Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,

just to mention that deseq2-1-8-2 (requiring r-3-2-1) also installs fine!

Best regards,
Hans
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi Marius,

I bow to your efforts in appreciation - it seems to install without flaws!!

I tried the new cairo-1-12-14 and then r-3-2-1 in a frest postgresqldb/galaxy 
instance … everything got installed and shows the green label ;-)

requirements on top of Mac OS Xcode/command line tools are:
- gfortran (I used the OS X 10.11  gfortran 5.2 installer from here 
https://gcc.gnu.org/wiki/GFortranBinaries 
)
- libiconv-1.14 (from http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz 
) - (which I put into 
/usr/local where it seems to be found without editing my $PATH)

This is great! Many thanks again!
Hans


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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,

I now learned that R-3.2.2 binaries for Mac OS X are available 
(https://cran.r-project.org/bin/macosx/) - could that be a potential help for 
R-related problems in galaxy on Mac OS X?

Cheers,
Hans
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,

not sure whether that helps, but I tried to compile r-3-2-1 outside galaxy on 
the same machine:

1.straight ./configure yields error: "cannot compile a simple Fortran program."
To remedie this, I installed gfortran (=gf) 5.2 for OS X (10.11) from 
https://gcc.gnu.org/wiki/GFortranBinaries 


and with gf installed, ./configure now completes, but make fails with "dyld: 
Symbol not found: _libiconv_open"

2. I then installed libiconv-1.4 as suggested in this tip for R-on-OS X: 
http://blog.qiubio.com:8080/archives/3897 

and put /usr/local/lib into $PATH
now make finishes …


I made mistakes running ./configure and make/install
first omitting the epxort LD_LIBRARY_PATH= command … and I don’t have proper 
records ;-)

Not sure how to clean this up - but I wanted to let you know my findings with 
respect to compiling r-3-2-1

Cheers,

Hans



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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,
I hope I am up-to-date:
$ xcode-select —install yields:
xcode-select: error: command line tools are already installed, use "Software 
Update" to install updates

and software-update doesn’t show anything

Cheers,
Hans___
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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi,

I use Mac OS X 10.11.1 (El Capitan) - I append terminal output during the 
r-package installation and R INSTALLATION.LOG
Cheers,
Hans

tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2015-12-02 
23:04:16,463 Successfully downloaded from url: 
http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,017 checking host system 
type... x86_64-apple-darwin15.0.0
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,031 loading build-specific 
script './config.site'
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,049 checking whether 
builddir is srcdir... yes
checking build system type... x86_64-apple-darwin15.0.0
checking host system type... x86_64-apple-darwin15.0.0
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,221 checking for working 
autoconf... found
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,519 checking for working 
autoheader... found
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,526 checking for mawk... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,526 checking for awk... awk
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,526 checking for bison... 
bison -y
checking for working autoheader... found
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether ln -s works... yes
checking for bison... bison -y
checking for ar... ar
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,557 checking for a 
BSD-compatible install... /usr/bin/install -c
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,560 checking for which... 
/usr/bin/which
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,564 checking for gtar... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,565 checking for tar... 
/usr/bin/tar
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,568 checking for pdftex... 
no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,575 checking for 
makeindex... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,576 checking for 
texi2dvi... /usr/bin/texi2dvi
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,580 checking for latex 
inconsolata package... checking for unzip... /usr/bin/unzip
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,583 checking for gzip... 
/usr/bin/gzip
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,585 checking for 
firefox... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,588 checking for galeon... 
no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,591 checking for 
xdg-open... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,593 checking for 
gnome-moz-remote... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,595 using default browser 
... /usr/bin/open
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,598 checking for 
acroread4... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,600 checking for evince... 
no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,603 checking for gv... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,606 checking for ggv... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,608 checking for kpdf... no
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,612 checking for 
notangle... false
install_environment.STDOUT DEBUG 2015-12-02 23:04:17,616 checking for 
pkg-config... /opt/local/bin/pkg-config
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /usr/bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... no
checking for tar... /usr/bin/tar
checking for tex... no
checking for pdftex... no
checking for pdflatex... no
checking for makeindex... no
checking for texi2any... no
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /usr/bin/gzip
checking for bzip2... /opt/local/bin/bzip2
checking for firefox... no
checking for mozilla... no
checking for galeon... no
checking for opera... no
checking for xdg-open... no
checking for kfmclient... no
checking for gnome-moz-remote... no
checking for open... /usr/bin/open
using default browser ... /usr/bin/open
checking for acroread... no
checking for acroread4... no
checking for xdg-open... no
checking for evince... no
checking for xpdf... no
checking for gv... no
checking for gnome-gv... no
checking for ggv... no
checking for okular... no
checking for kpdf... no
checking for open... /usr/bin/open
checking for notangle... false
checking for realpath... false
checking for pkg-config... /opt/local/bin/pkg-config
checking for gcc... gcc
configure:

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hi Björn,

thanks very much for your efforts. Unfortunately, installation of the new 
deseq2-1-8-2 (uic, 2015-12-02) still fails for me -

apparently due to the included package_r_3_2_1 which fails with "configure: 
error: C compiler cannot create executables”
and the R error status stops deseq2 installation with error "/bin/sh: line 7: 
Rscript: command not found”.

But all the other dependencies in the deseq2-1-8-2 package:

atlas-3-10
cairo-1-12-14
fontconfig-2-11-1
freetype-2-5-2
libpng-1-6-7
libxml2-2-9-1
ncurses-6-0
pixman-0.32-4
pixman-0-32-6
readline-6-3

show the green label “installed” as installation status.

Best regards,
Hans




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Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Thanks to Marius and Martin for fixing pixman-0.32.4!

This new pixman-0.32.4 version (owned by devteam) is also used by the new 
devteam cairo-1-12-14 package … both installed properly into galaxy on OS X.

I am curious/unclear on how to proceed with other packages, e.g. deseq2-1-8-2 
(uic),
which still seem to use the "old" cairo-1-12-14 (uic) and pixman-0-32-4 (uic) 
versions … which won’t work on OS X.

What am I missing?

Best regards,
Hans


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[galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Hans Rudolph]

Hello Galaxy-devs,

I am setting up galaxy on current os x 10.11 and encounter this trouble using 
galaxy to install pixman-0.32.4:
the package gets downloaded successfully from 
http://cairographics.org/releases/pixman-0.32.4.tar.gz 

… while following the installation process in terminal I see this output during 
the process …presumably indicating an gcc problem
...
install_environment.STDOUT DEBUG 2015-12-01 10:44:18,096 checking build system 
type... x86_64-apple-darwin15.0.0
install_environment.STDOUT DEBUG 2015-12-01 10:44:18,099 checking for gcc... gcc
checking build system type... x86_64-apple-darwin15.0.0
checking host system type... x86_64-apple-darwin15.0.0
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in 
`/Users/hans/galaxy/database/tmp/tmp-toolshed-mtdKC9F_F/pixman-0.32.4':
configure: error: C compiler cannot create executables
See `config.log' for more details

Curiously, if I download the pixman package (same URL) outside of galaxy and 
run ./configure … gcc seems to work :
...
checking build system type... x86_64-apple-darwin15.0.0
checking host system type... x86_64-apple-darwin15.0.0
checking for gcc... gcc
checking whether the C compiler works… yes
...
and ./configure finishes OK.

to actually compile/make pixman properly, I have to use the ./configure 
—disable-mmx option to avoid another known error
(pixman-mmx.c:100:20: error: constraint 'K' expects an integer constant 
expression
: "y" (__A), "K" (__N))

Perhaps someone is using galaxy on Mac OS X how this difference in gcc handling 
arises?
Thanks very much,

Hans Rudolph___
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