RStudio 1.2.1578 fails to start on Mac

[ivanek]

System details

RStudio Edition : Desktop
RStudio Version : 1.2.1578
OS Version      :  macOS 10.14.6
R Version       :   3.6.1 Patched (2019-09-14 r77193)

Steps to reproduce the problem

Install RStusio 1.2.1578 (dmg downloaded from the website)
Started Rstudio with /Applications/RStudio.app/Contents/MacOS/RStudio

Describe the problem in detail

There is an error message in the terminal: "Uncaught TypeError: Cannot read property 'notifyRCrashed' of undefined"
And the RStudio fails to start, showing only white window with text:

This site can’t be reached
127.0.0.1 refused to connect.
Try:

Checking the connection
Checking the proxy and the firewall
ERR_CONNECTION_REFUSED 

Describe the behavior you expected

Should simply start (the version 1.2.1335 starts normally).

1. The output of sessionInfo()

R version 3.6.1 Patched (2019-09-14 r77193)
Platform: x86_64-apple-darwin18.7.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.dylib
LAPACK: /usr/local/lib/R/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
[1] compiler_3.6.1

2. The R code in question <none>

3. A diagnostics report from affected version is not created.

Command: /Applications/RStudio.app/Contents/MacOS/RStudio --run-diagnostics shows only following:

Using R script: /usr/local/bin/R

Attempting to launch R session...
  R_HOME=/usr/local/lib/R
  R_DOC_DIR=/usr/local/lib/R/doc
  R_INCLUDE_DIR=/usr/local/lib/R/include
  R_SHARE_DIR=/usr/local/lib/R/share
  PATH=/Users/ivanek/perl5/bin:/usr/local/opt/mysql-client/bin:/usr/local/opt/libxml2/bin:/usr/local/opt/tcl-tk/bin:/usr/local/bin:/usr/local/sbin:/Users/ivanek/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/MacGPG2/bin:/opt/X11/bin:/Applications/Wireshark.app/Contents/MacOS
  HOME=/Users/ivanek

R session launched, attempting to connect on port 24591...
dyld: Library not loaded: libRblas.dylib
  Referenced from: /usr/local/lib/R/lib/libR.dylib
  Reason: image not found

Connected to R session, attempting to initialize...

However the version 1.2.1335 (which works) creates this diagnostic report:

[1] "1.2.1335"

$R
[1] "/usr/local/bin/R"

$pdflatex
[1] "/usr/local/bin/pdflatex"

$bibtex
[1] "/usr/local/bin/bibtex"

$gcc
[1] "/usr/bin/gcc"

$git
[1] "/usr/bin/git"

$svn
[1] "/usr/bin/svn"

R version 3.6.1 Patched (2019-09-14 r77193)
Platform: x86_64-apple-darwin18.7.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /usr/local/lib/R/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1   

SysInfo:
                                                                                           sysname 
                                                                                          "Darwin" 
                                                                                           release 
                                                                                          "18.7.0" 
                                                                                           version 
"Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64" 
                                                                                          nodename 
                                                                        "dbm203-190.dbm.unibas.ch" 
                                                                                           machine 
                                                                                          "x86_64" 
                                                                                             login 
                                                                                          "ivanek" 
                                                                                              user 
                                                                                          "ivanek" 
                                                                                    effective_user 
                                                                                          "ivanek" 

R Version:
               _                                          
platform       x86_64-apple-darwin18.7.0                  
arch           x86_64                                     
os             darwin18.7.0                               
system         x86_64, darwin18.7.0                       
status         Patched                                    
major          3                                          
minor          6.1                                        
year           2019                                       
month          09                                         
day            14                                         
svn rev        77193                                      
language       R                                          
version.string R version 3.6.1 Patched (2019-09-14 r77193)
nickname       Action of the Toes                         
$Apple_PubSub_Socket_Render
[1] "/private/tmp/com.apple.launchd.iVF7kYsCiZ/Render"

$CLICOLOR_FORCE
[1] "1"

$COLORFGBG
[1] "15;0"

$COLORTERM
[1] "truecolor"

$CPPFLAGS
[1] "-I/usr/local/opt/openblas/include"

$DISPLAY
[1] "/private/tmp/com.apple.launchd.m3W9YpYJVg/org.macosforge.xquartz:0"

$DYLD_FALLBACK_LIBRARY_PATH
[1] "/usr/local/lib/R/lib:/Users/ivanek/lib:/usr/local/lib:/usr/lib:::/lib:/Library/Java/JavaVirtualMachines/adoptopenjdk-12.jdk/Contents/Home/lib/server"

$EDITOR
[1] "vi"

$GIT_ASKPASS
[1] "rpostback-askpass"

$HISTCONTROL
[1] "ignoreboth:erasedups"

$HOME
[1] "/Users/ivanek"

$ITERM_ORIG_PS1
[1] "\\[\033[32m\\]\\u@\\h\\[\033[37m\\]:\\[\033[34m\\]\\W\\[\033[37m\\]$ \\[\033(B\033[m\\]"

$ITERM_PREV_PS1
[1] "\\[\033]133;D;$?\a\033]133;A\a\\]\\[\033[32m\\]\\u@\\h\\[\033[37m\\]:\\[\033[34m\\]\\W\\[\033[37m\\]$ \\[\033(B\033[m\\]\\[\033]133;B\a\\]"

$ITERM_PROFILE
[1] "Default"

$ITERM_SESSION_ID
[1] "w0t4p0:7F2BE21C-E335-4C6A-82D1-5BA0354A19D2"

$LANG
[1] "en_US.UTF-8"

$LC_COLLATE
[1] "C"

$LC_CTYPE
[1] "en_US.UTF-8"

$LC_TERMINAL
[1] "iTerm2"

$LC_TERMINAL_VERSION
[1] "3.3.4"

$LC_TYPE
[1] "en_US.UTF-8"

$LDFLAGS
[1] "-L/usr/local/opt/openblas/lib"

$LN_S
[1] "ln -s"

$LOGNAME
[1] "ivanek"

$MAKE
[1] "make"

$PAGER
[1] "/usr/bin/less"

$PATH
[1] "/Users/ivanek/perl5/bin:/usr/local/opt/mysql-client/bin:/usr/local/opt/libxml2/bin:/usr/local/opt/tcl-tk/bin:/usr/local/bin:/usr/local/sbin:/Users/ivanek/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/MacGPG2/bin:/opt/X11/bin:/Applications/Wireshark.app/Contents/MacOS"

$PERL5LIB
[1] "/Users/ivanek/perl5/lib/perl5"

$PERL_LOCAL_LIB_ROOT
[1] "/Users/ivanek/perl5"

$PERL_MB_OPT
[1] "--install_base \"/Users/ivanek/perl5\""

$PERL_MM_OPT
[1] "INSTALL_BASE=/Users/ivanek/perl5"

$PKG_CONFIG_PATH
[1] "/usr/local/opt/openblas/lib/pkgconfig"

$PS1
[1] "\\[\033[32m\\]\\u@\\h\\[\033[37m\\]:\\[\033[34m\\]\\W\\[\033[37m\\]$ \\[\033(B\033[m\\]"

$PWD
[1] "/Users/ivanek"

$RMARKDOWN_MATHJAX_PATH
[1] "/Applications/RStudio.app/Contents/Resources/resources/mathjax-26"

$RSTUDIO
[1] "1"

$RSTUDIO_CONSOLE_COLOR
[1] "256"

$RSTUDIO_CONSOLE_WIDTH
[1] "80"

$RSTUDIO_PANDOC
[1] "/Applications/RStudio.app/Contents/MacOS/pandoc"

$RSTUDIO_SESSION_PORT
[1] "28617"

$RSTUDIO_USER_IDENTITY
[1] "ivanek"

$RSTUDIO_WINUTILS
[1] "bin/winutils"

$RS_PPM_FD_READ
[1] "15"

$RS_PPM_FD_WRITE
[1] "16"

$RS_RPOSTBACK_PATH
[1] "/Applications/RStudio.app/Contents/MacOS/rpostback"

$RS_SHARED_SECRET
[1] "2824752491622650073984943658"

$R_BROWSER
[1] "/usr/bin/open"

$R_BZIPCMD
[1] "/usr/bin/bzip2"

$R_DOC_DIR
[1] "/usr/local/lib/R/doc"

$R_GZIPCMD
[1] "/usr/bin/gzip"

$R_HOME
[1] "/usr/local/lib/R"

$R_INCLUDE_DIR
[1] "/usr/local/lib/R/include"

$R_LIBS_SITE
[1] ""

$R_LIBS_USER
[1] "~/Library/R/3.6/library"

$R_PAPERSIZE
[1] "a4"

$R_PDFVIEWER
[1] "/usr/bin/open"

$R_PLATFORM
[1] "x86_64-apple-darwin18.7.0"

$R_PRINTCMD
[1] "lpr"

$R_RD4PDF
[1] "times,inconsolata,hyper"

$R_SESSION_TMPDIR
[1] "/var/folders/cb/xv8tc7250x132tsz1l0rpqzw0000gr/T//Rtmpd7kYUB"

$R_SHARE_DIR
[1] "/usr/local/lib/R/share"

$R_STRIP_SHARED_LIB
[1] "strip -x"

$R_STRIP_STATIC_LIB
[1] "strip -S"

$R_SYSTEM_ABI
[1] "osx,gcc,gxx,gfortran,gfortran"

$R_TEXI2DVICMD
[1] "/usr/local/Cellar/texinfo/6.6/bin/texi2dvi"

$R_UNZIPCMD
[1] "/usr/bin/unzip"

$R_ZIPCMD
[1] "/usr/bin/zip"

$SED
[1] "/usr/bin/sed"

$SHELL
[1] "/bin/bash"

$SHLVL
[1] "1"

$SSH_ASKPASS
[1] "rpostback-askpass"

$SSH_AUTH_SOCK
[1] "/private/tmp/com.apple.launchd.m6hl01oM2s/Listeners"

$TAR
[1] "/usr/bin/tar"

$TERM
[1] "xterm-256color"

$TERM_PROGRAM
[1] "iTerm.app"

$TERM_PROGRAM_VERSION
[1] "3.3.4"

$TERM_SESSION_ID
[1] "w0t4p0:7F2BE21C-E335-4C6A-82D1-5BA0354A19D2"

$TMPDIR
[1] "/var/folders/cb/xv8tc7250x132tsz1l0rpqzw0000gr/T/"

$TZ
[1] "Europe/Zurich"

$USER
[1] "ivanek"

$XPC_FLAGS
[1] "0x0"

$XPC_SERVICE_NAME
[1] "0"

$`_`
[1] "/Applications/RStudio.app/Contents/MacOS/RStudio"

$`__CF_USER_TEXT_ENCODING`
[1] "0x1F8:0x0:0x0"

 [1] ".GlobalEnv"        "tools:rstudio"     "package:stats"     "package:graphics"  "package:grDevices"
 [6] "package:utils"     "package:datasets"  "package:methods"   "Autoloads"         "package:base"     
Log file: rdesktop.log
--------------------------------------------------

(Empty)

Log file: rsession-ivanek.log
--------------------------------------------------

16 Sep 2019 09:42:03 [rsession-ivanek] ERROR system error 2 (No such file or directory) [path=/Users/ivanek/.Rhistory]; OCCURRED AT: rstudio::core::Error rstudio::core::FilePath::open_w(boost::shared_ptr<std::ostream> *, bool) const /Users/vagrant/workspace/IDE/macos-v1.2/src/cpp/core/FilePath.cpp:1165; LOGGED FROM: void rstudio::r::session::reportHistoryAccessError(const std::string &, const rstudio::core::FilePath &, const rstudio::core::Error &) /Users/vagrant/workspace/IDE/macos-v1.2/src/cpp/r/session/RInit.cpp:391
16 Sep 2019 09:56:02 [rsession-ivanek] WARNING Process supervisor did not terminate within 1 second; LOGGED FROM: void (anonymous namespace)::rCleanup(bool) /Users/vagrant/workspace/IDE/macos-v1.2/src/cpp/session/SessionMain.cpp:1193
16 Sep 2019 15:04:25 [rsession-ivanek] WARNING Private command disabled, unsupported $HISTCONTROL: [ignoreboth:erasedups]; LOGGED FROM: bool rstudio::core::terminal::PrivateCommand::output(const std::string &) /Users/vagrant/workspace/IDE/macos-v1.2/src/cpp/core/terminal/PrivateCommand.cpp:243

[ronblum]

@ivanek Thank you for raising this issue. I can't reproduce it, both with the initial R 3.6.1 and the 9/14 patched version. Can you try resetting RStudio's state—any change in behavior? https://support.rstudio.com/hc/en-us/articles/200534577-Resetting-RStudio-Desktop-s-State

[kevinushey]

How did you install R? It looks like you're not using CRAN R.

[kevinushey]

I have a copy of R built from sources on my own machine that I can run against RStudio without issue so I suspect there is something unique about the copy of R you have installed.

[ivanek]

I reset the preferences, but that did not help.

My R installation: I installed the required libraries using brew and afterwards I compiled R itself form source. I did not have any issue with that before. The error message is a bit cryptic for me. What could be the problem with openblas? The older version of Rstudio starts fine.

otool -L /usr/local/lib/R/lib/libR.dylib
/usr/local/lib/R/lib/libR.dylib:
	libR.dylib (compatibility version 3.6.0, current version 3.6.1)
	libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/usr/local/opt/gcc/lib/gcc/9/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.250.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1575.17.0)
	/usr/lib/libedit.3.dylib (compatibility version 2.0.0, current version 3.0.0)
	/usr/local/opt/pcre/lib/libpcre.1.dylib (compatibility version 4.0.0, current version 4.11.0)
	/usr/local/opt/xz/lib/liblzma.5.dylib (compatibility version 8.0.0, current version 8.4.0)
	/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 62.1.0)
	/usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)

and

otool -L /usr/local/lib/R/lib/libRblas.dylib
/usr/local/lib/R/lib/libRblas.dylib:
	libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/usr/local/opt/gcc/lib/gcc/9/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.250.1)

[ivanek]

What would be the way to debug it further? (the issue persists also with RStudio-daily)

[kevinushey]

You can try fixing the library lookup path:

install_name_tool -change \
    libRblas.dylib /usr/local/lib/R/lib/libRblas.dylb \
    /usr/local/lib/R/lib/libR.dylib

It looks like my locally-compiled version of R works because I compiled and linked to an external BLAS.

[kevinushey]

And compare that with what you see with a regular CRAN build of R:

kevinushey@Kevins-MacBook-Pro:/Library/Frameworks/R.framework/Resources/lib
$ otool -L libR.dylib
libR.dylib:
        /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib (compatibility version 3.6.0, current version 3.6.1)
        /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
        /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
        /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)
        /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1259.11.0)
        /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib (compatibility version 5.0.0, current version 5.2.0)
        /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)
        /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5)
        /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 55.1.0)
        /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
        /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libomp.dylib (compatibility version 5.0.0, current version 5.0.0)

Note that libRblas.dylib is explicitly referenced with a full path.

[kevinushey]

And finally -- these restricted are being imposed upon us by Apple with the hardened runtime; there's not much more we can do on the RStudio side about this.

[ivanek]

Indeed, the relative path to the R lib files might be an issue. If I start the RStudio from /usr/local/lib/R/lib directory, it starts fine. However I cannot switch to any projects. It starts to complain about the missing libR.dylib library. Now I need to figure out how to install R and also packages with absolute path for lib files.

[kevinushey]

Did you see my advice regarding the use of install_name_tool? That lets you change these library paths as necessary.

[ivanek]

I had to execute install_name_tool on several libraries:

1. On R libs and libs from default packages in order to start the Rstudio:

install_name_tool -change libR.dylib /usr/local/lib/R/lib/libR.dylib /usr/local/lib/R/lib/libRblas.dylib
install_name_tool -change libRblas.dylib /usr/local/lib/R/lib/libRblas.dylib /usr/local/lib/R/lib/libR.dylib
install_name_tool -change libR.dylib /usr/local/lib/R/lib/libR.dylib /usr/local/lib/R/lib/libRlapack.dylib
install_name_tool -change libRblas.dylib /usr/local/lib/R/lib/libRblas.dylib /usr/local/lib/R/lib/libRlapack.dylib


install_name_tool -change libR.dylib /usr/local/lib/R/lib/libR.dylib /usr/local/lib/R/library/utils/libs/utils.so
install_name_tool -change libR.dylib /usr/local/lib/R/lib/libR.dylib /usr/local/lib/R/library/grDevices/libs/grDevices.so

2. There were still error messages that default libraries cannot be loaded, so I applied it to few others:

install_name_tool -change libR.dylib /usr/local/lib/R/lib/libR.dylib /usr/local/lib/R/library/methods/libs/methods.so
install_name_tool -change libR.dylib /usr/local/lib/R/lib/libR.dylib /usr/local/lib/R/library/stats/libs/stats.so
install_name_tool -change libRblas.dylib /usr/local/lib/R/lib/libRblas.dylib /usr/local/lib/R/library/stats/libs/stats.so
install_name_tool -change libRlapack.dylib /usr/local/lib/R/lib/libRlapack.dylib /usr/local/lib/R/library/stats/libs/stats.so
install_name_tool -change libR.dylib /usr/local/lib/R/lib/libR.dylib /usr/local/lib/R/library/tools/libs/tools.so

3. Plus the following, but these were not directly required.

install_name_tool -change libR.dylib /usr/local/lib/R/lib/libR.dylib /usr/local/lib/R/library/grDevices/libs/cairo.so
install_name_tool -change libR.dylib /usr/local/lib/R/lib/libR.dylib /usr/local/lib/R/library/graphics/libs/graphics.so

Afterwards Rstudio can start, however I cannot load other libraries (almost each lib complains about the missing path to libR.dylib library. So I would have to check each *.so file if the links are absolute.

On top of it, the help pages do not work, there is this error message:

Error in tools::startDynamicHelp() : internet routines cannot be loaded

[ivanek]

After reinstalling R into /Library/Frameworks/R.framework everything works. Thanks for help.