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Published
20 hours ago •
r-lib
r-lib
Error: can't convert package with RemoteType 'bioc' to remote
For one, this generic message isn’t very helpful if you use update_packages. Fixed in #397.
I figured out the offending package was XVector. I assume its RemoteType field was added by an older version of devtools or remotes? If so, this should be handled in a backwards-compatible fashion
I am seeing a similar error on GitHub actions (private repo):
Run devtools::install(dependencies = TRUE) devtools::install(dependencies = TRUE) shell: /usr/local/bin/Rscript {0} env: GITHUB_PAT: *** R_LIBS_USER: /home/runner/work/_temp/Library TZ: UTC R_CHECK_SYSTEM_CLOCK: FALSE NOT_CRAN: true RSPM: https://packagemanager.rstudio.com/all/linux/focal/latest Error in FUN(X[[i]], ...) : can't convert package lintr with RemoteType 'any' to remote Calls: <Anonymous> ... dev_package_deps -> package_deps -> structure -> lapply -> FUN Execution halted Error: Process completed with exit code 1.
Session info:
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.2.[1](https://github.com/user/repo/actions/runs/3056077432/jobs/4929856680#step:6:1) (2022-06-23)
os Ubuntu 20.04.5 LTS
system x86_64, linux-gnu
ui X[11](https://github.com/user/repo/actions/runs/3056077432/jobs/4929856680#step:6:12)
language (EN)
collate C.UTF-8
ctype C.UTF-8
tz UTC
date 2022-09-14
pandoc 2.5 @ /usr/bin/pandoc
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] RSPM (R 4.2.0)
affy 1.74.0 2022-04-26 [1] Bioconductor
affyio 1.66.0 2022-04-26 [1] Bioconductor
annotate 1.74.0 2022-04-26 [1] Bioconductor
AnnotationDbi 1.58.0 2022-04-26 [1] Bioconductor
anytime 0.3.9 2020-08-27 [1] RSPM (R 4.2.0)
askpass 1.1 2019-01-13 [1] RSPM
backports 1.4.1 2021-[12](https://github.com/user/repo/actions/runs/3056077432/jobs/4929856680#step:6:13)-[13](https://github.com/user/repo/actions/runs/3056077432/jobs/4929856680#step:6:14) [1] RSPM
base * 4.2.1 2022-09-09 [2] local
base64enc 0.1-3 2015-07-28 [1] RSPM
bayestestR 0.12.1 2022-05-02 [1] RSPM (R 4.2.0)
BH 1.78.0-0 2021-12-15 [1] RSPM (R 4.2.0)
Biobase 2.56.0 2022-04-26 [1] Bioconductor
BiocGenerics 0.42.0 2022-04-26 [1] Bioconductor
BiocManager 1.30.18 2022-05-18 [1] RSPM (R 4.2.0)
Biostrings 2.64.1 2022-08-18 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] RSPM (R 4.2.0)
bit64 4.0.5 2020-08-30 [1] RSPM (R 4.2.0)
bitops 1.0-7 2021-04-24 [1] RSPM (R 4.2.0)
blob 1.2.3 2022-04-10 [1] RSPM (R 4.2.0)
boot 1.3-28 2021-05-03 [2] CRAN (R 4.2.1)
brew 1.0-7 2022-02-04 [1] RSPM
brio 1.1.3 2021-11-30 [1] RSPM
broom 1.0.1 2022-08-29 [1] RSPM (R 4.2.0)
bslib 0.4.0 2022-07-16 [1] RSPM
cachem 1.0.6 2021-08-19 [1] RSPM
callr 3.7.2 2022-08-22 [1] RSPM
car 3.1-0 2022-06-15 [1] RSPM (R 4.2.0)
carData 3.0-5 2022-01-06 [1] RSPM (R 4.2.0)
Category 2.62.0 2022-04-26 [1] Bioconductor
cellHTS2 2.60.0 2022-04-26 [1] Bioconductor
cellranger 1.1.0 2016-07-27 [1] RSPM (R 4.2.0)
checkmate 2.1.0 2022-04-21 [1] RSPM (R 4.2.0)
circlize 0.4.15 2022-05-10 [1] RSPM (R 4.2.0)
class 7.3-20 2022-01-16 [2] CRAN (R 4.2.1)
cli 3.4.0 2022-09-08 [1] RSPM
clipr 0.8.0 2022-02-22 [1] RSPM
clue 0.3-61 2022-05-30 [1] RSPM (R 4.2.0)
cluster 2.1.3 2022-03-28 [2] CRAN (R 4.2.1)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.2.1)
colorspace 2.0-3 2022-02-21 [1] RSPM (R 4.2.0)
commonmark 1.8.0 2022-03-09 [1] RSPM
compiler 4.2.1 2022-09-09 [2] local
ComplexHeatmap 2.12.1 2022-08-09 [1] Bioconductor
corrplot 0.92 2021-11-18 [1] RSPM (R 4.2.0)
cowplot 1.1.1 2020-12-30 [1] RSPM (R 4.2.0)
cpp11 0.4.2 2021-11-30 [1] RSPM
crayon 1.5.1 2022-03-26 [1] RSPM
credentials 1.3.2 2021-11-29 [1] RSPM
crosstalk 1.2.0 2021-11-04 [1] RSPM (R 4.2.0)
curl 4.3.2 2021-06-23 [1] RSPM
cyclocomp 1.1.0 2016-09-10 [1] RSPM
data.table 1.[14](https://github.com/user/repo/actions/runs/3056077432/jobs/4929856680#step:6:15).2 2021-09-27 [1] RSPM (R 4.2.0)
datasets * 4.2.1 2022-09-09 [2] local
datawizard 0.5.1 2022-08-17 [1] RSPM (R 4.2.0)
DBI 1.1.3 2022-06-18 [1] RSPM (R 4.2.0)
desc 1.4.2 2022-09-08 [1] RSPM
devtools 2.4.4 2022-07-20 [1] any (@2.4.4)
diffobj 0.3.5 2021-10-05 [1] RSPM
digest 0.6.29 2021-12-01 [1] RSPM
doParallel 1.0.17 2022-02-07 [1] RSPM (R 4.2.0)
downlit 0.4.2 2022-07-05 [1] RSPM
dplyr 1.0.10 2022-09-01 [1] RSPM (R 4.2.0)
DT 0.25 2022-09-12 [1] RSPM (R 4.2.0)
e1071 1.7-11 2022-06-07 [1] RSPM (R 4.2.0)
EBImage 4.38.0 2022-04-26 [1] Bioconductor
ellipsis 0.3.2 2021-04-29 [1] RSPM
evaluate 0.16 2022-08-09 [1] RSPM
fansi 1.0.3 2022-03-24 [1] RSPM
farver 2.1.1 2022-07-06 [1] RSPM (R 4.2.0)
fastmap 1.1.0 2021-01-25 [1] RSPM
fftwtools 0.9-11 2021-03-01 [1] RSPM (R 4.2.0)
fontawesome 0.3.0 2022-07-20 [1] RSPM
foreach 1.5.2 2022-02-02 [1] RSPM (R 4.2.0)
foreign 0.8-82 2022-01-16 [2] CRAN (R 4.2.1)
fs 1.5.2 2021-12-08 [1] RSPM
future 1.28.0 2022-09-02 [1] RSPM (R 4.2.0)
genefilter 1.78.0 2022-04-26 [1] Bioconductor
generics 0.1.3 2022-07-05 [1] RSPM (R 4.2.0)
GenomeInfoDb 1.32.4 2022-09-06 [1] Bioconductor
GenomeInfoDbData 1.2.8 2022-09-14 [1] Bioconductor
gert 1.8.0 2022-09-06 [1] RSPM
GetoptLong 1.0.5 2020-12-[15](https://github.com/user/repo/actions/runs/3056077432/jobs/4929856680#step:6:16) [1] RSPM (R 4.2.0)
ggplot2 3.3.6 2022-05-03 [1] RSPM (R 4.2.0)
ggpubr 0.4.0 2020-06-27 [1] RSPM (R 4.2.0)
ggrepel 0.9.1 2021-01-15 [1] RSPM (R 4.2.0)
ggsci 2.9 2018-05-14 [1] RSPM (R 4.2.0)
ggsignif 0.6.3 2021-09-09 [1] RSPM (R 4.2.0)
gh 1.3.1 2022-09-08 [1] RSPM
git2r 0.30.1 2022-03-16 [1] RSPM (R 4.2.0)
gitcreds 0.1.2 2022-09-08 [1] RSPM
GlobalOptions 0.1.2 2020-06-10 [1] RSPM (R 4.2.0)
globals 0.16.1 2022-08-28 [1] RSPM (R 4.2.0)
glue 1.6.2 2022-02-24 [1] RSPM
graph 1.74.0 2022-04-26 [1] Bioconductor
graphics * 4.2.1 2022-09-09 [2] local
grDevices * 4.2.1 2022-09-09 [2] local
grid 4.2.1 2022-09-09 [2] local
gridExtra 2.3 2017-09-09 [1] RSPM (R 4.2.0)
GSEABase 1.58.0 2022-04-26 [1] Bioconductor
gtable 0.3.1 2022-09-01 [1] RSPM (R 4.2.0)
highr 0.9 2021-04-16 [1] RSPM
hms 1.1.2 2022-08-19 [1] RSPM (R 4.2.0)
htmltools 0.5.3 2022-07-18 [1] RSPM
htmlwidgets 1.5.4 2021-09-08 [1] RSPM
httpuv 1.6.6 2022-09-08 [1] RSPM
httr 1.4.4 2022-08-17 [1] RSPM
hwriter 1.3.2.1 2022-04-08 [1] RSPM (R 4.2.0)
igraph 1.3.4 2022-07-19 [1] RSPM (R 4.2.0)
imageHTS 1.45.1 2022-01-06 [1] Bioconductor
ini 0.3.1 2018-05-20 [1] RSPM
insight 0.18.2 2022-08-10 [1] RSPM (R 4.2.0)
IRanges 2.30.1 2022-08-18 [1] Bioconductor
isoband 0.2.5 2021-07-13 [1] RSPM (R 4.2.0)
iterators 1.0.14 2022-02-05 [1] RSPM (R 4.2.0)
jpeg 0.1-9 2021-07-24 [1] RSPM (R 4.2.0)
jquerylib 0.1.4 2021-04-26 [1] RSPM
jsonlite 1.8.0 2022-02-22 [1] RSPM
KEGGREST 1.36.3 2022-07-12 [1] Bioconductor
KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.2.1)
knitr 1.40 2022-08-24 [1] RSPM
labeling 0.4.2 2020-10-20 [1] RSPM (R 4.2.0)
later 1.3.0 2021-08-18 [1] RSPM
lattice 0.20-45 2021-09-22 [2] CRAN (R 4.2.1)
lazyeval 0.2.2 2019-03-15 [1] RSPM
lifecycle 1.0.2 2022-09-09 [1] RSPM
limma 3.52.3 2022-09-11 [1] Bioconductor
lintr 3.0.1 2022-09-13 [1] any (@3.0.1)
listenv 0.8.0 2019-12-05 [1] RSPM (R 4.2.0)
lme4 1.1-30 2022-07-08 [1] RSPM (R 4.2.0)
locfit 1.5-9.6 2022-07-11 [1] RSPM (R 4.2.0)
logger 0.2.2 2021-10-19 [1] RSPM (R 4.2.0)
magrittr 2.0.3 2022-03-30 [1] RSPM
maptools 1.1-4 2022-04-17 [1] RSPM (R 4.2.0)
MASS 7.3-57 2022-04-22 [2] CRAN (R 4.2.1)
Matrix 1.5-1 2022-09-13 [1] RSPM (R 4.2.0)
MatrixModels 0.5-1 2022-09-11 [1] RSPM (R 4.2.0)
matrixStats 0.62.0 2022-04-19 [1] RSPM (R 4.2.0)
memoise 2.0.1 2021-11-26 [1] RSPM
methods * 4.2.1 2022-09-09 [2] local
mgcv 1.8-40 2022-03-29 [2] CRAN (R 4.2.1)
mime 0.12 2021-09-28 [1] RSPM
miniUI 0.1.1.1 2018-05-18 [1] RSPM
minqa 1.2.4 2014-10-09 [1] RSPM (R 4.2.0)
munsell 0.5.0 2018-06-12 [1] RSPM (R 4.2.0)
nlme 3.1-157 2022-03-25 [2] CRAN (R 4.2.1)
nloptr 2.0.3 2022-05-26 [1] RSPM (R 4.2.0)
nnet 7.3-17 2022-01-16 [2] CRAN (R 4.2.1)
nplr 0.1-7 2016-12-28 [1] RSPM (R 4.2.0)
numDeriv 2016.8-1.1 2019-06-06 [1] RSPM (R 4.2.0)
OmnipathR 3.4.0 2022-04-26 [1] Bioconductor
openssl 2.0.2 2022-05-24 [1] RSPM
openxlsx 4.2.5 2021-12-14 [1] RSPM (R 4.2.0)
pak 0.3.0 2022-04-12 [1] local
parallel 4.2.1 2022-09-09 [2] local
parallelly 1.32.1 2022-07-21 [1] RSPM (R 4.2.0)
patchwork 1.1.2 2022-08-19 [1] RSPM (R 4.2.0)
pbkrtest 0.5.1 2021-03-09 [1] RSPM (R 4.2.0)
pillar 1.8.1 2022-08-19 [1] RSPM
pkgbuild 1.3.1 2021-12-20 [1] RSPM
pkgconfig 2.0.3 2019-09-22 [1] RSPM
pkgdown 2.0.6 2022-07-16 [1] RSPM
pkgload 1.3.0 2022-06-27 [1] RSPM
plogr 0.2.0 2018-03-25 [1] RSPM (R 4.2.0)
plotly 4.10.0 2021-10-09 [1] RSPM (R 4.2.0)
png 0.1-7 2013-12-03 [1] RSPM (R 4.2.0)
polynom 1.4-1 2022-04-11 [1] RSPM (R 4.2.0)
praise 1.0.0 2015-08-11 [1] RSPM
preprocessCore 1.58.0 2022-04-26 [1] Bioconductor
prettyunits 1.1.1 2020-01-24 [1] RSPM
processx 3.7.0 2022-07-07 [1] RSPM
profvis 0.3.7 2020-11-02 [1] RSPM
progress 1.2.2 2019-05-16 [1] RSPM (R 4.2.0)
promises 1.2.0.1 2021-02-11 [1] RSPM
proxy 0.4-27 2022-06-09 [1] RSPM (R 4.2.0)
ps 1.7.1 2022-06-18 [1] RSPM
purrr 0.3.4 2020-04-17 [1] RSPM
quantreg 5.94 2022-07-20 [1] RSPM (R 4.2.0)
R6 2.5.1 2021-08-19 [1] RSPM
ragg 1.2.2 2022-02-21 [1] RSPM
rappdirs 0.3.3 2021-01-31 [1] RSPM
RBGL 1.72.0 2022-04-26 [1] Bioconductor
rcmdcheck 1.4.0 2021-09-27 [1] RSPM
RColorBrewer 1.1-3 2022-04-03 [1] RSPM (R 4.2.0)
Rcpp 1.0.9 2022-07-08 [1] RSPM
RcppEigen 0.3.3.9.2 2022-04-08 [1] RSPM (R 4.2.0)
RCurl 1.98-1.8 2022-07-30 [1] RSPM (R 4.2.0)
readr 2.1.2 2022-01-30 [1] RSPM (R 4.2.0)
readxl 1.4.1 2022-08-17 [1] RSPM (R 4.2.0)
rematch 1.0.1 2016-04-21 [1] RSPM (R 4.2.0)
rematch2 2.1.2 2020-05-01 [1] RSPM
remotes 2.4.2 2021-11-30 [1] RSPM
rex 1.2.1 2021-11-26 [1] RSPM
rjson 0.2.21 2022-01-09 [1] RSPM (R 4.2.0)
rlang 1.0.5 2022-08-31 [1] RSPM
rmarkdown 2.16 2022-08-24 [1] RSPM
roxygen2 7.2.1 2022-07-18 [1] RSPM
rpart 4.1.16 2022-01-24 [2] CRAN (R 4.2.1)
rprojroot 2.0.3 2022-04-02 [1] RSPM
RSQLite 2.2.17 2022-09-10 [1] RSPM (R 4.2.0)
rstatix 0.7.0 2021-02-13 [1] RSPM (R 4.2.0)
rstudioapi 0.14 2022-08-22 [1] RSPM
rversions 2.1.2 2022-08-31 [1] RSPM
S4Vectors 0.34.0 2022-04-26 [1] Bioconductor
sass 0.4.2 2022-07-16 [1] RSPM
scales 1.2.1 2022-08-20 [1] RSPM (R 4.2.0)
sessioninfo 1.2.2 2021-12-06 [1] RSPM
shape 1.4.6 2021-05-19 [1] RSPM (R 4.2.0)
shiny 1.7.2 2022-07-19 [1] RSPM
shinyjs 2.1.0 2021-12-23 [1] RSPM (R 4.2.0)
shinythemes 1.2.0 2021-01-25 [1] RSPM (R 4.2.0)
shinyWidgets 0.7.3 2022-08-31 [1] RSPM (R 4.2.0)
sourcetools 0.1.7 2018-04-25 [1] RSPM
sp 1.5-0 2022-06-05 [1] RSPM (R 4.2.0)
SparseM 1.81 2021-02-18 [1] RSPM (R 4.2.0)
spatial 7.3-15 2022-01-16 [2] CRAN (R 4.2.1)
splines 4.2.1 2022-09-09 [2] local
splots 1.62.0 2022-04-26 [1] Bioconductor
stats * 4.2.1 2022-09-09 [2] local
stats4 4.2.1 2022-09-09 [2] local
stringi 1.7.8 2022-07-11 [1] RSPM
stringr 1.4.1 2022-08-20 [1] RSPM
survival 3.3-1 2022-03-03 [2] CRAN (R 4.2.1)
sys 3.4 2020-07-23 [1] RSPM
systemfonts 1.0.4 2022-02-11 [1] RSPM
tcltk 4.2.1 2022-09-09 [2] local
testthat 3.1.4 2022-04-26 [1] RSPM
textshaping 0.3.6 2021-10-13 [1] RSPM
tibble 3.1.8 2022-07-22 [1] RSPM
tidyr 1.2.1 2022-09-08 [1] RSPM (R 4.2.0)
tidyselect 1.1.2 2022-02-21 [1] RSPM (R 4.2.0)
tiff 0.1-11 2022-01-31 [1] RSPM (R 4.2.0)
tinytex 0.41 2022-08-16 [1] RSPM
tools 4.2.1 2022-09-09 [2] local
tzdb 0.3.0 2022-03-28 [1] RSPM (R 4.2.0)
urlchecker 1.0.1 2021-11-30 [1] RSPM
usethis 2.1.6 2022-05-25 [1] RSPM
utf8 1.2.2 2021-07-24 [1] RSPM
utils * 4.2.1 2022-09-09 [2] local
vctrs 0.4.1 2022-04-13 [1] RSPM
viridisLite 0.4.1 2022-08-22 [1] RSPM (R 4.2.0)
vroom 1.5.7 2021-11-30 [1] RSPM (R 4.2.0)
vsn 3.64.0 2022-04-26 [1] Bioconductor
waldo 0.4.0 2022-03-16 [1] RSPM
whisker 0.4 2019-08-28 [1] RSPM
withr 2.5.0 2022-03-03 [1] RSPM
xfun 0.33 2022-09-12 [1] RSPM
XML 3.99-0.10 2022-06-09 [1] RSPM (R 4.2.0)
xml2 1.3.3 2021-11-30 [1] RSPM
xmlparsedata 1.0.5 2021-03-06 [1] RSPM
xopen 1.0.0 2018-09-17 [1] RSPM
xtable 1.8-4 2019-04-21 [1] RSPM
XVector 0.36.0 2022-04-26 [1] Bioconductor
yaml 2.3.5 2022-02-21 [1] RSPM
zeallot 0.1.0 2018-01-28 [1] RSPM (R 4.2.0)
zip 2.2.1 2022-09-08 [1] RSPM
zlibbioc 1.42.0 2022-04-26 [1] Bioconductor
[1] /home/runner/work/_temp/Library
[2] /opt/R/4.2.1/lib/R/library
──────────────────────────────────────────────────────────────────────────────
Workflow steps:
- name: Checkout repository
uses: actions/checkout@v3
- name: Setup R
uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
- name: Install and cache dependencies
uses: r-lib/actions/setup-r-dependencies@v2
with:
packages: any::devtools
# https://github.com/igraph/rigraph/issues/209
# https://github.com/igraph/rigraph/issues/418
- name: Install libglpk.so.40
run: sudo apt-get install -y libglpk40
- name: Install package
run: devtools::install(dependencies = TRUE)
shell: Rscript {0}
I also have another workflow that uses packages: any::lintr, and I feel that installing a package via r-lib/actions/setup-r-dependencies/with writes some RemoteType that devtools does not understand. (And that may have an influence here through caching.)
Use pak to install packages on GHA, it is already installed by setup-r-dependencies@v2.
It’s interesting to see the R world replacing the whole ecosystem with modern alternatives.
Now you only need nested namespaces and explicit named imports (without breaking S4 methods), and R is mostly fixed!