most problems caused by manual install on cygwin platform. package installation on cygwin is realy a great challenge.

first of all we come to one of the most common problem always get after updating or installing packages.

Sometimes, after updating or installing packages, you′ll start to get strange errors related to “fork()” or .dll loading. These errors are usually solved by rebasing your packages.

Now that no Cygwin services are running, you can rebase your packages. Open a Windows command prompt (by going to the Run menu and entering cmd). Once there, type or right-click and paste the following commands. Be patient, this′ll take a minute:

\cygwin\bin\dash -c '/usr/bin/rebaseall'
exit

Under Windows 7 (and possibly Vista), the above may not be able to rebase everything due to permissions. So instead, go to C:\cygwin\bin, and via right-click run the file dash.exe as Administrator, and then at the dash command prompt, type the following commands:

/usr/bin/rebaseall -v
exit

Rebasing all your packages will take a few minutes but should resolve the forking errors. Unfortunately, this seems to be machine-specific and can′t be done by Cygwin′s upstream.

If you want to execute this in an BATCH installation script, you can use:

D:\cygwin\bin\dash.exe -c '/usr/bin/rebaseall -v'

ruby rebase

run rubyrebase directly in bash

SAC [ok]

@ 2014/05/22, cygwin:

install sac-101.5 on cygwin, source-code copy from ubuntu.

# check README for instruction
cd /usr/local/local_software/sac-101.5
make
make install     # default install on /usr/local/sac
vim ~/.bashrc    

For bash, edit ~/.bashrc adding the lines

export SACHOME=/usr/local/sac     
source ${SACHOME}/bin/sacinit.sh     

HDF5 [ok]

@ 2014/05/22, cygwin:

view http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_Cygwin.txt for instruction
h5cc -showconfig to check configuration or view your_hdf5_install_path/lib/libhdf5.settings, README.txt

Dependencies

• zlib : exist
• Szip : download from http://www.hdfgroup.org/doc_resource/SZIP/, ./configure --prefix=/usr/local, make,make install

Install HDF5 on Cygwin

pre-build binary:

• download pre-build binary distribution hdf5-1.8.13-cygwin32-static.tar.gz from http://www.hdfgroup.org/HDF5/release/obtain5.html
• extract to /usr/local/local_software/hdf5-1.8.13-pre-build-binary-cygwin32-static-CYGWIN_NT-6.11.7.28
• uninstall old version and update to pre-build cygwin version.

hdf5-1.8.13-cygwin32-static.tar.gz include fortran interface ,however have conflict with the version problem. Fatal Error: Wrong module version '10' (expected '4') for file 'hdf5.mod' opened at (1) , resort to self compile.

 cd hdf5-1.8.10-patch1
 make uninstall ; make uninstall-all 
 cp /usr/local/local_software/hdf5-1.8.13-pre-build-binary-cygwin32-static-CYGWIN_NT-6.11.7.28 /usr/local/hdf5

source code for all platform:

• download src files via http://www.hdfgroup.org/HDF5/release/obtainsrc.html

  ./configure 
      --with-szlib=/usr/local/ 
      --with-zlib=/usr/include,/usr/lib 
      --prefix=/usr/local/hdf5 
      --enable-cxx 
      --enable-fortran
  make                   # make > "make_out_info"  
  make check             # make check > "make_check_out_info"
  make install           # make install > "make_instal_out_info"

@ 2014/07/05, cygwin:

update cygwin gcc to 4.8.3 now use prebuild hdf5-1.8.13-cygwin32-static.tar.gz which by gcc-4.8.2

libmseed [ok]

@ 2014/05/22, cygwin:

download libmseed-2.12.tar.gz from https://seiscode.iris.washington.edu/projects/libmseed/files
extract to /usr/local/local_software/libmseed-2.12

  # check `INSTALL` and `Makefile` for instruction
  make gcc                               #  default with "cc"
  cp libmseed.a /usr/local/lib/
  cp *.h /usr/local/include/

kiwi [ binary ok ]

@ 2014/05/22, cygwin:

view https://github.com/emolch/kiwi/wiki/Installation for instruction

Dependencies

• FFTW3
• libmseed

• sac

• cd /usr/local/local_software

• git clone git://github.com/emolch/kiwi.git kiwi
• cp Makefile.local.example Makefile.local
• Edit Makefile.local
• Edit hostinfo.pl add $os = 'linux' if $uname_a =~ /Cygwin/i; treat Cygwin as linux.
• make
• make check

$ cat Makefile.local
## Fortran 95 compiler:
FORTRANC = gfortran

## Adjust if HDF5 is installed at a custom location
INCHDF = -I/usr/local/hdf5/include
LIBHDF = -L/usr/local/hdf5/lib -lhdf5_fortran -lhdf5 -lz -lsz

## Adjust if FFTW is installed at a custom location
INCFFTW = -I/usr/include
LIBFFTW = -L/usr -lfftw3f

## Uncomment to disable SAC IO support to not depend on libsacio
LIBSAC = `sac-config -c -l sacio sac`

edit ~/.bashrc, add following environment variables:

export PATH=$PATH:/usr/local/kiwi/bin
export KIWI_HOME=/usr/local/kiwi/share/kiwi

Install kiwi python modules ```brush: bash

in the kiwi source directory:

cd python sudo python setup.py install ```

Pyrocko

pyrocko < scipy < numpy,atlas,lapack < …

nose [ok]

@ 2014/05/22, cygwin:
only for test numpy, not for use it. see INSTALL.txt in numpy-1.8.1

 tar xzf nose-1.3.3.tar.gz
 cd nose-1.3.3/
 python setup.py build
 python setup.py install

lapack [ ok ]

@ 2014/05/22, cygwin:
[ build lib: ok, testing: failed, cp *.a /usr/local/lib; cygwin already exist in /usr/lib ]

tar zxf lapack-3.5.0.tgz
cd lapack-3.5.0/
cp make.inc.example make.inc
vim Makefile   # edit line: set variable, "lib: blaslib variants lapacklib tmglib"
make lib       # make : default make all, would test, however fail when test TESTING/xeights  " (core dumped) ./xeigtsts < sed.in" 
cp librefblas.a libblas.a   && cp *.a /usr/local/lib
cd .. && rm lapack-3.5.0/

atlas

@ 2014/05/24, cygwin:
atlas3.10.1.tar.bz2 [install got some problems]

• configure need without -Fa alg
• need modify CONFIG/src/atlconf_misc.c add following code in function char *GetPathEnvVar(void)

      else if (path[i] == '(')
      {
         *p = '\\';
     p[1] = '(';
     p += 2;
      }
      else if (path[i] == ')')
      {
         *p = '\\';
     p[1] = ')';
     p += 2;
      }

 tar jxvf atlas3.10.1.tar.bz2
 cd ATLAS/
 # view  INSTALL.txt for instructions
 mkdir atlas_build_cygwin ; cd atlas_build_cygwin
 ../configure -b 32 -D c -DPentiumCPS=2494  --with-netlib-lapack-tarfile=/usr/local/local_software/lapack-3.5.0.tgz   --shared   --prefix=/usr/local/ATLAS
 make              # tune and compile library
 make check        # perform sanity tests,
 make ptcheck      # checks of threaded code for multiprocessor systems
 make time         # provide performance summary as % of clock rate
 make install      # Copy library and include files to other directories :: 
                   #   make install:  configure with shared, lib***.a :ok lib***.so failed. 

NumPy

@ 2014/05/24, cygwin:

view site.cfg.example, INSTALL.txt Prerequisites: []: means optional, ATLAS (or OpenBLAS, or MKL), [ FFTW ( or djbfft) ], [ UMFPACK ] …

 tar zxf numpy-1.8.1.tar.gz
 cd  numpy-1.8.1
 # view INSTALL.txt for instructions
 # view site.cfg    for instructions
 cp site.cfg.example site.cfg
 vim site.cfg   # Edit site.cfg for cumstom setting
 python setup.py build --fcompiler=gnu95    
 python setup.py install

$cat site.cfg

[atlas]
libraries = lapack,f77blas,cblas,atlas
library_dirs = /usr/local/ATLAS/lib
include_dirs = /usr/local/ATLAS/include
[amd]
amd_libs = amd
[umfpack]
umfpack_libs = umfpack
[fftw]
libraries = fftw3

scipy

 python setup.py build --fcompiler=gnu95    
 python setup.py install  # address space needed by 'lapack_lite.dll' (0x610000) is already occupied

cygwin ash rebase

rdseed [pre-build ok]

#download src code from `http://www.iris.edu/forms/rdseed_request.htm`
tar xzf rdseedv5.3.1.tar.gz
cd rdseedv5.3.1
cp rdseed.windows.cygwin_32.exe /usr/local/bin

view README

Already five excutables, if you do not want use pre-build version, then recompile it. for 32-bit comilation

uncomment the cflags line #CFLAGS = -O -m32 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE to force 32-bit compilation.

cp   Makefile makefile_cygwin
vim  makefile_cygwin         # edit cflags  
make clean                 
make -f makefile_cygwin      # faild can not find -lnsl

GMT

gmtpy

view http://emolch.github.io/gmtpy/install.html

pycdf

view `http://pysclint.sourceforge.net/pycdf/INSTALL To install, follow these steps.

1-Install the Python devel package, holding the python libraries and header files.

2-Install the netcdf library. Source code is available at:
http://www.unidata.ucar.edu/software/netcdf . Binary packages
are available for most popular environments.

3-Install one of the python Numeric or numarray packages.
Numeric source code is available at: numpy.sourceforge.net,
and numarray source code at http://sourceforge.net/projects/numpy .
Binary packages are available for most popular environments.

4-Uncompress and untar the pycdf tar ball, then cd to the
pycdf-xxx directory just created.

5-Edit the setup.py file, and locate the line reading USE = ....
Set USE = NUMERIC to create a Numeric-based version of pycdf.
Set USE = NUMARRAY to create a numarray-based version.

5-If your netcdf library lives in a non-standard directory
(eg not on the standard library search path),
edit the setup.py file and locate the line reading:

#library_dirs=["non standard path where libs live"],   

Remove the pound sign to uncomment the line, and enter the non- standard path in quotes between the square brackets. For ex.:

library_dirs = ["/usr/local/netcdf-3.5.0/lib"],

6-As root, execute the command: python setup.py install

python-progressbar [ok]

tar xzf progressbar-2.2.tar.gz
cd progressbar-2.2/
python setup.py build
python setup.py install

example:

$ python
>>> from progressbar import ProgressBar
>>> pbar = ProgressBar(10)
>>> for i in range(10):
...     pbar.update(i+1)
... 
100% |######################################################################|

Cheetah [ok]

模板引擎

tar xzf Cheetah-2.4.4.tar.gz
cd Cheetah-2.4.4/
python setup.py build
python setup.py install

convert [ok]

 #download `ImageMagick-i686-pc-cygwin.tar.gz` via `http://www.imagemagick.org/script/binary-releases.php#unix`
 tar xzf ImageMagick-i686-pc-cygwin.tar.gz
 cd ImageMagick-6.8.8/
 # pre-build
 vim ~/.bashrc  # export MAGICK_HOME="$HOME/ImageMagick-6.8.8" ; export PATH="$MAGICK_HOME/bin:$PATH"

matplotlib [ok]

@ 2014/05/24, cygwin:

lib/matplotlib/tri/_tri.cpp:2180:28: 4mNs#:expected unqualified-id before numeric constant

There is a variable called “C” defined in lib/matplotlib/tri/tri.h on line 821 and invoked in tri.cpp on lines 2180 and 2186. For some reason gcc doesn′t like this (is it a reserved word in some architecture?). I just renamed the variable to “_Co” in both tri.h and tri.cpp, and the compilation finished successfully.

/usr/share/python2.7/CXX/cxxsupport.cxx:40:38: error: Src/Python2/cxxsupport.cxx: No such file or directory

cp CXX/Python2 src/Python2 -r

python setup.py build
python setup.py install 

ruby-2.1.2

ruby-2.1.2: troubleshooting vim ruby-2.1.2/ext/digest/md5/Makefile /ruby-2.1.2/ext/digest/sha1/Makefile /ruby-2.1.2/ext/digest/sha1/Makefile add cflag -DHAVE_OPENSSL_MD5_H -DSHA2_USE_OPENSSL

lapack95

make.inc

#
#  -- LAPACK95 interface driver routine (version 2.0) --
#     UNI-C, Denmark; Univ. of Tennessee, USA; NAG Ltd., UK
#     August 5, 2000
#
FC   = gfortran -ffree-form
FC1      = gfortran -ffixed-form
# -dcfuns  Enable recognition of non-standard double
#          precision  complex intrinsic functions
# -dusty   Allows the compilation and execution of "legacy"
#          software by downgrading the category  of  common
#          errors  found  in  such software from "Error" to
# -ieee=full enables all IEEE arithmetic facilities
#          including non-stop arithmetic.

OPTS0    = 
MODLIB   = -I./../lapack95_modules
OPTS1    = -c $(OPTS0)
OPTS3    = $(OPTS1) $(MODLIB)
OPTL     = -o 
OPTLIB   =

LAPACK_PATH = /usr/lib/

LAPACK95 = ../lapack95.a
LAPACK77 = $(LAPACK_PATH)/liblapack.a
TMG77    = $(LAPACK_PATH)/libtmglib.a
BLAS     = $(LAPACK_PATH)/libblas.a

LIBS     = $(LAPACK95) $(TMG77) $(LAPACK77) $(BLAS)
SUF      = f90

XX = 'rm' -f $@; \
        'rm' -f $@.res; \
    $(FC) $(OPTS0) -o $@ $(MODLIB) $@.$(SUF) $(OPTLIB) $(LIBS); \
        $@ < $@.dat > $@.res; \
        'rm' -f $@

YY = $(FC) $(OPTS0) -o $@ $(MODLIB) $@.$(SUF) $(OPTLIB) $(LIBS)

.SUFFIXES: .f90 .f .o

.$(SUF).o: 
    $(FC) $(OPTS3) $<

.f.o:
    $(FC1) $(OPTS3) $<

vim make.inc
cd SRC
make single_double_complex_dcomplex
mkdir -p /usr/local/lapack95/include
mkdir -p /usr/local/lapack95/lib
cp ../lapack95.a /usr/local/lapack95/lib/liblapack95.a
cp ../lapack95_modules/*.mod /usr/local/lapack95/include/