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broom.mixed installs correctly but raises errors and is not loaded #12

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DesiQuintans opened this issue Feb 15, 2019 · 1 comment
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@DesiQuintans
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DesiQuintans commented Feb 15, 2019

Ran into an issue where a GitHub package (bbolker/broom.mixed) correctly installed but shelf() reports that the package "failed to install and was not attached" (see Output 1 below for console dump). But it did indeed install — I can see it in my R Library folder — so only the latter part of that error is true.

Trying to attach the package with shelf() raises the same error (Output 2), making it clear that a) the package is installed because shelf() can see it, and b) shelf fails to attach it. Attaching it with base R method library() works just fine, and since library() is what shelf() uses internally, the package must not be getting to the attachment phase at all.

Is this an issue with the . in the package name?


Output 1

> shelf(bbolker/broom.mixed)
Downloading GitHub repo bbolker/broom.mixed@master
√  checking for file 'C:\Users\Desi\AppData\Local\Temp\Rtmpop1ag9\remotes21c461c437cf\bbolker-broom.mixed-7a0ed67/DESCRIPTION' ... 
-  preparing 'broom.mixed':
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'broom.mixed_0.2.4.tar.gz'
   
* installing *source* package 'broom.mixed' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'broom.mixed'
    finding HTML links ... done
    augment.ranef.mer                       html  
    brms_tidiers                            html  
    compact                                 html  
    extractEffects                          html  
    fixef.MCMCglmm                          html  
    gamlss_tidiers                          html  
    glmmTMB_tidiers                         html  
    glmmadmb_tidiers                        html  
    insert_NAs                              html  
    lme4_tidiers                            html  
Rd warning: C:/Users/Desi/AppData/Local/Temp/Rtmp44fkdV/R.INSTALL225c255e6cb0/broom.mixed/man/lme4_tidiers.Rd:29: file link 'coef.merMod' in package 'lme4' does not exist and so has been treated as a topic
    mcmc_tidiers                            html  
    nlme_tidiers                            html  
    paramNamesMCMCglmm                      html  
    ranef.MCMCglmm                          html  
    ranefLevels                             html  
    reexports                               html  
Rd warning: C:/Users/Desi/AppData/Local/Temp/Rtmp44fkdV/R.INSTALL225c255e6cb0/broom.mixed/man/reexports.Rd:16: file link 'tidy' in package 'broom' does not exist and so has been treated as a topic
Rd warning: C:/Users/Desi/AppData/Local/Temp/Rtmp44fkdV/R.INSTALL225c255e6cb0/broom.mixed/man/reexports.Rd:16: file link 'glance' in package 'broom' does not exist and so has been treated as a topic
Rd warning: C:/Users/Desi/AppData/Local/Temp/Rtmp44fkdV/R.INSTALL225c255e6cb0/broom.mixed/man/reexports.Rd:16: file link 'augment' in package 'broom' does not exist and so has been treated as a topic
    rstanarm_tidiers                        html  
    stdranef                                html  
    tidy.TMB                                html  
    unrowname                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (broom.mixed)
In R CMD INSTALL
Warning message:
In shelf(bbolker/broom.mixed) : 

  These packages failed to install and were not attached:

    broom.mixed

  Are they Bioconductor packages? If so, please install Bioconductor
  before running librarian::shelf().

  Are they from GitHub? Please supply both the GitHub username and
  package name, e.g. DesiQuintans/librarian

  Otherwise, check the spelling and capitalisation of the names.
  It's also possible that the packages are someone's private packages
  that are not being shared online.

Output 2

> shelf(bbolker/broom.mixed)
Skipping install of 'broom.mixed' from a github remote, the SHA1 (7a0ed673) has not changed since last install.
  Use `force = TRUE` to force installation
Warning message:
In shelf(bbolker/broom.mixed) : 

  These packages failed to install and were not attached:

    broom.mixed

  Are they Bioconductor packages? If so, please install Bioconductor
  before running librarian::shelf().

  Are they from GitHub? Please supply both the GitHub username and
  package name, e.g. DesiQuintans/librarian

  Otherwise, check the spelling and capitalisation of the names.
  It's also possible that the packages are someone's private packages
  that are not being shared online.
@DesiQuintans DesiQuintans added the bug Something isn't working label Feb 15, 2019
@DesiQuintans DesiQuintans self-assigned this Feb 15, 2019
@amywilderson
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I have the same issue

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