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
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/BiocPkgTools
-* Number of recursive dependencies: 164
-
-Run `revdepcheck::cloud_details(, "BiocPkgTools")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# biodb
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/biodb
-* Number of recursive dependencies: 124
-
-Run `revdepcheck::cloud_details(, "biodb")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# biomaRt
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/biomaRt
-* Number of recursive dependencies: 102
-
-Run `revdepcheck::cloud_details(, "biomaRt")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# cola
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/cola
-* Number of recursive dependencies: 244
-
-Run `revdepcheck::cloud_details(, "cola")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# CompoundDb
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/CompoundDb
-* Number of recursive dependencies: 124
-
-Run `revdepcheck::cloud_details(, "CompoundDb")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# ELMER
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/ELMER
-* Number of recursive dependencies: 231
-
-Run `revdepcheck::cloud_details(, "ELMER")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# EpiTxDb
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/EpiTxDb
-* Number of recursive dependencies: 161
-
-Run `revdepcheck::cloud_details(, "EpiTxDb")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# ExpressionAtlas
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/ExpressionAtlas
-* Number of recursive dependencies: 84
-
-Run `revdepcheck::cloud_details(, "ExpressionAtlas")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# GenomicDataCommons
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/GenomicDataCommons
-* Number of recursive dependencies: 160
-
-Run `revdepcheck::cloud_details(, "GenomicDataCommons")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# GEOexplorer
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/GEOexplorer
-* Number of recursive dependencies: 223
-
-Run `revdepcheck::cloud_details(, "GEOexplorer")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# GEOfastq
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/GEOfastq
-* Number of recursive dependencies: 98
-
-Run `revdepcheck::cloud_details(, "GEOfastq")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# GEOquery
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/GEOquery
-* Number of recursive dependencies: 85
-
-Run `revdepcheck::cloud_details(, "GEOquery")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# Gviz
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/Gviz
-* Number of recursive dependencies: 162
-
-Run `revdepcheck::cloud_details(, "Gviz")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# healthyControlsPresenceChecker
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/healthyControlsPresenceChecker
-* Number of recursive dependencies: 94
-
-Run `revdepcheck::cloud_details(, "healthyControlsPresenceChecker")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# HPAanalyze
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/HPAanalyze
-* Number of recursive dependencies: 120
-
-Run `revdepcheck::cloud_details(, "HPAanalyze")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# immunotation
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/immunotation
-* Number of recursive dependencies: 103
-
-Run `revdepcheck::cloud_details(, "immunotation")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# InterMineR
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/InterMineR
-* Number of recursive dependencies: 157
-
-Run `revdepcheck::cloud_details(, "InterMineR")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# levi
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/levi
-* Number of recursive dependencies: 97
-
-Run `revdepcheck::cloud_details(, "levi")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# Macarron
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/Macarron
-* Number of recursive dependencies: 205
-
-Run `revdepcheck::cloud_details(, "Macarron")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# MACSQuantifyR
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/MACSQuantifyR
-* Number of recursive dependencies: 97
-
-Run `revdepcheck::cloud_details(, "MACSQuantifyR")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# MBQN
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/MBQN
-* Number of recursive dependencies: 102
-
-Run `revdepcheck::cloud_details(, "MBQN")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# memes
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/memes
-* Number of recursive dependencies: 162
-
-Run `revdepcheck::cloud_details(, "memes")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# mosbi
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/mosbi
-* Number of recursive dependencies: 110
-
-Run `revdepcheck::cloud_details(, "mosbi")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# ncRNAtools
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/ncRNAtools
-* Number of recursive dependencies: 72
-
-Run `revdepcheck::cloud_details(, "ncRNAtools")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# OmnipathR
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/OmnipathR
-* Number of recursive dependencies: 166
-
-Run `revdepcheck::cloud_details(, "OmnipathR")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# ORFik
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/ORFik
-* Number of recursive dependencies: 156
-
-Run `revdepcheck::cloud_details(, "ORFik")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# PhyloProfile
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/PhyloProfile
-* Number of recursive dependencies: 145
-
-Run `revdepcheck::cloud_details(, "PhyloProfile")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# RBioFormats
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/RBioFormats
-* Number of recursive dependencies: 70
-
-Run `revdepcheck::cloud_details(, "RBioFormats")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# rfaRm
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/rfaRm
-* Number of recursive dependencies: 78
-
-Run `revdepcheck::cloud_details(, "rfaRm")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# RGMQL
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/RGMQL
-* Number of recursive dependencies: 93
-
-Run `revdepcheck::cloud_details(, "RGMQL")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# rpx
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/rpx
-* Number of recursive dependencies: 86
-
-Run `revdepcheck::cloud_details(, "rpx")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# RTCGA
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/RTCGA
-* Number of recursive dependencies: 181
-
-Run `revdepcheck::cloud_details(, "RTCGA")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# SBGNview
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/SBGNview
-* Number of recursive dependencies: 103
-
-Run `revdepcheck::cloud_details(, "SBGNview")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# scPipe
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/scPipe
-* Number of recursive dependencies: 263
-
-Run `revdepcheck::cloud_details(, "scPipe")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# scRNAseqApp
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/scRNAseqApp
-* Number of recursive dependencies: 236
-
-Run `revdepcheck::cloud_details(, "scRNAseqApp")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# simona
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/simona
-* Number of recursive dependencies: 138
-
-Run `revdepcheck::cloud_details(, "simona")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# spatialHeatmap
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/spatialHeatmap
-* Number of recursive dependencies: 300
-
-Run `revdepcheck::cloud_details(, "spatialHeatmap")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# surfaltr
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/surfaltr
-* Number of recursive dependencies: 158
-
-Run `revdepcheck::cloud_details(, "surfaltr")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# syntenet
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/syntenet
-* Number of recursive dependencies: 145
-
-Run `revdepcheck::cloud_details(, "syntenet")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# TCGAbiolinks
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/TCGAbiolinks
-* Number of recursive dependencies: 354
-
-Run `revdepcheck::cloud_details(, "TCGAbiolinks")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# TCGAutils
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/TCGAutils
-* Number of recursive dependencies: 228
-
-Run `revdepcheck::cloud_details(, "TCGAutils")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# topdownr
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/topdownr
-* Number of recursive dependencies: 118
-
-Run `revdepcheck::cloud_details(, "topdownr")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# treeio
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/treeio
-* Number of recursive dependencies: 106
-
-Run `revdepcheck::cloud_details(, "treeio")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# tRNAdbImport
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/tRNAdbImport
-* Number of recursive dependencies: 116
-
-Run `revdepcheck::cloud_details(, "tRNAdbImport")` for more info
-
-</details>
-
-## 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
-
-<details>
-
-* 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
-
-</details>
-
-## 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 -> <Anonymous>
- 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
-
-<details>
-
-* 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
-
-</details>
-
-## 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