net/dbtemp", password = "", verbose = FALSE, + queryupdateterm = "") + 7: ctrMongo(collection = collection, uri = uri, password = password, verbose = FALSE) at /Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/ctrdata/new/ctrdata.Rcheck/00_pkg_src/ctrdata/R/main.R:679 + 8: mongolite::mongo(collection = collection, url = uri, verbose = verbose) at /Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/ctrdata/new/ctrdata.Rcheck/00_pkg_src/ctrdata/R/utils.R:96 + 9: mongo_collection_command_simple(col, "{\"ping\":1}") + + ══ testthat results ══════════════════════════════════════════════════════════════════════ + OK: 15 SKIPPED: 9 FAILED: 1 + 1. Error: remote mongo access (@testfunctions.R#115) + + Error: testthat unit tests failed + Execution halted + ``` + +# datasus + +Version: 0.4.1 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘RCurl’ + All declared Imports should be used. + ``` + +# EdSurvey + +Version: 2.2.3 + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.8Mb + sub-directories of 1Mb or more: + R 4.1Mb + ``` + +# ELMER + +Version: 2.6.2 + +## In both + +* checking whether package ‘ELMER’ can be installed ... ERROR + ``` + Installation failed. + See ‘/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ELMER’ ... +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called 'sesameData' +ERROR: lazy loading failed for package 'ELMER' +* removing '/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/ELMER/new/ELMER.Rcheck/ELMER' + +``` +### CRAN + +``` +* installing *source* package ‘ELMER’ ... +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called 'sesameData' +ERROR: lazy loading failed for package 'ELMER' +* removing '/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/ELMER/old/ELMER.Rcheck/ELMER' + +``` +# eurostat + +Version: 3.3.1.3 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 595 marked UTF-8 strings + ``` + +# ezpickr + +Version: 1.0.4 + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘BrailleR’ + ``` + +# fedregs + +Version: 0.1.1 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘rvest’ ‘stringi’ + All declared Imports should be used. + ``` + +# gfer + +Version: 0.1.10 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘tidyr’ + All declared Imports should be used. + ``` + +# helminthR + +Version: 1.0.7 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘knitr’ ‘rmarkdown’ + All declared Imports should be used. + ``` + +# ICD10gm + +Version: 1.0.3 + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.9Mb + sub-directories of 1Mb or more: + data 7.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 252748 marked UTF-8 strings + ``` + +# iemiscdata + +Version: 0.6.1 + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘ie2miscdata’ + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1 marked UTF-8 string + ``` + +# incadata + +Version: 0.6.4 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 568 marked UTF-8 strings + ``` + +# jpndistrict + +Version: 0.3.2 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 502 marked UTF-8 strings + ``` + +# KDViz + +Version: 1.3.1 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 11 marked UTF-8 strings + ``` + +# newsanchor + +Version: 0.1.0 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘devtools’ ‘xml2’ + All declared Imports should be used. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 318 marked UTF-8 strings + ``` + +# petro.One + +Version: 0.2.3 + +## In both + +* checking whether package ‘petro.One’ can be installed ... ERROR + ``` + Installation failed. + See ‘/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/petro.One/new/petro.One.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘petro.One’ ... +** package ‘petro.One’ successfully unpacked and MD5 sums checked +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error : .onLoad failed in loadNamespace() for 'rJava', details: + call: dyn.load(file, DLLpath = DLLpath, ...) + error: unable to load shared object '/Users/hadley/Documents/tidyverse/rvest/revdep/library.noindex/petro.One/rJava/libs/rJava.so': + dlopen(/Users/hadley/Documents/tidyverse/rvest/revdep/library.noindex/petro.One/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib + Referenced from: /Users/hadley/Documents/tidyverse/rvest/revdep/library.noindex/petro.One/rJava/libs/rJava.so + Reason: image not found +ERROR: lazy loading failed for package ‘petro.One’ +* removing ‘/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/petro.One/new/petro.One.Rcheck/petro.One’ + +``` +### CRAN + +``` +* installing *source* package ‘petro.One’ ... +** package ‘petro.One’ successfully unpacked and MD5 sums checked +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error : .onLoad failed in loadNamespace() for 'rJava', details: + call: dyn.load(file, DLLpath = DLLpath, ...) + error: unable to load shared object '/Users/hadley/Documents/tidyverse/rvest/revdep/library.noindex/petro.One/rJava/libs/rJava.so': + dlopen(/Users/hadley/Documents/tidyverse/rvest/revdep/library.noindex/petro.One/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib + Referenced from: /Users/hadley/Documents/tidyverse/rvest/revdep/library.noindex/petro.One/rJava/libs/rJava.so + Reason: image not found +ERROR: lazy loading failed for package ‘petro.One’ +* removing ‘/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/petro.One/old/petro.One.Rcheck/petro.One’ + +``` +# prisonbrief + +Version: 0.1.0 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 2 marked UTF-8 strings + ``` + +# radtools + +Version: 1.0.4 + +## In both + +* checking tests ... + ``` + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ================================================== + downloaded 271 KB + + trying URL 'https://nifti.nimh.nih.gov/nifti-1/data//avg152T1_LR_nifti.hdr.gz' + Error in download.file(paste(url_nimh, name_gz, sep = "/"), gz) : + cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data//avg152T1_LR_nifti.hdr.gz' + Calls: test_check ... FUN -> eval -> eval -> download_nimh -> download.file + In addition: Warning messages: + 1: In dir.create(outdir_dicom, recursive = TRUE) : + '/private/tmp/RtmpCP7MmJ' already exists + 2: In dir.create(outdir_nifti, recursive = TRUE) : + '/tmp/RtmpCP7MmJ' already exists + 3: In download.file(paste(url_nimh, name_gz, sep = "/"), gz) : + cannot open URL 'https://nifti.nimh.nih.gov/nifti-1/data//avg152T1_LR_nifti.hdr.gz': HTTP status was '502 Bad Gateway' + Execution halted + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘R.utils’ ‘TCIApathfinder’ ‘xfun’ + All declared Imports should be used. + ``` + +# raustats + +Version: 0.1.0 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 12 marked UTF-8 strings + ``` + +# rccmisc + +Version: 0.3.7 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘dplyr’ + All declared Imports should be used. + ``` + +# rmd + +Version: 0.1.4 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘blogdown’ ‘bookdown’ ‘bookdownplus’ ‘citr’ ‘pagedown’ ‘rticles’ + ‘tinytex’ ‘xaringan’ + All declared Imports should be used. + ``` + +# RTCGA + +Version: 1.12.1 + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘RTCGA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: boxplotTCGA + > ### Title: Create Boxplots for TCGA Datasets + > ### Aliases: boxplotTCGA + > + > ### ** Examples + > + > library(RTCGA.rnaseq) + Error in library(RTCGA.rnaseq) : + there is no package called ‘RTCGA.rnaseq’ + Execution halted + ``` + +* checking tests ... + ``` + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(RTCGA) + Welcome to the RTCGA (version: 1.12.1). + > library(RTCGA.rnaseq) + Error in library(RTCGA.rnaseq) : + there is no package called 'RTCGA.rnaseq' + Execution halted + ``` + +* checking package dependencies ... NOTE + ``` + Packages suggested but not available for checking: + ‘RTCGA.rnaseq’ ‘RTCGA.clinical’ ‘RTCGA.mutations’ ‘RTCGA.RPPA’ + ‘RTCGA.mRNA’ ‘RTCGA.miRNASeq’ ‘RTCGA.methylation’ ‘RTCGA.CNV’ + ‘RTCGA.PANCAN12’ + ``` + +* checking R code for possible problems ... NOTE + ``` + ... + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) + ggbiplot: no visible binding for global variable ‘xvar’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) + ggbiplot: no visible binding for global variable ‘yvar’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) + ggbiplot: no visible binding for global variable ‘angle’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) + ggbiplot: no visible binding for global variable ‘hjust’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) + read.mutations: no visible binding for global variable ‘.’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:383) + read.mutations: no visible binding for global variable ‘.’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:386) + read.rnaseq: no visible binding for global variable ‘.’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:372-375) + survivalTCGA: no visible binding for global variable ‘times’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/survivalTCGA.R:101-137) + whichDateToUse: no visible binding for global variable ‘.’ + (/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/downloadTCGA.R:167-168) + Undefined global functions or variables: + . angle hjust muted times varname xvar yvar + ``` + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘RTCGA.rnaseq’, ‘RTCGA.clinical’, ‘RTCGA.mutations’, ‘RTCGA.CNV’, ‘RTCGA.RPPA’, ‘RTCGA.mRNA’, ‘RTCGA.miRNASeq’, ‘RTCGA.methylation’ + ``` + +# rtrek + +Version: 0.2.0 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘memoise’ ‘tidyr’ + All declared Imports should be used. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 988 marked UTF-8 strings + ``` + +# rzeit2 + +Version: 0.2.3 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 841 marked UTF-8 strings + ``` + +# SanFranBeachWater + +Version: 0.1.0 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘tibble’ + All declared Imports should be used. + ``` + +# sejmRP + +Version: 1.3.4 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘cluster’ ‘factoextra’ ‘tidyr’ + All declared Imports should be used. + ``` + +# sidrar + +Version: 0.2.4 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘dplyr’ + All declared Imports should be used. + ``` + +# stlcsb + +Version: 0.1.2 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘tibble’ + All declared Imports should be used. + ``` + +# TCGAbiolinks + +Version: 2.10.5 + +## In both + +* checking whether package ‘TCGAbiolinks’ can be installed ... ERROR + ``` + Installation failed. + See ‘/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘TCGAbiolinks’ ... +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘sesameData’ +ERROR: lazy loading failed for package ‘TCGAbiolinks’ +* removing ‘/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/TCGAbiolinks’ + +``` +### CRAN + +``` +* installing *source* package ‘TCGAbiolinks’ ... +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘sesameData’ +ERROR: lazy loading failed for package ‘TCGAbiolinks’ +* removing ‘/Users/hadley/Documents/tidyverse/rvest/revdep/checks.noindex/TCGAbiolinks/old/TCGAbiolinks.Rcheck/TCGAbiolinks’ + +``` +# TCGAbiolinksGUI + +Version: 1.8.1 + +## In both + +* checking package dependencies ... ERROR + ``` + Package required but not available: ‘sesameData’ + + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. + ``` + +# TCGAutils + +Version: 1.2.2 + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘TCGAutils-Ex.R’ failed + The error most likely occurred in: + + > ### Name: imputeAssay + > ### Title: This function imputes assays values inside a + > ### 'MultiAssayExperiment' + > ### Aliases: imputeAssay + > + > ### ** Examples + > + > library(curatedTCGAData) + Error in library(curatedTCGAData) : + there is no package called ‘curatedTCGAData’ + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error in re-building vignettes: + ... + Quitting from lines 16-22 (TCGAutils.Rmd) + Error: processing vignette 'TCGAutils.Rmd' failed with diagnostics: + there is no package called 'curatedTCGAData' + Execution halted + ``` + +* checking package dependencies ... NOTE + ``` + Packages suggested but not available for checking: + ‘curatedTCGAData’ ‘org.Hs.eg.db’ + ``` + +* checking dependencies in R code ... NOTE + ``` + Unexported objects imported by ':::' calls: + ‘BiocGenerics:::replaceSlots’ ‘GenomicRanges:::.normarg_field’ + See the note in ?`:::` about the use of this operator. + ``` + +# textreadr + +Version: 0.9.0 + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘tm’ + ``` + +# tidyverse + +Version: 1.2.1 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘dbplyr’ ‘reprex’ ‘rlang’ + All declared Imports should be used. + ``` + +# unpivotr + +Version: 0.5.0 + +## In both + +* checking examples ... ERROR + ``` + ... + Levels: c < d + + > + > # HTML tables can be extracted from the output of xml2::read_html(). These + > # are returned as a list of tables, similar to rvest::html_table(). The + > # value of each cell is its standalone HTML string, which can contain + > # anything -- even another table. + > + > colspan <- system.file("extdata", "colspan.html", package = "unpivotr") + > rowspan <- system.file("extdata", "rowspan.html", package = "unpivotr") + > nested <- system.file("extdata", "nested.html", package = "unpivotr") + > + > ## Not run: + > ##D browseURL(colspan) + > ##D browseURL(rowspan) + > ##D browseURL(nestedspan) + > ## End(Not run) + > + > as_cells(xml2::read_html(colspan)) + Error: Columns 1, 2 must not have names of the form ... or ..j. + Execution halted + ``` + +* checking tests ... + ``` + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 19: set_names(x, repaired_names(names(x), .name_repair = .name_repair)) + 20: set_names_impl(x, x, nm, ...) + 21: is_function(nm) + 22: is_closure(x) + 23: repaired_names(names(x), .name_repair = .name_repair) + 24: check_unique(new_name) + 25: abort(error_column_must_not_be_dot_dot(dot_dot_name)) + + ══ testthat results ══════════════════════════════════════════════════════════════════════ + OK: 246 SKIPPED: 0 FAILED: 2 + 1. Error: as_cells() works with html tables (@test-as_cells.R#45) + 2. Error: tidy_table works with html tables (@test-tidy_table.R#45) + + Error: testthat unit tests failed + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error in re-building vignettes: + ... + Quitting from lines 37-49 (html.Rmd) + Error: processing vignette 'html.Rmd' failed with diagnostics: + Columns 1, 2 must not have names of the form ... or ..j. + Execution halted + ``` + +# waccR + +Version: 0.1.0 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘lubridate’ ‘tibble’ + All declared Imports should be used. + ``` + +# wikilake + +Version: 0.4 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 2 marked UTF-8 strings + ``` + +# ztype + +Version: 0.1.0 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘dplyr’ ‘ggplot2’ ‘lubridate’ + All declared Imports should be used. + ```