Error: Vignette re-building failed

[feosborne]

Error when installing remora package from github.

I have installed "remotes" package and ran the command remotes : : install_github ('IMOS-AnimalTracking/remora', build_vignettes = TRUE)
But have had no success installing the package with vignettes.

SUMMARY: processing the following files failed:
'extractorMoor.Rmd' 'runQC.Rmd'

Error: Vignettes re-building failed.
Execution halted
Error: Failed to install 'remora' from GitHub
instalation of package 'systemfonts' had non-zero exit status.

[fmaron]

@feosborne thank you for reporting this. Could you paste the whole error and the output of sessionInfo()? It seems that there is an error with another package systemfonts. You could try installing this package separately with install.packages("systemfonts") and re-install remora.

[feosborne]

@fmaron thanks for getting back to me so quickly. I have tried the suggested and still have errors and fails please see below.

install.packages("systemfonts")
Error in install.packages : Updating loaded packages

Restarting R session...

install.packages("systemfonts")

There is a binary version available but the source version is later:
binary source needs_compilation
systemfonts 1.0.2 1.0.3 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘systemfonts’

trying URL 'https://cran.rstudio.com/src/contrib/systemfonts_1.0.3.tar.gz'
Content type 'application/x-gzip' length 81722 bytes (79 KB)

downloaded 79 KB

• installing source package ‘systemfonts’ ...
  ** package ‘systemfonts’ successfully unpacked and MD5 sums checked
  ** using staged installation
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  --------------------------- [SYSTEMFONTS] -----------------------------
  Configuration failed to find an Objective-C compiler.
  systemfonts require the use of Objective-C code on macOS to access
  the system-native font matching API.
  Please ensure that your build system is setup with an Objective-C
  compiler to install systemfonts on macOS

---

ERROR: configuration failed for package ‘systemfonts’

• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/systemfonts’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/systemfonts’
  Warning in install.packages :
  installation of package ‘systemfonts’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/n6/jjpbvkp95q74mlnw0pg1w1h00000gp/T/RtmpHPCryq/downloaded_packages’

library('systemfonts')
remotes::install_github('IMOS-AnimalTracking/remora', build_vignettes = TRUE)
Downloading GitHub repo IMOS-AnimalTracking/remora@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: systemfonts (1.0.2 -> 1.0.3) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
systemfonts (1.0.2 -> 1.0.3) [CRAN]
Installing 1 packages: systemfonts

There is a binary version available but the source version is later:
binary source needs_compilation
systemfonts 1.0.2 1.0.3 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘systemfonts’

trying URL 'https://cran.rstudio.com/src/contrib/systemfonts_1.0.3.tar.gz'
Content type 'application/x-gzip' length 81722 bytes (79 KB)

downloaded 79 KB

• installing source package ‘systemfonts’ ...
  ** package ‘systemfonts’ successfully unpacked and MD5 sums checked
  ** using staged installation
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  --------------------------- [SYSTEMFONTS] -----------------------------
  Configuration failed to find an Objective-C compiler.
  systemfonts require the use of Objective-C code on macOS to access
  the system-native font matching API.
  Please ensure that your build system is setup with an Objective-C
  compiler to install systemfonts on macOS

---

ERROR: configuration failed for package ‘systemfonts’

• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/systemfonts’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/systemfonts’

The downloaded source packages are in
‘/private/var/folders/n6/jjpbvkp95q74mlnw0pg1w1h00000gp/T/RtmpHPCryq/downloaded_packages’
✓ checking for file ‘/private/var/folders/n6/jjpbvkp95q74mlnw0pg1w1h00000gp/T/RtmpHPCryq/remotes12f63308667e3/IMOS-AnimalTracking-remora-a0d8193/DESCRIPTION’ (616ms)
─ preparing ‘remora’: (1.4s)
✓ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes
E creating vignettes (1m 23.2s)
--- re-building ‘extractEnv.Rmd’ using rmarkdown
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'tidyverse'
--- finished re-building ‘extractEnv.Rmd’

--- re-building ‘extractMoor.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

   between, first, last

The following objects are masked from 'package:stats':

   filter, lag

The following objects are masked from 'package:base':

   intersect, setdiff, setequal, union

Linking to GEOS 3.8.1, GDAL 3.2.1, PROJ 7.2.1

Attaching package: 'lubridate'

The following objects are masked from 'package:data.table':

   hour, isoweek, mday, minute, month, quarter, second, wday, week,
   yday, year

The following objects are masked from 'package:base':

   date, intersect, setdiff, union

Quitting from lines 49-53 (extractMoor.Rmd)
Error: processing vignette 'extractMoor.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘extractMoor.Rmd’

--- re-building ‘runQC.Rmd’ using rmarkdown
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'tidyverse'
Loading required package: tidyverse
Quitting from lines 130-136 (runQC.Rmd)
Error: processing vignette 'runQC.Rmd' failed with diagnostics:
could not find function "unnest"
--- failed re-building ‘runQC.Rmd’

--- re-building ‘shinyReport_receivers.Rmd’ using rmarkdown
--- finished re-building ‘shinyReport_receivers.Rmd’

--- re-building ‘shinyReport_transmitters.Rmd’ using rmarkdown
--- finished re-building ‘shinyReport_transmitters.Rmd’

SUMMARY: processing the following files failed:
‘extractMoor.Rmd’ ‘runQC.Rmd’

Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'remora' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> --- finished re-building ‘shinyReport_receivers.Rmd’
E>
E> --- re-building ‘shinyReport_transmitters.Rmd’ using rmarkdown
E> --- finished re-building ‘shinyReport_transmitters.Rmd’
E>
E> SUMMARY: processing the following files failed:
E> ‘extractMoor.Rmd’ ‘runQC.Rmd’
E>
E> Error: Vignette re-building failed.
E> Execution halted
In addition: Warning message:
In i.p(...) :
installation of package ‘systemfonts’ had non-zero exit status

[fmaron]

This is a problem related to systemfonts. You can try what it's suggested here. In summary, select "no" when install.packages("systemfonts") asks for compilation OR download Xcode for Mac users here.

When the issue with installing systemfonts is fixed, try re-installing remora.

[feosborne]

@fmaron Thank you, I have installed systemfonts downloaded Xcode and updated all R and Rstudio packages and I am still unable to install the remora package.

I now get this error:
SUMMARY: processing the following files failed:
‘extractMoor.Rmd’ ‘runQC.Rmd’

Error: Vignette re-building failed.
Execution halted
STDERR:

Error: Failed to install 'remora' from GitHub:
Failed to R CMD build package, try build = FALSE.

I can install it with build = FALSE, but then have no vignettes, any idea on whats happening here?
Thanks Kindly

[fmaron]

@feosborne, I'm sorry you couldn't install the package with the vignettes. I'll investigate this error in further detail (@ianjonsen @RossDwyer @fjaine, any thoughts?). Meanwhile, you can access the vignettes from the package website:

https://imos-animaltracking.github.io/remora/

[ianjonsen]

@feosborne A short-term fix would be to install using build = FALSE, as you say the package installs when not building the vignettes. You can access the vignettes via https://imos-animaltracking.github.io/remora/ - all the vignettes are in a tab on the right side of the menu bar. I realize this may not be ideal but it should get you going while we investigate the install issue.