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install_github() fails with blogdown #309

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kevinushey opened this issue Mar 11, 2019 · 0 comments
Closed

install_github() fails with blogdown #309

kevinushey opened this issue Mar 11, 2019 · 0 comments

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@kevinushey
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kevinushey commented Mar 11, 2019

remotes::install_github("rstudio/blogdown")
#> Downloading GitHub repo rstudio/blogdown@master
#> Error in FUN(X[[i]], ...): is.remote(remote) is not TRUE

Created on 2019-03-10 by the reprex package (v0.2.1)

Session info
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#>  setting  value                                      
#>  version  R version 3.5.2 Patched (2019-01-14 r75994)
#>  os       macOS Mojave 10.14.3                       
#>  system   x86_64, darwin15.6.0                       
#>  ui       X11                                        
#>  language (EN)                                       
#>  collate  en_US.UTF-8                                
#>  ctype    en_US.UTF-8                                
#>  tz       America/Los_Angeles                        
#>  date     2019-03-10                                 
#> 
#> ─ Packages ──────────────────────────────────────────────────────────────
#>  package     * version    date       lib source                        
#>  assertthat    0.2.0      2017-04-11 [1] CRAN (R 3.5.0)                
#>  backports     1.1.3      2018-12-14 [1] CRAN (R 3.5.0)                
#>  callr         3.1.1      2018-12-21 [1] CRAN (R 3.5.0)                
#>  cli           1.0.1      2018-09-25 [1] CRAN (R 3.5.0)                
#>  crayon        1.3.4      2017-09-16 [1] CRAN (R 3.5.0)                
#>  curl          3.3        2019-01-10 [1] CRAN (R 3.5.2)                
#>  desc          1.2.0      2018-05-01 [1] CRAN (R 3.5.0)                
#>  devtools      2.0.1      2018-10-26 [1] CRAN (R 3.5.2)                
#>  digest        0.6.18     2018-10-10 [1] CRAN (R 3.5.0)                
#>  evaluate      0.13       2019-02-12 [1] CRAN (R 3.5.2)                
#>  fs            1.2.6      2018-08-23 [1] CRAN (R 3.5.0)                
#>  glue          1.3.0      2018-07-17 [1] CRAN (R 3.5.0)                
#>  highr         0.7        2018-06-09 [1] standard (@0.7)               
#>  htmltools     0.3.6      2017-04-28 [1] standard (@0.3.6)             
#>  knitr         1.22       2019-03-08 [1] CRAN (R 3.5.2)                
#>  magrittr      1.5        2014-11-22 [1] CRAN (R 3.5.0)                
#>  memoise       1.1.0      2017-04-21 [1] CRAN (R 3.5.0)                
#>  pkgbuild      1.0.2      2018-10-16 [1] CRAN (R 3.5.0)                
#>  pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.5.0)                
#>  prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.5.0)                
#>  processx      3.3.0      2019-03-10 [1] CRAN (R 3.5.2)                
#>  ps            1.3.0      2018-12-21 [1] CRAN (R 3.5.0)                
#>  R6            2.4.0      2019-02-14 [1] CRAN (R 3.5.2)                
#>  Rcpp          1.0.0      2018-11-07 [1] CRAN (R 3.5.0)                
#>  remotes       2.0.2.9000 2019-03-11 [1] Github (r-lib/remotes@6212345)
#>  rlang         0.3.1      2019-01-08 [1] CRAN (R 3.5.2)                
#>  rmarkdown     1.11       2018-12-08 [1] standard (@1.11)              
#>  rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.5.0)                
#>  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.5.0)                
#>  stringi       1.3.1      2019-02-13 [1] CRAN (R 3.5.2)                
#>  stringr       1.4.0      2019-02-10 [1] CRAN (R 3.5.2)                
#>  testthat      2.0.1      2018-10-13 [1] standard (@2.0.1)             
#>  usethis       1.4.0      2018-08-14 [1] CRAN (R 3.5.0)                
#>  withr         2.1.2      2018-03-15 [1] CRAN (R 3.5.0)                
#>  xfun          0.5        2019-02-20 [1] CRAN (R 3.5.2)                
#>  yaml          2.2.0      2018-07-25 [1] standard (@2.2.0)             
#> 
#> [1] /Users/kevin/Library/R/3.5/library
#> [2] /Library/Frameworks/R.framework/Versions/3.5/Resources/library

Looks like things are failing while attempting to update some other packages:

> remotes::install_github("rstudio/blogdown")
Downloading GitHub repo rstudio/blogdown@master
Error in FUN(X[[i]], ...) : is.remote(remote) is not TRUE

Enter a frame number, or 0 to exit   

 1: remotes::install_github("rstudio/blogdown")
 2: install_remotes(remotes, auth_token = auth_token, host = host, dependencies = dependencies, upgrade = upgrade,
 3: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
 4: FUN(X[[i]], ...)
 5: install(source, dependencies = dependencies, upgrade = upgrade, force = force, quiet = quiet, build = build, b
 6: install_deps(pkgdir, dependencies = dependencies, quiet = quiet, build = build, build_opts = build_opts, upgra
 7: update(packages, dependencies = dep_deps, quiet = quiet, upgrade = upgrade, build = build, build_opts = build_
 8: update.package_deps(packages, dependencies = dep_deps, quiet = quiet, upgrade = upgrade, build = build, build_
 9: install_remotes(object$remote[!object$is_cran & behind], dependencies = dependencies, upgrade = upgrade, force
10: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
11: FUN(X[[i]], ...)
12: stopifnot(is.remote(remote))

Looks like this is caused by NULL entries sneaking into the set of package dependencies:

> str(remotes::package_deps("rmarkdown"))
Classes 'package_deps' and 'data.frame':	18 obs. of  6 variables:
 $ package  : chr  "base64enc" "digest" "evaluate" "glue" ...
 $ installed: chr  "0.1-3" "0.6.18" "0.13" "1.3.0" ...
 $ available: chr  "0.1-3" "0.6.18" "0.13" "1.3.0" ...
 $ diff     : int  0 0 0 0 0 0 0 0 0 0 ...
 $ is_cran  : logi  TRUE TRUE TRUE TRUE FALSE FALSE ...
 $ remote   :List of 18
  ..$ :List of 4
  .. ..$ name    : chr "base64enc"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "0.1-3"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ :List of 4
  .. ..$ name    : chr "digest"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "0.6.18"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ :List of 4
  .. ..$ name    : chr "evaluate"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "0.13"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ :List of 4
  .. ..$ name    : chr "glue"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "1.3.0"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ : NULL
  ..$ : NULL
  ..$ :List of 4
  .. ..$ name    : chr "jsonlite"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "1.6"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ :List of 4
  .. ..$ name    : chr "knitr"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "1.22"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ :List of 4
  .. ..$ name    : chr "magrittr"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "1.5"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ : NULL
  ..$ :List of 4
  .. ..$ name    : chr "mime"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "0.6"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ :List of 4
  .. ..$ name    : chr "Rcpp"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "1.0.0"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ : NULL
  ..$ :List of 4
  .. ..$ name    : chr "stringi"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "1.3.1"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ :List of 4
  .. ..$ name    : chr "stringr"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "1.4.0"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ : NULL
  ..$ :List of 4
  .. ..$ name    : chr "xfun"
  .. ..$ repos   : Named chr "https://cran.rstudio.com"
  .. .. ..- attr(*, "names")= chr "CRAN"
  .. ..$ pkg_type: chr "both"
  .. ..$ sha     : chr "0.5"
  .. ..- attr(*, "class")= chr  "cran_remote" "remote"
  ..$ : NULL
  ..- attr(*, "class")= chr "remotes"
 - attr(*, "repos")= Named chr "https://cran.rstudio.com"
  ..- attr(*, "names")= chr "CRAN"
 - attr(*, "type")= chr "both"

I believe this is because some of the packages I have were installed by pak, and list their RemoteType as standard which is not yet understood by the remotes package.

> str(remotes:::package2remote("highr"))
 NULL
> str(read.dcf(system.file("DESCRIPTION", package = "highr"), all = TRUE))
'data.frame':	1 obs. of  25 variables:
 $ Package         : chr "highr"
 $ Type            : chr "Package"
 $ Title           : chr "Syntax Highlighting for R Source Code"
 $ Version         : chr "0.7"
 $ Authors@R       : chr "c(person(\"Christopher\", \"Gandrud\", role = \"ctb\"),\nperson(\"Qiang\", \"Li\", role = \"ctb\"),\nperson(\"Y"| __truncated__
 $ Maintainer      : chr "Yihui Xie <xie@yihui.name>"
 $ Description     : chr "Provides syntax highlighting for R source code. Currently it\nsupports LaTeX and HTML output. Source code of ot"| __truncated__
 $ Depends         : chr "R (>= 3.0.2)"
 $ Suggests        : chr "knitr, testit"
 $ License         : chr "GPL"
 $ URL             : chr "https://github.com/yihui/highr"
 $ BugReports      : chr "https://github.com/yihui/highr/issues"
 $ VignetteBuilder : chr "knitr"
 $ RoxygenNote     : chr "6.0.1"
 $ NeedsCompilation: chr "no"
 $ Packaged        : chr "2018-06-09 07:37:11 UTC; yihui"
 $ Author          : chr "Christopher Gandrud [ctb],\nQiang Li [ctb],\nYixuan Qiu [aut],\nYihui Xie [aut, cre]"
 $ Repository      : chr "CRAN"
 $ Date/Publication: chr "2018-06-09 15:46:28 UTC"
 $ Built           : chr "R 3.5.0; ; 2018-06-10 13:59:10 UTC; unix"
 $ RemoteType      : chr "standard"
 $ RemoteRef       : chr "highr"
 $ RemoteRepos     : chr "https://cloud.r-project.org"
 $ RemotePkgType   : chr "macos"
 $ RemoteSha       : chr "0.7"
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