`ggnetwork` error: `Error in `if (stringsAsFactors) x <- factor(x)`: argument is of length zero`
bschilder opened this issue · comments
1. Bug description
ThreeWayTest:::networkmap_ggnetwork fails only on Linux GHA machine. I've noticed this with other packages of mine recently and I think it has to do with some recent changes to ggnetwork package. Will sort this out since I need to figure it out for my other packages anyways.
##https://github.com/bschilder/ThreeWayTest/actions/runs/4363979376/jobs/7630734336#step:4:1172# Console output
https://github.com/bschilder/ThreeWayTest/actions/runs/4363979376/jobs/7630734336#step:4:1172
── Test failures ───────────────────────────────────────────────── testthat ────
> desc_path <- list.files("../","^DESCRIPTION$",
+ full.names = TRUE, recursive = TRUE)[1]
> pkg <- read.dcf(desc_path, fields = "Package")[1]
> library(testthat)
> library(pkg, character.only = TRUE)
>
> test_check(pkg)
Loading required namespace: heatmaply
Loading required namespace: tidygraph
Loading required namespace: ggnetwork
Loading required namespace: pals
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-networkmap.R:4'): networkmap works ─────────────────────────────
Error in `if (stringsAsFactors) x <- factor(x)`: argument is of length zero
Backtrace:
▆
1. └─ThreeWayTest::networkmap(dat = dat) at test-networkmap.R:4:4
2. └─ThreeWayTest:::networkmap_ggnetwork(...)
3. ├─base::suppressWarnings(ggnetwork::fortify(ig, list(layout = "graphopt")))
4. │ └─base::withCallingHandlers(...)
5. ├─ggnetwork::fortify(ig, list(layout = "graphopt"))
6. └─ggnetwork:::fortify.igraph(ig, list(layout = "graphopt"))
7. └─ggnetwork:::format_fortify(...)
8. └─base::cbind.data.frame(...)
9. └─base::data.frame(..., check.names = FALSE)
10. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
11. └─base::as.data.frame.list(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
12. ├─base::do.call(data.frame, c(x, alis))
13. └─base (local) `<fn>`(...)
14. ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
15. └─base::as.data.frame.character(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
Error: Test failures
Execution halted
2 errors ✖ | 0 warnings ✔ | 1 note ✖
Expected behaviour
Runs with no errors.
2. Reproducible example
Error in if (stringsAsFactors) x <- factor(x): argument is of length zero
3. Session info
https://github.com/bschilder/ThreeWayTest/actions/runs/4363979376/jobs/7630734336#step:4:761
─ Session info ───────────────────────────────────────────────────────────────────────────────────
setting value
version R Under development (unstable) (2023-03-02 r83926)
os Ubuntu 22.04.2 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz UTC
date 2023-03-08
pandoc 2.19.2 @ /usr/local/bin/pandoc
─ Packages ───────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
askpass 1.1 2019-01-13 [1] CRAN (R 4.3.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.3.0)
badger 0.2.3 2023-01-28 [1] CRAN (R 4.3.0)
base * 4.3.0 2023-03-03 [3] local
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.3.0)
BH 1.81.0-1 2023-01-22 [1] CRAN (R 4.3.0)
Biobase 2.59.0 2022-11-01 [1] Bioconductor
BiocCheck 1.35.12 2023-02-27 [1] any (@1.35.12)
BiocFileCache 2.7.2 2023-02-17 [1] Bioconductor
BiocGenerics 0.45.0 2022-11-01 [1] Bioconductor
BiocManager 1.30.20 2023-02-24 [1] CRAN (R 4.3.0)
BiocVersion 3.17.1 2022-11-04 [2] Bioconductor
biocViews 1.67.2 2022-12-22 [1] Bioconductor
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
blob 1.2.3 2022-04-10 [1] CRAN (R 4.3.0)
boot 1.3-28.1 2022-11-22 [3] CRAN (R 4.3.0)
brew 1.0-8 2022-09-29 [2] CRAN (R 4.3.0)
brio 1.1.3 2021-11-30 [1] CRAN (R 4.3.0)
bslib 0.4.2 2022-12-16 [1] CRAN (R 4.3.0)
ca 0.71.1 2020-01-24 [1] CRAN (R 4.3.0)
cachem 1.0.7 2023-02-24 [1] CRAN (R 4.3.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
class 7.3-21 2023-01-23 [3] CRAN (R 4.3.0)
cli 3.6.0 2023-01-09 [1] CRAN (R 4.3.0)
clipr 0.8.0 2022-02-22 [1] CRAN (R 4.3.0)
cluster 2.1.4 2022-08-22 [3] CRAN (R 4.3.0)
coda 0.19-4 2020-09-30 [1] CRAN (R 4.3.0)
codetools 0.2-19 2023-02-01 [3] CRAN (R 4.3.0)
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commonmark 1.8.1 2022-10-14 [1] CRAN (R 4.3.0)
compiler 4.3.0 2023-03-03 [3] local
covr 3.6.1 2022-08-26 [1] CRAN (R 4.3.0)
cpp11 0.4.3 2022-10-12 [1] CRAN (R 4.3.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
credentials 1.3.2 2021-11-29 [1] CRAN (R 4.3.0)
crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.3.0)
curl 5.0.0 2023-01-12 [1] CRAN (R 4.3.0)
data.table 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
datasets * 4.3.0 2023-03-03 [3] local
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.3.0)
dbplyr 2.3.1 2023-02-24 [1] CRAN (R 4.3.0)
dendextend 1.16.0 2022-07-04 [1] CRAN (R 4.3.0)
desc 1.4.2 2022-09-08 [1] CRAN (R 4.3.0)
devtools 2.4.5 2022-10-11 [2] CRAN (R 4.3.0)
dichromat 2.0-0.1 2022-05-02 [1] CRAN (R 4.3.0)
diffobj 0.3.5 2021-10-05 [1] CRAN (R 4.3.0)
digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0)
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docopt 0.7.1 2020-06-24 [2] CRAN (R 4.3.0)
downlit 0.4.2 2022-07-05 [2] CRAN (R 4.3.0)
dplyr 1.1.0 2023-01-29 [1] CRAN (R 4.3.0)
egg 0.4.5 2019-07-13 [1] CRAN (R 4.3.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
evaluate 0.20 2023-01-17 [1] CRAN (R 4.3.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
filelock 1.0.2 2018-10-05 [1] CRAN (R 4.3.0)
fontawesome 0.5.0 2023-01-25 [2] CRAN (R 4.3.0)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
foreign 0.8-84 2022-12-06 [3] CRAN (R 4.3.0)
fs 1.6.1 2023-02-06 [1] CRAN (R 4.3.0)
gclus 1.3.2 2019-01-07 [1] CRAN (R 4.3.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
gert 1.9.2 2022-12-05 [1] CRAN (R 4.3.0)
ggnetwork 0.5.10 2021-07-06 [1] CRAN (R 4.3.0)
ggplot2 3.4.1 2023-02-10 [1] CRAN (R 4.3.0)
ggrepel 0.9.3 2023-02-03 [1] CRAN (R 4.3.0)
gh 1.4.0 2023-02-22 [1] CRAN (R 4.3.0)
gitcreds 0.1.2 2022-09-08 [1] CRAN (R 4.3.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
graph 1.77.2 2023-02-24 [1] Bioconductor
graphics * 4.3.0 2023-03-03 [3] local
grDevices * 4.3.0 2023-03-03 [3] local
grid 4.3.0 2023-03-03 [3] local
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.0)
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.3.0)
heatmaply 1.4.2 2023-01-07 [1] CRAN (R 4.3.0)
here 1.0.1 2020-12-13 [1] CRAN (R 4.3.0)
highr 0.10 2022-12-22 [1] CRAN (R 4.3.0)
htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.3.0)
htmlwidgets 1.6.1 2023-01-07 [1] CRAN (R 4.3.0)
httpuv 1.6.9 2023-02-14 [2] CRAN (R 4.3.0)
httr 1.4.5 2023-02-24 [1] CRAN (R 4.3.0)
httr2 0.2.2 2022-09-25 [1] CRAN (R 4.3.0)
igraph 1.4.1 2023-02-24 [1] CRAN (R 4.3.0)
ini 0.3.1 2018-05-20 [1] CRAN (R 4.3.0)
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iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0)
jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.3.0)
KernSmooth 2.23-20 2021-05-03 [3] CRAN (R 4.3.0)
knitr 1.42 2023-01-25 [1] CRAN (R 4.3.0)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.3.0)
later 1.3.0 2021-08-18 [1] CRAN (R 4.3.0)
lattice 0.20-45 2021-09-22 [3] CRAN (R 4.3.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
littler 0.3.17 2022-10-29 [2] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
mapproj 1.2.11 2023-01-12 [1] CRAN (R 4.3.0)
maps 3.4.1 2022-10-30 [1] CRAN (R 4.3.0)
markdown 1.5 2023-01-31 [1] CRAN (R 4.3.0)
MASS 7.3-58.2 2023-01-23 [3] CRAN (R 4.3.0)
Matrix 1.5-3 2022-11-11 [3] CRAN (R 4.3.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
methods * 4.3.0 2023-03-03 [3] local
mgcv 1.8-42 2023-03-02 [3] CRAN (R 4.3.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [2] CRAN (R 4.3.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
network 1.18.1 2023-01-24 [1] CRAN (R 4.3.0)
nlme 3.1-162 2023-01-31 [3] CRAN (R 4.3.0)
nnet 7.3-18 2022-09-28 [3] CRAN (R 4.3.0)
openssl 2.0.5 2022-12-06 [1] CRAN (R 4.3.0)
pals 1.7 2021-04-17 [1] CRAN (R 4.3.0)
parallel 4.3.0 2023-03-03 [3] local
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pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.3.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
pkgdown 2.0.7 2022-12-14 [1] CRAN (R 4.3.0)
pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.3.0)
plogr 0.2.0 2018-03-25 [1] CRAN (R 4.3.0)
plotly 4.10.1 2022-11-07 [1] CRAN (R 4.3.0)
plyr 1.8.8 2022-11-11 [1] CRAN (R 4.3.0)
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RBGL 1.75.0 2022-11-01 [1] Bioconductor
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roxygen2 7.2.3 2022-12-08 [2] CRAN (R 4.3.0)
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RSQLite 2.3.0 2023-02-17 [1] CRAN (R 4.3.0)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.3.0)
RUnit 0.4.32 2018-05-18 [1] CRAN (R 4.3.0)
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rversions 2.1.2 2022-08-31 [2] CRAN (R 4.3.0)
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seriation 1.4.1 2023-01-07 [1] CRAN (R 4.3.0)
sessioninfo * 1.2.2 2021-12-06 [1] any (@1.2.2)
shiny 1.7.4 2022-12-15 [2] CRAN (R 4.3.0)
sna 2.7-1 2023-01-24 [1] CRAN (R 4.3.0)
sourcetools 0.1.7-1 2023-02-01 [2] CRAN (R 4.3.0)
spatial 7.3-16 2023-01-23 [3] CRAN (R 4.3.0)
splines 4.3.0 2023-03-03 [3] local
statnet.common 4.8.0 2023-01-24 [1] CRAN (R 4.3.0)
stats * 4.3.0 2023-03-03 [3] local
stats4 4.3.0 2023-03-03 [3] local
stringdist 0.9.10 2022-11-07 [1] CRAN (R 4.3.0)
stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0)
stringr 1.5.0 2022-12-02 [1] CRAN (R 4.3.0)
survival 3.5-3 2023-02-12 [3] CRAN (R 4.3.0)
sys 3.4.1 2022-10-18 [1] CRAN (R 4.3.0)
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tcltk 4.3.0 2023-03-03 [3] local
testthat 3.1.6 2022-12-09 [1] CRAN (R 4.3.0)
textshaping 0.3.6 2021-10-13 [2] CRAN (R 4.3.0)
ThreeWayTest 1.0.1 2023-03-03 [1] local
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.3.0)
tidygraph 1.2.3 2023-02-01 [1] CRAN (R 4.3.0)
tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.3.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
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TSP 1.2-2 2023-01-25 [1] CRAN (R 4.3.0)
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whisker 0.4.1 2022-12-05 [1] CRAN (R 4.3.0)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.3.0)
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XML 3.99-0.13 2022-12-04 [1] CRAN (R 4.3.0)
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zip 2.2.2 2022-10-26 [1] CRAN (R 4.3.0)
[1] /__w/_temp/Library
[2] /usr/local/lib/R/site-library
[3] /usr/local/lib/R/library
Oddly, I noticed the version on the Linux GHA is actually older than the one on my local machine. GHA might be using the cached installation with the bug in it, so will rerun with /nocache flag in commit message.
Version used on GHA Linux:
ggnetwork 0.5.10 2021-07-06 [1] CRAN (R 4.3.0)
Version used on my local Mac:
ggnetwork * 0.5.12 2023-03-06 [1] CRAN (R 4.2.1)
Oddly, I noticed the version on the Linux GHA is actually older than the one on my local machine. GHA might be using the cached installation with the bug in it, so will rerun with
/nocacheflag in commit message.
This did the trick! ThreeWayTestis now passing on all GHA runners.