Error: Unable to retrieve package records for the following packages: - "grDevices", "graphics", "grid", "methods", "stats", "tools", "utils"

[tbsund]

I am getting this error when I try to deploy my shiny app to shinyapps.io:

Error: Unable to retrieve package records for the following packages:

• "grDevices", "graphics", "grid", "methods", "stats", "tools", "utils"

These are all base packages so I can't use install.packages() for them, and the only libraries that are loaded in my shiny app are readxl, ggplot2, and reshape2 which are all CRAN packages.

[jspiewak]

Could you please include the full output of the deployment?
What is the output of rsconnect::appDependencies()?

[tbsund]

Here is the output of the deployment:

rsconnect::deployApp('C:/Users/tsunderl/Desktop/folder')
Preparing to deploy application...DONE
Uploading bundle for application: 352639...Error: Unable to retrieve package records for the following packages:

• "grDevices", "graphics", "grid", "methods", "stats", "tools", "utils"
  In addition: Warning messages:
  1: In FUN(X[[i]], ...) :
  Failed to infer source for package 'BH'; using latest available version on CRAN instead
  2: In FUN(X[[i]], ...) :
  3: In FUN(X[[i]], ...) :
  4: In FUN(X[[i]], ...) :
  5: In FUN(X[[i]], ...) :
  6: In FUN(X[[i]], ...) :
  7: In FUN(X[[i]], ...) :
  8: In FUN(X[[i]], ...) :

And here is the output of appDependencies:

rsconnect::appDependencies('C:/Users/tsunderl/Desktop/folder')
Error: Unable to retrieve package records for the following packages:

• "grDevices", "graphics", "grid", "methods", "stats", "tools", "utils"
  In addition: Warning messages:
  1: In FUN(X[[i]], ...) :
  Failed to infer source for package 'BH'; using latest available version on CRAN instead
  2: In FUN(X[[i]], ...) :
  3: In FUN(X[[i]], ...) :
  4: In FUN(X[[i]], ...) :
  5: In FUN(X[[i]], ...) :
  6: In FUN(X[[i]], ...) :
  7: In FUN(X[[i]], ...) :
  8: In FUN(X[[i]], ...) :

Thanks!!

[jspiewak]

And what files are in 'C:/Users/tsunderl/Desktop/folder'?

[tbsund]

My program, app.R, is the only file in the folder

[jspiewak]

@jmcphers any suggestions for tracking this down further?

[kevinushey]

@tbsund, what is the output of:

ip <- as.data.frame(installed.packages(), stringsAsFactors = FALSE)
ip[ip$Priority %in% "base", ]

[tbsund]

ip <- as.data.frame(installed.packages(), stringsAsFactors = FALSE)
ip[ip$Priority %in% "base", ]
[1] Package LibPath Version Priority Depends Imports
[7] LinkingTo Suggests Enhances License License_is_FOSS License_restricts_use
[13] OS_type Archs MD5sum NeedsCompilation Built
<0 rows> (or 0-length row.names)

[kevinushey]

How did you install R? For some reason, R does not believe any of the installed packages have "base" priority. On my machine (with a CRAN binary of R on macOS) I see:

> ip <- as.data.frame(installed.packages(), stringsAsFactors = FALSE)
> ip[ip$Priority %in% "base", ]
            Package                                                        LibPath Version Priority Depends                    Imports LinkingTo                                 Suggests        Enhances         License License_is_FOSS
base           base /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>                       <NA>      <NA>                                  methods            <NA> Part of R 3.5.0            <NA>
compiler   compiler /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>                       <NA>      <NA>                                     <NA>            <NA> Part of R 3.5.0            <NA>
datasets   datasets /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>                       <NA>      <NA>                                     <NA>            <NA> Part of R 3.5.0            <NA>
graphics   graphics /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>                  grDevices      <NA>                                     <NA>            <NA> Part of R 3.5.0            <NA>
grDevices grDevices /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>                       <NA>      <NA>                               KernSmooth            <NA> Part of R 3.5.0            <NA>
grid           grid /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>           grDevices, utils      <NA>                                  lattice            <NA> Part of R 3.5.0            <NA>
methods     methods /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>               utils, stats      <NA>                                codetools            <NA> Part of R 3.5.0            <NA>
parallel   parallel /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>            tools, compiler      <NA>                                  methods snow, nws, Rmpi Part of R 3.5.0            <NA>
splines     splines /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>            graphics, stats      <NA>                          Matrix, methods            <NA> Part of R 3.5.0            <NA>
stats         stats /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA> utils, grDevices, graphics      <NA> MASS, Matrix, SuppDists, methods, stats4            <NA> Part of R 3.5.0            <NA>
stats4       stats4 /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>   graphics, methods, stats      <NA>                                     <NA>            <NA> Part of R 3.5.0            <NA>
tcltk         tcltk /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>                      utils      <NA>                                     <NA>            <NA> Part of R 3.5.0            <NA>
tools         tools /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>                       <NA>      <NA>           codetools, methods, xml2, curl            <NA> Part of R 3.5.0            <NA>
utils         utils /Library/Frameworks/R.framework/Versions/3.5/Resources/library   3.5.0     base    <NA>                       <NA>      <NA>                methods, xml2, commonmark            <NA> Part of R 3.5.0            <NA>
          License_restricts_use OS_type MD5sum NeedsCompilation Built
base                       <NA>    <NA>   <NA>             <NA> 3.5.0
compiler                   <NA>    <NA>   <NA>             <NA> 3.5.0
datasets                   <NA>    <NA>   <NA>             <NA> 3.5.0
graphics                   <NA>    <NA>   <NA>              yes 3.5.0
grDevices                  <NA>    <NA>   <NA>              yes 3.5.0
grid                       <NA>    <NA>   <NA>              yes 3.5.0
methods                    <NA>    <NA>   <NA>              yes 3.5.0
parallel                   <NA>    <NA>   <NA>              yes 3.5.0
splines                    <NA>    <NA>   <NA>              yes 3.5.0
stats                      <NA>    <NA>   <NA>              yes 3.5.0
stats4                     <NA>    <NA>   <NA>             <NA> 3.5.0
tcltk                      <NA>    <NA>   <NA>              yes 3.5.0
tools                      <NA>    <NA>   <NA>              yes 3.5.0
utils                      <NA>    <NA>   <NA>              yes 3.5.0

[kevinushey]

I'd also be curious to see what the output of:

tools:::.get_standard_package_names()

is. This sounds suspiciously similar to rstudio/packrat#381.

[tbsund]

I downloaded it from the CRAN website. It is my work computer, so there's a chance it's a permissions issue. I'm the only R user in my office, so if you think the permissions is the issue, do you have any advice I could relay to IT to get it fixed? Everything, including my shiny app works fine on my computer, it is only deploying it that is an issue.

Her is that output:

tools:::.get_standard_package_names()
$base
[1] "base" "tools" "utils" "grDevices" "graphics" "stats" "datasets" "methods" "grid" "splines" "stats4"
[12] "tcltk" "compiler" "parallel"

$recommended
[1] "MASS" "lattice" "Matrix" "nlme" "survival" "boot" "cluster" "codetools" "foreign" "KernSmooth"
[11] "rpart" "class" "nnet" "spatial" "mgcv"

[kevinushey]

Strange -- can you share the whole output of:

installed.packages()

The only thing I can initially guess is that R somehow lacks permissions to read some of the package metadata required when querying installed.packages()...

[tbsund]

Are either of these what you meant? I feel like neither are very informative...

install.packages()
Error in install.packages : argument "pkgs" is missing, with no default
install.packages
function (...)
.rs.callAs(name, hook, original, ...)
<environment: 0x00000000082a5c70>

[kevinushey]

Sorry, I meant installed.packages() -- I since edited the post to update but not fast enough!

[tbsund]

installed.packages()
Package LibPath Version Priority Depends Imports LinkingTo Suggests Enhances License License_is_FOSS License_restricts_use OS_type
Archs MD5sum NeedsCompilation Built

[kevinushey]

That makes even less sense! What is the output of:

.libPaths()

on your machine? Are you actually able to load any of those packages? Does library(stats) succeed for you?

[tbsund]

I edited the output a little just because I don't know much about stuff and didn't know if the network name is sensitive.

.libPaths()
[1] "\\network.corp/Personal$/tsunderl/My Documents/R/win-library/3.5"
[2] "\\network.corp/Personal$/tsunderl/My Documents/R/R-3.5.0/library"

and library(stats) did not give any error messages, so I assume it succeeds!

[kevinushey]

Interesting. I can only guess that installed.packages() is failing to query the set of installed packages because your R libraries are located on a networked drive.

We could potentially work around this in Packrat.

[tbsund]

Okay! How?

Btw, thanks for all your help! :)

[kevinushey]

This will require some work on the Packrat side, so unfortunately there's nothing to be done on your side until we get those fixes in.

Can you by any chance provide the output of:

list.files(.libPaths()[1])

[tbsund]

list.files(.libPaths()[1])
[1] "assertthat" "base64enc" "bitops" "cellranger" "cli" "colorspace" "crayon"
[8] "dichromat" "digest" "file1ed43486f49" "file614128c20b7" "filea04566c4702" "filed8c64675d8" "ggplot2"
[15] "glue" "gtable" "htmltools" "httpuv" "jsonlite" "labeling" "later"
[22] "lattice" "lazyeval" "lme4" "magrittr" "MASS" "Matrix" "mime"
[29] "minqa" "munsell" "nlme" "nloptr" "packrat" "pillar" "PKI"
[36] "plyr" "promises" "R6" "RColorBrewer" "Rcpp" "RcppEigen" "RCurl"
[43] "readxl" "rematch" "reshape2" "RJSONIO" "rlang" "rsconnect" "rstudioapi"
[50] "scales" "shiny" "sourcetools" "stringi" "stringr" "tibble" "utf8"
[57] "viridisLite" "xtable" "yaml"

[kevinushey]

Great! With that I should be able to get a workaround into Packrat.

[kevinushey]

I have a candidate fix in Packrat now. Can you try installing the development version with:

if (!requireNamespace("devtools")) install.packages("devtools")
devtools::install_github("rstudio/packrat")

and let me know if you have any better luck with deployment?

[tbsund]

It worked!!! It made me load a billion libraries, but once I did it worked. THANK YOU!! From: Kevin Ushey [mailto:notifications@github.com] Sent: Thursday, June 07, 2018 4:20 PM To: rstudio/rsconnect <rsconnect@noreply.github.com> Cc: Tiffany Sunderland <Tiffany.Sunderland@cabelas.com>; Mention <mention@noreply.github.com> Subject: Re: [rstudio/rsconnect] Error: Unable to retrieve package records for the following packages: - "grDevices", "graphics", "grid", "methods", "stats", "tools", "utils" (#278) I have a candidate fix in Packrat now. Can you try installing the development version with: if (!requireNamespace("devtools")) install.packages("devtools") devtools::install_github("rstudio/packrat") and let me know if you have any better luck with deployment? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rstudio_rsconnect_issues_278-23issuecomment-2D395568715&d=DwMFaQ&c=_mDkRWzOLjoVDgT8Mi46Yw&r=to7blI0sWWXXa6aO4OJKc2ufF5FJgacLay0qi5PxoYw&m=wlorVp_0kteNPjiTY7f7bS2vISlxlTvMPz-ZlWil4IU&s=BdX59-3klpxhqKfkyKg1WsCqsVKK0vD9ASvZL2JdBgI&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AmEQnBKFp4P3-5FHDoDV9X2P4HycrQE9Uiks5t6ZkFgaJpZM4UZPkr&d=DwMFaQ&c=_mDkRWzOLjoVDgT8Mi46Yw&r=to7blI0sWWXXa6aO4OJKc2ufF5FJgacLay0qi5PxoYw&m=wlorVp_0kteNPjiTY7f7bS2vISlxlTvMPz-ZlWil4IU&s=AYPDlPHyBlebrOq8OWMqFFSoNxMlGYO2RuRTXytwLa0&e=>.

[kevinushey]

Awesome! I'm glad to hear it :-)

[TMax66]

HI, all
meet an analogue problem when try to deploy my app
I get this message:

Preparing to deploy application...DONE
Uploading bundle for application: 369321...Errore: 
* Application depends on package "MASS" but it is not installed.
   Please resolve before continuing.

any suggestion??

no solution in other topic https://community.rstudio.com/t/error-during-deploy-shiny-app/9604
Massimo
Thanks

[kevinushey]

Can you confirm that an attempt to load the MASS package succeeds? E.g.

library(MASS)

In addition, what is the output of find.package("MASS")?

Does installing the latest version from CRAN with install.packages("MASS") help at all?

[TMax66]

Hi Kevin,
yes I I tried them all..no success!

[kevinushey]

What did you see in the R console after trying each of these steps?

[TMax66]

HI Kevin
I tried to install again MASSand it seems that it works now....

thanks
Max

[jmcphers]

Fixed on the packrat side; no work to do in rsconnect.