diff --git a/cran-comments.md b/cran-comments.md index 20257fd0..42ecefeb 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,10 @@ ## R CMD check results 0 errors | 0 warnings | 0 note + +## revdepcheck results + +We checked 570 reverse dependencies (526 from CRAN + 44 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. + + * We saw 0 new problems + * We failed to check 0 packages diff --git a/revdep/README.md b/revdep/README.md index 709b0bfb..52e12c71 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,58 +1,2 @@ # Revdeps -## Failed to check (44) - -|package |version |error |warning |note | -|:------------------------------|:-------|:-----|:-------|:----| -|BiocPkgTools |? | | | | -|biodb |? | | | | -|biomaRt |? | | | | -|cola |? | | | | -|CompoundDb |? | | | | -|ELMER |? | | | | -|EpiTxDb |? | | | | -|ExpressionAtlas |? | | | | -|GenomicDataCommons |? | | | | -|GEOexplorer |? | | | | -|GEOfastq |? | | | | -|GEOquery |? | | | | -|Gviz |? | | | | -|healthyControlsPresenceChecker |? | | | | -|HPAanalyze |? | | | | -|immunotation |? | | | | -|InterMineR |? | | | | -|levi |? | | | | -|Macarron |? | | | | -|MACSQuantifyR |? | | | | -|MBQN |? | | | | -|memes |? | | | | -|mosbi |? | | | | -|ncRNAtools |? | | | | -|OmnipathR |? | | | | -|ORFik |? | | | | -|PhyloProfile |? | | | | -|RBioFormats |? | | | | -|rfaRm |? | | | | -|RGMQL |? | | | | -|rpx |? | | | | -|RTCGA |? | | | | -|SBGNview |? | | | | -|scPipe |? | | | | -|scRNAseqApp |? | | | | -|simona |? | | | | -|spatialHeatmap |? | | | | -|surfaltr |? | | | | -|syntenet |? | | | | -|TCGAbiolinks |? | | | | -|TCGAutils |? | | | | -|topdownr |? | | | | -|treeio |? | | | | -|tRNAdbImport |? | | | | - -## New problems (2) - -|package |version |error |warning |note | -|:----------|:-------|:------|:-------|:----| -|[fhircrackr](problems.md#fhircrackr)|2.1.1 |__+2__ | | | -|[pmparser](problems.md#pmparser)|1.0.17 |__+2__ | | | - diff --git a/revdep/cran.md b/revdep/cran.md index 90a63b17..d07935b8 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,20 +1,7 @@ ## revdepcheck results -We checked 570 reverse dependencies (526 from CRAN + 44 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 2 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 2 new problems + * We saw 0 new problems * We failed to check 0 packages -Issues with CRAN packages are summarised below. - -### New problems -(This reports the first line of each new failure) - -* fhircrackr - checking examples ... ERROR - checking re-building of vignette outputs ... ERROR - -* pmparser - checking examples ... ERROR - checking tests ... ERROR - diff --git a/revdep/failures.md b/revdep/failures.md index ceb9214e..9a207363 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,1540 +1 @@ -# BiocPkgTools - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/BiocPkgTools -* Number of recursive dependencies: 164 - -Run `revdepcheck::cloud_details(, "BiocPkgTools")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# biodb - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/biodb -* Number of recursive dependencies: 124 - -Run `revdepcheck::cloud_details(, "biodb")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# biomaRt - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/biomaRt -* Number of recursive dependencies: 102 - -Run `revdepcheck::cloud_details(, "biomaRt")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# cola - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/cola -* Number of recursive dependencies: 244 - -Run `revdepcheck::cloud_details(, "cola")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# CompoundDb - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/CompoundDb -* Number of recursive dependencies: 124 - -Run `revdepcheck::cloud_details(, "CompoundDb")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# ELMER - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/ELMER -* Number of recursive dependencies: 231 - -Run `revdepcheck::cloud_details(, "ELMER")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# EpiTxDb - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/EpiTxDb -* Number of recursive dependencies: 161 - -Run `revdepcheck::cloud_details(, "EpiTxDb")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# ExpressionAtlas - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/ExpressionAtlas -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "ExpressionAtlas")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# GenomicDataCommons - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/GenomicDataCommons -* Number of recursive dependencies: 160 - -Run `revdepcheck::cloud_details(, "GenomicDataCommons")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# GEOexplorer - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/GEOexplorer -* Number of recursive dependencies: 223 - -Run `revdepcheck::cloud_details(, "GEOexplorer")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# GEOfastq - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/GEOfastq -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "GEOfastq")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# GEOquery - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/GEOquery -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "GEOquery")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# Gviz - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/Gviz -* Number of recursive dependencies: 162 - -Run `revdepcheck::cloud_details(, "Gviz")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# healthyControlsPresenceChecker - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/healthyControlsPresenceChecker -* Number of recursive dependencies: 94 - -Run `revdepcheck::cloud_details(, "healthyControlsPresenceChecker")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# HPAanalyze - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/HPAanalyze -* Number of recursive dependencies: 120 - -Run `revdepcheck::cloud_details(, "HPAanalyze")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# immunotation - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/immunotation -* Number of recursive dependencies: 103 - -Run `revdepcheck::cloud_details(, "immunotation")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# InterMineR - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/InterMineR -* Number of recursive dependencies: 157 - -Run `revdepcheck::cloud_details(, "InterMineR")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# levi - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/levi -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "levi")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# Macarron - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/Macarron -* Number of recursive dependencies: 205 - -Run `revdepcheck::cloud_details(, "Macarron")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# MACSQuantifyR - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/MACSQuantifyR -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "MACSQuantifyR")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# MBQN - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/MBQN -* Number of recursive dependencies: 102 - -Run `revdepcheck::cloud_details(, "MBQN")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# memes - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/memes -* Number of recursive dependencies: 162 - -Run `revdepcheck::cloud_details(, "memes")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# mosbi - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/mosbi -* Number of recursive dependencies: 110 - -Run `revdepcheck::cloud_details(, "mosbi")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# ncRNAtools - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/ncRNAtools -* Number of recursive dependencies: 72 - -Run `revdepcheck::cloud_details(, "ncRNAtools")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# OmnipathR - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/OmnipathR -* Number of recursive dependencies: 166 - -Run `revdepcheck::cloud_details(, "OmnipathR")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# ORFik - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/ORFik -* Number of recursive dependencies: 156 - -Run `revdepcheck::cloud_details(, "ORFik")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# PhyloProfile - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/PhyloProfile -* Number of recursive dependencies: 145 - -Run `revdepcheck::cloud_details(, "PhyloProfile")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# RBioFormats - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/RBioFormats -* Number of recursive dependencies: 70 - -Run `revdepcheck::cloud_details(, "RBioFormats")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# rfaRm - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/rfaRm -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "rfaRm")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# RGMQL - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/RGMQL -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "RGMQL")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# rpx - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/rpx -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "rpx")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# RTCGA - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/RTCGA -* Number of recursive dependencies: 181 - -Run `revdepcheck::cloud_details(, "RTCGA")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# SBGNview - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/SBGNview -* Number of recursive dependencies: 103 - -Run `revdepcheck::cloud_details(, "SBGNview")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# scPipe - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/scPipe -* Number of recursive dependencies: 263 - -Run `revdepcheck::cloud_details(, "scPipe")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# scRNAseqApp - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/scRNAseqApp -* Number of recursive dependencies: 236 - -Run `revdepcheck::cloud_details(, "scRNAseqApp")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# simona - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/simona -* Number of recursive dependencies: 138 - -Run `revdepcheck::cloud_details(, "simona")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# spatialHeatmap - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/spatialHeatmap -* Number of recursive dependencies: 300 - -Run `revdepcheck::cloud_details(, "spatialHeatmap")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# surfaltr - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/surfaltr -* Number of recursive dependencies: 158 - -Run `revdepcheck::cloud_details(, "surfaltr")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# syntenet - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/syntenet -* Number of recursive dependencies: 145 - -Run `revdepcheck::cloud_details(, "syntenet")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# TCGAbiolinks - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/TCGAbiolinks -* Number of recursive dependencies: 354 - -Run `revdepcheck::cloud_details(, "TCGAbiolinks")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# TCGAutils - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/TCGAutils -* Number of recursive dependencies: 228 - -Run `revdepcheck::cloud_details(, "TCGAutils")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# topdownr - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/topdownr -* Number of recursive dependencies: 118 - -Run `revdepcheck::cloud_details(, "topdownr")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# treeio - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/treeio -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "treeio")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# tRNAdbImport - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/tRNAdbImport -* Number of recursive dependencies: 116 - -Run `revdepcheck::cloud_details(, "tRNAdbImport")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` +*Wow, no problems at all. :)* \ No newline at end of file diff --git a/revdep/problems.md b/revdep/problems.md index 4e284ccd..9a207363 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,127 +1 @@ -# fhircrackr - -
- -* Version: 2.1.1 -* GitHub: https://github.com/POLAR-fhiR/fhircrackr -* Source code: https://github.com/cran/fhircrackr -* Date/Publication: 2023-02-10 09:30:07 UTC -* Number of recursive dependencies: 38 - -Run `revdepcheck::cloud_details(, "fhircrackr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘fhircrackr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: transaction_bundle_example - > ### Title: Toy examples to POST/PUT on a server - > ### Aliases: transaction_bundle_example example_resource1 example_resource2 - > ### example_resource3 - > ### Keywords: datasets - > - > ### ** Examples - > - > #unserialize xml objects before doing anything else with them! - > fhir_unserialize(bundles = transaction_bundle_example) - Error in xml2::xml_name(x = object) : Unexpected node type - Calls: fhir_unserialize ... anyStrings -> isTRUE -> validityMethod -> - Execution halted - ``` - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - --- re-building ‘downloadResources.Rmd’ using rmarkdown - - Quitting from lines 128-129 [unnamed-chunk-7] (downloadResources.Rmd) - Error: processing vignette 'downloadResources.Rmd' failed with diagnostics: - Unexpected node type - --- failed re-building ‘downloadResources.Rmd’ - - --- re-building ‘fhircrackr_intro.Rmd’ using rmarkdown - - ... - Error: processing vignette 'recreateResources.Rmd' failed with diagnostics: - Unexpected node type - --- failed re-building ‘recreateResources.Rmd’ - - SUMMARY: processing the following files failed: - ‘downloadResources.Rmd’ ‘fhircrackr_intro.Rmd’ ‘flattenResources.Rmd’ - ‘recreateResources.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# pmparser - -
- -* Version: 1.0.17 -* GitHub: https://github.com/hugheylab/pmparser -* Source code: https://github.com/cran/pmparser -* Date/Publication: 2023-05-23 23:32:04 UTC -* Number of recursive dependencies: 87 - -Run `revdepcheck::cloud_details(, "pmparser")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pmparser-Ex.R’ failed - The error most likely occurred in: - - > ### Name: parseElement - > ### Title: Parse elements from a PubMed XML file - > ### Aliases: parseElement parsePmidStatus parseArticleId parseArticle - > ### parsePubHistory parseJournal parsePubType parseMesh parseKeyword - > ### parseGrant parseChemical parseDataBank parseComment parseAbstract - > ### parseOther parseAuthor parseInvestigator - > - ... - > dPmidRaw = pmidStatusList[[2L]] - > dPmid = dPmidRaw[status != 'Deleted', !'status'] - > - > dArticleId = parseArticleId(pmXml, dPmid) - > dArticle = parseArticle(pmXml, dPmid) - > dJournal = parseJournal(pmXml, dPmid) - Error in xml_attr(xml_find_first(x1[idx], "CitedMedium")) : - argument "attr" is missing, with no default - Calls: parseJournal -> data.table -> xml_attr - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(pmparser) - > - > test_check('pmparser') - [ FAIL 4 | WARN 0 | SKIP 4 | PASS 158 ] - - ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ - ... - ▆ - 1. └─parseFuncs[[i]](pmXml, dPmid) at test_parse_element_no_rows.R:14:5 - 2. ├─data.table::data.table(...) - 3. └─xml2::xml_attr(xml_find_first(x1[idx], "CitedMedium")) - - [ FAIL 4 | WARN 0 | SKIP 4 | PASS 158 ] - Error: Test failures - In addition: Warning message: - call dbDisconnect() when finished working with a connection - Execution halted - ``` - +*Wow, no problems at all. :)* \ No newline at end of file