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rtminstall.packages

Can't install "tm", "NLP" or "slam" package on R 3.3.2 (macOS Sierra)

Installing the "tm" package with:

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

Fails with the following output:

During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MESSAGES failed, using "C"
3: Setting LC_MONETARY failed, using "C"
* installing *source* package ‘NLP’ ...
** package ‘NLP’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - R
ERROR: sub-architecture 'R' is not installed
*** arch - R.html
ERROR: sub-architecture 'R.html' is not installed
ERROR: loading failed for ‘R’, ‘R.html’
* removing ‘/usr/local/lib/R/3.3/site-library/NLP’
During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MESSAGES failed, using "C"
3: Setting LC_MONETARY failed, using "C"
* installing *source* package ‘slam’ ...
** package ‘slam’ successfully unpacked and MD5 sums checked
** libs
make: *** No rule to make target `apply.o', needed by `slam.so'.  Stop.
*** arch - R.html
Warning in file(con, "r") :
  cannot open file '/usr/local/Cellar/r/3.3.2/R.framework/Resources/etc/R.html/Makeconf': No such file or directory
Error in file(con, "r") : cannot open the connection
* removing ‘/usr/local/lib/R/3.3/site-library/slam’
During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MESSAGES failed, using "C"
3: Setting LC_MONETARY failed, using "C"
* installing *source* package ‘filehash’ ...
** package ‘filehash’ successfully unpacked and MD5 sums checked
** libs
make: *** No rule to make target `hash.o', needed by `filehash.so'.  Stop.
*** arch - R.html
Warning in file(con, "r") :
  cannot open file '/usr/local/Cellar/r/3.3.2/R.framework/Resources/etc/R.html/Makeconf': No such file or directory
Error in file(con, "r") : cannot open the connection
* removing ‘/usr/local/lib/R/3.3/site-library/filehash’
During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MESSAGES failed, using "C"
3: Setting LC_MONETARY failed, using "C"
* installing *source* package ‘Rpoppler’ ...
** package ‘Rpoppler’ successfully unpacked and MD5 sums checked
checking for pkg-config... /usr/local/bin/pkg-config
checking whether pkg-config knows about poppler-glib >= 0.18.0... no
configure: error: cannot determine poppler-glib compile/link flags
ERROR: configuration failed for package ‘Rpoppler’
* removing ‘/usr/local/lib/R/3.3/site-library/Rpoppler’
During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MESSAGES failed, using "C"
3: Setting LC_MONETARY failed, using "C"
* installing *source* package ‘SnowballC’ ...
** package ‘SnowballC’ successfully unpacked and MD5 sums checked
** libs
make: *** No rule to make target `api.o', needed by `SnowballC.so'.  Stop.
*** arch - R.html
Warning in file(con, "r") :
  cannot open file '/usr/local/Cellar/r/3.3.2/R.framework/Resources/etc/R.html/Makeconf': No such file or directory
Error in file(con, "r") : cannot open the connection
* removing ‘/usr/local/lib/R/3.3/site-library/SnowballC’
During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MESSAGES failed, using "C"
3: Setting LC_MONETARY failed, using "C"
ERROR: dependencies ‘NLP’, ‘slam’ are not available for package ‘tm’
* removing ‘/usr/local/lib/R/3.3/site-library/tm’

The downloaded source packages are in
    ‘/private/var/folders/19/b59kndv96js71_09xrz9ssdc0000gn/T/RtmptEhVgC/downloaded_packages’
Warning messages:
1: In install.packages("tm", dependencies = TRUE) :
  installation of package ‘NLP’ had non-zero exit status
2: In install.packages("tm", dependencies = TRUE) :
  installation of package ‘slam’ had non-zero exit status
3: In install.packages("tm", dependencies = TRUE) :
  installation of package ‘filehash’ had non-zero exit status
4: In install.packages("tm", dependencies = TRUE) :
  installation of package ‘Rpoppler’ had non-zero exit status
5: In install.packages("tm", dependencies = TRUE) :
  installation of package ‘SnowballC’ had non-zero exit status
6: In install.packages("tm", dependencies = TRUE) :
  installation of package ‘tm’ had non-zero exit status

Session info:

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin16.1.0 (64-bit)
Running under: macOS Sierra 10.12.2

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_3.3.2

PS: Trying to install "NLP" or "slam" separately fails too.

> install.packages("NLP", dependencies = TRUE)
Installing package into ‘/usr/local/lib/R/3.3/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://lib.ugent.be/CRAN/src/contrib/NLP_0.1-9.tar.gz'
Content type 'application/x-gzip' length 134347 bytes (131 KB)
==================================================
downloaded 131 KB

During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MESSAGES failed, using "C"
3: Setting LC_MONETARY failed, using "C"
* installing *source* package ‘NLP’ ...
** package ‘NLP’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - R
ERROR: sub-architecture 'R' is not installed
*** arch - R.html
ERROR: sub-architecture 'R.html' is not installed
ERROR: loading failed for ‘R’, ‘R.html’
* removing ‘/usr/local/lib/R/3.3/site-library/NLP’

The downloaded source packages are in
    ‘/private/var/folders/19/b59kndv96js71_09xrz9ssdc0000gn/T/RtmptEhVgC/downloaded_packages’
Warning message:
In install.packages("NLP", dependencies = TRUE) :
  installation of package ‘NLP’ had non-zero exit status


> install.packages("slam", dependencies = TRUE)
Installing package into ‘/usr/local/lib/R/3.3/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://lib.ugent.be/CRAN/src/contrib/slam_0.1-40.tar.gz'
Content type 'application/x-gzip' length 50146 bytes (48 KB)
==================================================
downloaded 48 KB

During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MESSAGES failed, using "C"
3: Setting LC_MONETARY failed, using "C"
* installing *source* package ‘slam’ ...
** package ‘slam’ successfully unpacked and MD5 sums checked
** libs
make: *** No rule to make target `apply.o', needed by `slam.so'.  Stop.
*** arch - R.html
Warning in file(con, "r") :
  cannot open file '/usr/local/Cellar/r/3.3.2/R.framework/Resources/etc/R.html/Makeconf': No such file or directory
Error in file(con, "r") : cannot open the connection
* removing ‘/usr/local/lib/R/3.3/site-library/slam’

The downloaded source packages are in
    ‘/private/var/folders/19/b59kndv96js71_09xrz9ssdc0000gn/T/RtmptEhVgC/downloaded_packages’
Warning message:
In install.packages("slam", dependencies = TRUE) :
  installation of package ‘slam’ had non-zero exit status

Links:

Solution

  • Ok, something weird was wrong.

    R uses this line to determine the architectures:

    archs  <- dir(file.path(R.home("bin"), "exec"))

    As seen here: src/library/toolsR/install.R#1479

    In my case the bin/exec directory could be found here:

    > R.home("bin/exec")
[1] "/usr/local/Cellar/r/3.3.2/R.framework/Resources/bin/exec"

    For some reason that directory contained a R.html file with the contents NA. This was causing R to think there was an architecture called R.html.

    After removing the file I was able to install everything.