colearendt
commented
5 years ago More weirdness afoot that can hopefully help. I have never seen this error before, and have seen it with regularity in a clean environment reproducing these issues:
Warning messages:
1: In `[<-.data.frame`(`*tmp*`, , c("Source", "Repository"), value = list( :
replacement element 1 has 252 rows to replace 130 rows
2: In `[<-.data.frame`(`*tmp*`, , c("Source", "Repository"), value = list( :
replacement element 2 has 252 rows to replace 130 rowsAnd kinda the inverse problem, I have seen the mapping from "Repository: RSPM" to "Source: RSPM" be pretty flaky. I wrote three manifests in the same project (different subfolders). I got:
"lubridate": {
"Source": "github",
"Repository": null,
--
"lubridate": {
"Source": "CRAN",
"Repository": "https://cluster.rstudiopm.com/cran/__linux__/bionic/latest",
--
"lubridate": {
"Source": "RSPM",
"Repository": "https://cluster.rstudiopm.com/cran/__linux__/bionic/latest",For all three (the package installation / R session / everything is the same... just different working directories / apps), the package description specifies Repository: RSPM.
The really troubling one is "github", but "CRAN" is nearly as troubling. It's almost like we're round-robining or something.
I can't easily share the manifest (too big). LMK if it'd be helpful to pair through tomorrow! It is a shared environment, so I can also give you creds if that's helpful.
Another jq workaround:
cat pre-manifest.json | jq '.packages |= map_values(. | (if .GithubRepo == null and .Source == "github" then .Source |= "RSPM" | .Repository |= "https://cluster.rstudiopm.com/cran/__linux__/bionic/latest" else . end))' > manifest.jsonmanifest.json - lubridate entry - github
``` "lubridate": { "Source": "github", "Repository": null, "GithubRepo": null, "GithubUsername": null, "GithubRef": null, "GithubSha1": null, "description": { "Package": "lubridate", "Type": "Package", "Version": "1.7.4", "Title": "Make Dealing with Dates a Little Easier", "Description": "Functions to work with date-times and time-spans: fast and user\n friendly parsing of date-time data, extraction and updating of components of\n a date-time (years, months, days, hours, minutes, and seconds), algebraic\n manipulation on date-time and time-span objects. The 'lubridate' package has\n a consistent and memorable syntax that makes working with dates easy and\n fun.\n Parts of the 'CCTZ' source code, released under the Apache 2.0 License,\n are included in this package. Seemanifest.json - lubridate entry - CRAN version
``` "lubridate": { "Source": "CRAN", "Repository": "https://cluster.rstudiopm.com/cran/__linux__/bionic/latest", "GithubRepo": null, "GithubUsername": null, "GithubRef": null, "GithubSha1": null, "description": { "Package": "lubridate", "Type": "Package", "Version": "1.7.4", "Title": "Make Dealing with Dates a Little Easier", "Description": "Functions to work with date-times and time-spans: fast and user\n friendly parsing of date-time data, extraction and updating of components of\n a date-time (years, months, days, hours, minutes, and seconds), algebraic\n manipulation on date-time and time-span objects. The 'lubridate' package has\n a consistent and memorable syntax that makes working with dates easy and\n fun.\n Parts of the 'CCTZ' source code, released under the Apache 2.0 License,\n are included in this package. Seelubridate DESCRIPTION file
``` Package: lubridate Type: Package Version: 1.7.4 Title: Make Dealing with Dates a Little Easier Description: Functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun. Parts of the 'CCTZ' source code, released under the Apache 2.0 License, are included in this package. SeeAlso note that several of these packages came from RSPM binaries... that shouldn't make a difference, but it's worth noting 😄
kevinushey
jmcphers
I believe this is a bug in the dev version of the
rsconnectpackage and the way it builds manifests. Specifically, in some cases a GitHub package can be misrepresented and Connect (1.7.6-6) will try to install it from CRAN / RSPM.To reproduce:
rlangfrom GitHubrsconnect::writeManifestwith latest from GitHubYou should see something like:
It only breaks programmatic deployment, as far as I am aware, because IDE deployment does not use this part of the manifest.json. Not sure what, if any, effect would be had on shinyapps.io.
A hacky fix on the
bad-manifest.jsonusingjq:This is a minimal copy of the manifest.json that was created from my environment, just in case it helps diagnose:
manifest.json
``` { "version": 1, "locale": "C", "platform": "3.6.0", "metadata": { "appmode": "rmd-static", "primary_rmd": "file.Rmd", "primary_html": null, "content_category": null, "has_parameters": false }, "packages": { "Rcpp": { "Source": "RSPM", "Repository": "https://cluster.rstudiopm.com/cran/__linux__/bionic/688", "GithubRepo": null, "GithubUsername": null, "GithubRef": null, "GithubSha1": null, "description": { "Package": "Rcpp", "Title": "Seamless R and C++ Integration", "Version": "1.0.1", "Date": "2019-03-16", "Author": "Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,\n Nathan Russell, Douglas Bates and John Chambers", "Maintainer": "Dirk Eddelbuettel