Installation Error

sequenceserver
#1

Hi, I have been using sequenceserver for sometime now and when I switched to a new machine, I get the following error message when I try to install using: sudo gem install sequenceserver. Kindly assist

MacOSMojave, v10.13

ERROR: Error installing sequenceserver:
ERROR: Failed to build gem native extension.

current directory: /Library/Ruby/Gems/2.3.0/gems/ox-2.8.1/ext/ox
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby -r ./siteconf20181028-1554-f24lww.rb extconf.rb
>>>>> Creating Makefile for ruby version 2.3.7 on universal.x86_64-darwin18 <<<<<
creating Makefile

current directory: /Library/Ruby/Gems/2.3.0/gems/ox-2.8.1/ext/ox
make “DESTDIR=” clean

current directory: /Library/Ruby/Gems/2.3.0/gems/ox-2.8.1/ext/ox
make "DESTDIR="
make: *** No rule to make target /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/universal-darwin18/ruby/config.h', needed by base64.o’. Stop.

make failed, exit code 2

Gem files will remain installed in /Library/Ruby/Gems/2.3.0/gems/ox-2.8.1 for inspection.
Results logged to /Library/Ruby/Gems/2.3.0/extensions/universal-darwin-18/2.3.0/ox-2.8.1/gem_make.out

the gem_make.out file contains the following:

current directory: /Library/Ruby/Gems/2.3.0/gems/ox-2.8.1/ext/ox
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby -r ./siteconf20181028-1554-f24lww.rb extconf.rb
>>>>> Creating Makefile for ruby version 2.3.7 on universal.x86_64-darwin18 <<<<<
creating Makefile

current directory: /Library/Ruby/Gems/2.3.0/gems/ox-2.8.1/ext/ox
make “DESTDIR=” clean

current directory: /Library/Ruby/Gems/2.3.0/gems/ox-2.8.1/ext/ox
make "DESTDIR="
make: *** No rule to make target /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/universal-darwin18/ruby/config.h', needed by base64.o’. Stop.

make failed, exit code 2

#2

Hi Kevin,

I am running seqserv on Mojave without any problems. You said this is a new machine. Have you installed Xcode and CLI tools for Xcode yet? Both are needed on Mac to compile software. For seqserv, it’s the ox library that we use for XML parsing that runs some compilation steps during installation.

Priyam

#3

Hi, I installed both Xcode and CLI tools for Xcode and seqserv is up and running.

Thank you.

#4

Kevin and Priyam,

I am running macOS Sierra 10.12.6 and recently received an update that likely changed my version of Ruby from 2.0 to 2.3. When opening sequenceserver today, I received the following message:

MacBook-Pro-de-MJB:~ mjb$ sequenceserver

-bash: /usr/local/bin/sequenceserver: /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby: bad interpreter: No such file or directory

Then, with some help I tried to reinstall the latest version of sequenceserver, which failed and gave the following:

MacBook-Pro-de-MJB:~ mjb$ sudo gem install sequenceserver

Building native extensions. This could take a while…

ERROR: Error installing sequenceserver:

ERROR: Failed to build gem native extension.

current directory: /Library/Ruby/Gems/2.3.0/gems/ox-2.10.0/ext/ox

/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby -r ./siteconf20181109-820-17oz6gr.rb extconf.rb

mkmf.rb can’t find header files for ruby at /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/include/ruby.h

extconf failed, exit code 1

Gem files will remain installed in /Library/Ruby/Gems/2.3.0/gems/ox-2.10.0 for inspection.

Results logged to /Library/Ruby/Gems/2.3.0/extensions/universal-darwin-16/2.3.0/ox-2.10.0/gem_make.out

Please advise, as I am not able to use sequenceserver, and we also cannot locate the ruby.h header file, which was a previous problem with Ruby 2.0.

Could really use your assistance here!

Thanks, Michael

#5

Hi Michael,

Looks like you need to install Xcode and CLI tools for Xcode.

Priyam