some installation glitches

[Steve Cumming]

Hi:

A recent install on a mac works more or less correctly, except for the following error and warning which are pretty obscure to me. 

install_packages("SpaDES")

library(SpaDES)

each produce the following:

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Warning message:

running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1 

They don't seem to matter much, but can you suggest what should be done to make them go away?

Also, may I suggest a new tag: "installation" ?

Steve

[Alex Chubaty]

Hi Steve,

Can you confirm that you used install_packages()  -- or something from the devtools package -- instead of the base install.packages()? The latter is the recammended way to install from CRAN using a pre-build binary.

If you *do* want to install from source, you need to have the developer tools installed on your mac. These include the xcode command line tools (xcode-select --install). You also should have installed xquartz.

Alex

[Steve Cumming]

Pardon me: I used install.packages(), as per your rpubs installation guide.

update.packages(ask = FALSE, checkBuilt = TRUE)
install.packages(c("devtools", "knitr", "profvis", "rmarkdown", "SpaDES"),
                 dependencies = TRUE)

 

[Alex Chubaty]

I'm not sure why you'd be getting the error for the SpaDES installation, since there is a prebuilt binary for macOS on CRAN (https://cran.r-project.org/bin/macosx/mavericks/contrib/3.3/SpaDES_1.3.1.tgz).

Can you run the install.packages() command only for "SpaDES" and see if you still get an error?

install.packages("SpaDES", dependencies = TRUE)

If that works, then the error is being generated by one of the other packages in that list...

[Steve Cumming]

This is the result, Alex, of install.packages() on a mac, R 3.2.3. 

Loading required package: sp

Loading required package: raster

Loading required package: SpaDES

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Default paths for SpaDES directories set to:

  cachePath: /var/folders/46/mvz8rwm14p1btgf8vsly26280000gn/T/SpaDES/cache

  inputPath: /var/folders/46/mvz8rwm14p1btgf8vsly26280000gn/T/SpaDES/inputs

  modulePath: /var/folders/46/mvz8rwm14p1btgf8vsly26280000gn/T/SpaDES/modules

  outputPath: /var/folders/46/mvz8rwm14p1btgf8vsly26280000gn/T/SpaDES/outputs

These can be changed by setting the appropriate option using:

  e.g., options(spades.cachePath = "/path/to/my/cache")

Attaching package: ‘SpaDES’

The following objects are masked from ‘package:stats’:

    end, start, time

> install.packages("SpaDES")

Error in install.packages : Updating loaded packages

Warning messages:

1: package ‘sp’ was built under R version 3.2.5 

2: package ‘raster’ was built under R version 3.2.5 

3: running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1 

> install.packages("SpaDES")

installing the source package ‘SpaDES’

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0 56 1628k   56  912k    0     0  1493k      0  0:00:01 --:--:--  0:00:01 1494k100 1628k  100 1628k    0     0  1773k      0 --:--:-- --:--:-- --:--:-- 1772k

* installing *source* package ‘SpaDES’ ...

** package ‘SpaDES’ successfully unpacked and MD5 sums checked

** R

** demo

** inst

** byte-compile and prepare package for lazy loading

Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘DBI’: not turning on duplicate class definitions for this class.

Note: the specification for S3 class “difftime” in package ‘lubridate’ seems equivalent to one from package ‘DBI’: not turning on duplicate class definitions for this class.

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Warning: running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1

Creating a new generic function for ‘cache’ in package ‘SpaDES’

Creating a new generic function for ‘copy’ in package ‘SpaDES’

Creating a new generic function for ‘digest’ in package ‘SpaDES’

Creating a generic function for ‘ls’ from package ‘base’ in package ‘SpaDES’

Creating a generic function for ‘objects’ from package ‘base’ in package ‘SpaDES’

Creating a generic function for ‘ls.str’ from package ‘utils’ in package ‘SpaDES’

Creating a new generic function for ‘time’ in package ‘SpaDES’

Creating a new generic function for ‘end’ in package ‘SpaDES’

Creating a new generic function for ‘start’ in package ‘SpaDES’

Creating a new generic function for ‘gpar’ in package ‘SpaDES’

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘DBI’: not turning on duplicate class definitions for this class.

Note: the specification for S3 class “difftime” in package ‘lubridate’ seems equivalent to one from package ‘DBI’: not turning on duplicate class definitions for this class.

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Warning: running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1

* DONE (SpaDES)

The downloaded source packages are in

‘/private/var/folders/46/mvz8rwm14p1btgf8vsly26280000gn/T/RtmpAciOCT/downloaded_packages’

> 

[Alex Chubaty]

Per my first post, do you have the xcode command line tools and xquartz installed?

[Steve Cumming]

Alex:

xcode and xquartz were installed long ago. It appears an OS upgrade broke something.

running

xcode-select --install

from the command line did the trick (hat tip to http://stackoverflow.com/questions/32925000/git-doesnt-work-after-upgrading-mac-os-x-el-capitain)

There are still some duplicated S3 class specifications in the numerous packages that come along with SpaDES, but that is not a serious problem I am sure.

Thanks for the help.

Steve

[Alex Chubaty]

Yes, both need to be reinstalled after every major OS update:

From https://cran.r-project.org/bin/macosx/:

Note: the use of X11 (including tcltk) requires XQuartz to be installed since it is no longer part of OS X. Always re-install XQuartz when upgrading your OS X to a new major version.

Likewise, reinstalling xcode commandline tools is required by Apple after major updates -- you need to re-agree to the EULA.