Authentication - scrypt package install issue.

[Brian Holton]

I'm working on setting up Application Authentication according to the Getting Started Guide and running into trouble on the scrypt package install. 

I've installed RTools (it's a win7 x64 box) and the shinyapps package seems to install ok. When I run the highlighted script to install rscrypt, I get the error below:

Any thoughts?  (Aside from this, everything else seems to be fine and I'm able to deploy applications with no issues)

[Ameek Singh]

This was happening for me too. It worked after I restarted the R Session after installing the RTools package.

Is it persisting even after that ?

[Alex Ioannides]

I'm getting the same issue, even after re-starting R, RStudio and using a newly installed version of 'shinyapps'. Thanks.

[Josh Lindsteadt]

I'm getting the same thing, but I'm working on a Mac.  I tried restarting and newly installing shinyapps after downloading Command Line Tools, but still running into the same problem.

[Andy Kipp]

Josh,

Can you send the full output from install_github() that you are getting?

Thanks

-Andy

[Josh Lindsteadt]

Here you go:

> devtools::install_github('rstudio/rscrypt')

Installing github repo rscrypt/master from rstudio

Downloading rscrypt.zip from https://github.com/rstudio/rscrypt/archive/master.zip

Installing package from /var/folders/f_/0583lg7d3ml60nqfp2g9731w0000gn/T//RtmpANGQ6N/rscrypt.zip

arguments 'minimized' and 'invisible' are for Windows only

Installing scrypt

Installing dependencies for scrypt:

'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \

  '/private/var/folders/f_/0583lg7d3ml60nqfp2g9731w0000gn/T/RtmpANGQ6N/devtools8e1316b77a4e/rscrypt-master'  \

  --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library' --install-tests 

* installing *source* package 'scrypt' ...

+ cd src/scrypt-1.1.6/

+ ./configure

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... config.aux/install-sh -c -d

checking for gawk... no

checking for mawk... no

checking for nawk... no

checking for awk... awk

checking whether make sets $(MAKE)... yes

checking whether to enable maintainer-specific portions of Makefiles... no

checking for gcc... gcc

checking for C compiler default output file name... a.out

checking whether the C compiler works... yes

checking whether we are cross compiling... no

checking for suffix of executables... 

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for style of include used by make... GNU

checking dependency style of gcc... gcc3

checking how to run the C preprocessor... gcc -E

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking sys/endian.h usability... no

checking sys/endian.h presence... no

checking for sys/endian.h... no

checking whether be64enc is declared... no

checking err.h usability... yes

checking err.h presence... yes

checking for err.h... yes

checking for clock_gettime in -lrt... no

checking for clock_gettime... no

checking sys/sysinfo.h usability... no

checking sys/sysinfo.h presence... no

checking for sys/sysinfo.h... no

checking for sysinfo... no

checking for struct sysinfo... no

checking for struct sysinfo.totalram... no

checking for struct sysinfo.mem_unit... no

checking sys/param.h usability... yes

checking sys/param.h presence... yes

checking for sys/param.h... yes

checking for posix_memalign... yes

checking for special C compiler options needed for large files... no

checking for _FILE_OFFSET_BITS value needed for large files... no

configure: creating ./config.status

config.status: creating Makefile

config.status: creating config.h

config.status: executing depfiles commands

** libs

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./scrypt-1.1.6/ -I./scrypt-1.1.6/lib -I./scrypt-1.1.6/lib/util -DHAVE_CONFIG_H  -fPIC  -mtune=core2 -g -O2  -c scrypt-1.1.6/lib/crypto/sha256.c -o scrypt-1.1.6/lib/crypto/sha256.o

clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  -I./scrypt-1.1.6/ -I./scrypt-1.1.6/lib -I./scrypt-1.1.6/lib/util -DHAVE_CONFIG_H  -fPIC  -mtune=core2 -g -O2  -c scrypt-1.1.6/lib/crypto/crypto_scrypt-ref.c -o scrypt-1.1.6/lib/crypto/crypto_scrypt-ref.o

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I./scrypt-1.1.6/ -I./scrypt-1.1.6/lib -I./scrypt-1.1.6/lib/util -DHAVE_CONFIG_H -fPIC  -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I./scrypt-1.1.6/ -I./scrypt-1.1.6/lib -I./scrypt-1.1.6/lib/util -DHAVE_CONFIG_H -fPIC  -mtune=core2 -g -O2  -c scrypt.cpp -o scrypt.o

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I./scrypt-1.1.6/ -I./scrypt-1.1.6/lib -I./scrypt-1.1.6/lib/util -DHAVE_CONFIG_H -fPIC  -mtune=core2 -g -O2  -c base64.cpp -o base64.o

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"  `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I./scrypt-1.1.6/ -I./scrypt-1.1.6/lib -I./scrypt-1.1.6/lib/util -DHAVE_CONFIG_H -fPIC  -mtune=core2 -g -O2  -c util.cpp -o util.o

clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o scrypt.so scrypt-1.1.6/lib/crypto/sha256.o scrypt-1.1.6/lib/crypto/crypto_scrypt-ref.o RcppExports.o scrypt.o base64.o util.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/scrypt/libs

** R

** preparing package for lazy loading

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded

Error in dyn.load(file, DLLpath = DLLpath, ...) : 

  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/scrypt/libs/scrypt.so':

  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/scrypt/libs/scrypt.so, 6): Symbol not found: __ZNSoD0Ev

  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/scrypt/libs/scrypt.so

  Expected in: flat namespace

 in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/scrypt/libs/scrypt.so

Error: loading failed

Execution halted

ERROR: loading failed

* removing '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/scrypt'

Error: Command failed (1)

In addition: Warning message:

package ‘’ is not available (for R version 3.0.2) 

[Andy Kipp]

Josh,

Are you are running OSX Mavericks? What version of Xcode command line tools are you running?

-Andy

[Josh Lindsteadt]

I am.  I'm not exactly sure what version, because I'm unfamiliar with the Terminal commands.  I downloaded it directly from the apple developer site.  It was names "Command Line Tools (OSX Mavericks) for Xcode - Late October 2013 release date was Oct 22, 2013. 

Thanks,

Josh

[Andy Kipp]

Josh,

I think you're hitting an issue with OSX Mavericks using a different compiler then R was compiled with (clang vs llvm). See this and this for more info if you're interested.

The work around is to install Rcpp from source using this command:

install.packages('Rcpp', type='source')

and then:

devtools::install_github('rstudio/rscrypt')

Let me know if that works!

-Andy

[Josh Lindsteadt]

Still not working.  I tried uninstalling Xcode & Command Line Tools and reinstalling, but I'm still getting the same error.  Below is the output from installing Rcpp and rscrypt.

> install.packages('Rcpp', type='source')

trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.11.0.tar.gz'

Content type 'application/x-gzip' length 1998844 bytes (1.9 Mb)

opened URL

==================================================

downloaded 1.9 Mb

* installing *source* package ‘Rcpp’ ...

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

** libs

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Date.cpp -o Date.o

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Module.cpp -o Module.o

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Rcpp_init.cpp -o Rcpp_init.o

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c api.cpp -o api.o

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c attributes.cpp -o attributes.o

clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c barrier.cpp -o barrier.o

clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/libs

** R

** inst

** preparing package for lazy loading

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (Rcpp)

The downloaded source packages are in

‘/private/var/folders/f_/0583lg7d3ml60nqfp2g9731w0000gn/T/RtmpqxJPlO/downloaded_packages’

> library(Rcpp)

> devtools::install_github('rstudio/rscrypt')

Installing github repo rscrypt/master from rstudio

Downloading rscrypt.zip from https://github.com/rstudio/rscrypt/archive/master.zip

Installing package from /var/folders/f_/0583lg7d3ml60nqfp2g9731w0000gn/T//RtmpqxJPlO/rscrypt.zip

arguments 'minimized' and 'invisible' are for Windows only

Installing scrypt

Installing dependencies for scrypt:

'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \

  '/private/var/folders/f_/0583lg7d3ml60nqfp2g9731w0000gn/T/RtmpqxJPlO/devtoolsc6695e34c8d9/rscrypt-master'  \

clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o scrypt.so scrypt-1.1.6/lib/crypto/sha256.o scrypt-1.1.6/lib/crypto/crypto_scrypt-ref.o RcppExports.o scrypt.o base64.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/scrypt/libs

** R

** preparing package for lazy loading

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded

* DONE (scrypt)

Warning message:

package ‘’ is not available (for R version 3.0.2) 

[Andy Kipp]

Josh,

I may be confused, but from the output below, it looks like the package was installed successfully. The warning message can be ignored. Or are you seeing another error?

Andy

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[Andy Kipp]

Brian,

Did Ameek's suggestion of restarting R after you installed RTools correct this problem for you?

-Andy

[Josh Lindsteadt]

Sorry Andy,  you're right.  I think I was just up too late!