Can RPM packages be installed into Cygwin?

Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

Dear all,

I noticed that there is a command - rpm - under Cygwin 1.7. Does that 
mean RPM packages can be installed into Cygwin?

I tried to install ncbi-blast-2.2.26+-3.i686.rpm (see: 
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ) into 
Cygwin 1.7.13 with the command "install -i 
ncbi-blast-2.2.26+-3.i686.rpm". However, error message appeared as 
below. I tried to search for the missing libs using the setup.exe of 
Cygwin. It seems that some of them were not present, such as libc.so.6, 
libdl.so.2,  libm.so.6,  libnsl.so.1, and  libz.so.1. Where can I get 
these libs? Thanks!

$ rpm -i ncbi-blast-2.2.26+-3.i686.rpm
error: Failed dependencies:
         /usr/bin/perl is needed by ncbi-blast-2.2.26+-3
         libbz2.so.1 is needed by ncbi-blast-2.2.26+-3
         libc.so.6 is needed by ncbi-blast-2.2.26+-3
         libc.so.6(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3
         libc.so.6(GLIBC_2.1) is needed by ncbi-blast-2.2.26+-3
         libc.so.6(GLIBC_2.1.2) is needed by ncbi-blast-2.2.26+-3
         libc.so.6(GLIBC_2.1.3) is needed by ncbi-blast-2.2.26+-3
         libc.so.6(GLIBC_2.2) is needed by ncbi-blast-2.2.26+-3
         libc.so.6(GLIBC_2.3) is needed by ncbi-blast-2.2.26+-3
         libdl.so.2 is needed by ncbi-blast-2.2.26+-3
         libdl.so.2(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3
         libdl.so.2(GLIBC_2.1) is needed by ncbi-blast-2.2.26+-3
         libgcc_s.so.1 is needed by ncbi-blast-2.2.26+-3
         libgcc_s.so.1(GCC_3.0) is needed by ncbi-blast-2.2.26+-3
         libgcc_s.so.1(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3
         libm.so.6 is needed by ncbi-blast-2.2.26+-3
         libnsl.so.1 is needed by ncbi-blast-2.2.26+-3
         libpthread.so.0 is needed by ncbi-blast-2.2.26+-3
         libpthread.so.0(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3
         libpthread.so.0(GLIBC_2.1) is needed by ncbi-blast-2.2.26+-3
         libpthread.so.0(GLIBC_2.2) is needed by ncbi-blast-2.2.26+-3
         libpthread.so.0(GLIBC_2.3.2) is needed by ncbi-blast-2.2.26+-3
         librt.so.1 is needed by ncbi-blast-2.2.26+-3
         libstdc++.so.6 is needed by ncbi-blast-2.2.26+-3
         libstdc++.so.6(CXXABI_1.3) is needed by ncbi-blast-2.2.26+-3
         libstdc++.so.6(GLIBCXX_3.4) is needed by ncbi-blast-2.2.26+-3
         libstdc++.so.6(GLIBCXX_3.4.5) is needed by ncbi-blast-2.2.26+-3
         libz.so.1 is needed by ncbi-blast-2.2.26+-3
         perl(Archive::Tar) is needed by ncbi-blast-2.2.26+-3
         perl(Digest::MD5) is needed by ncbi-blast-2.2.26+-3
         perl(File::Temp) is needed by ncbi-blast-2.2.26+-3
         perl(File::stat) is needed by ncbi-blast-2.2.26+-3
         perl(Getopt::Long) is needed by ncbi-blast-2.2.26+-3
         perl(Net::FTP) is needed by ncbi-blast-2.2.26+-3
         perl(Pod::Usage) is needed by ncbi-blast-2.2.26+-3
         perl(constant) is needed by ncbi-blast-2.2.26+-3
         perl(strict) is needed by ncbi-blast-2.2.26+-3
         perl(warnings) is needed by ncbi-blast-2.2.26+-3


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Re: Can RPM packages be installed into Cygwin?

[marco atzeri]

On 4/7/2012 9:40 AM, De-Jian Zhao wrote:
> Dear all,
>
> I noticed that there is a command - rpm - under Cygwin 1.7. Does that
> mean RPM packages can be installed into Cygwin?
>
> I tried to install ncbi-blast-2.2.26+-3.i686.rpm (see:
> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ) into
> Cygwin 1.7.13 with the command "install -i
> ncbi-blast-2.2.26+-3.i686.rpm". However, error message appeared as
> below. I tried to search for the missing libs using the setup.exe of
> Cygwin. It seems that some of them were not present, such as libc.so.6,
> libdl.so.2, libm.so.6, libnsl.so.1, and libz.so.1. Where can I get these
> libs? Thanks!
>
> $ rpm -i ncbi-blast-2.2.26+-3.i686.rpm
> error: Failed dependencies:
> /usr/bin/perl is needed by ncbi-blast-2.2.26+-3
> libbz2.so.1 is needed by ncbi-blast-2.2.26+-3
> libc.so.6 is needed by ncbi-blast-2.2.26+-3
{cut]
>
>
...isn't it?

from cygwin website (first page):

Cygwin is not:

-    a way to run native Linux apps on Windows. You must rebuild your 
application
      from source if you want it to run on Windows.
-    a way to magically make native Windows apps aware of UNIX® 
functionality like
      signals, ptys, etc. Again, you need to build your apps from source 
if you want
      to take advantage of Cygwin functionality.

Regards
Marco

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Re: Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

On 2012-4-7 16:12, marco atzeri wrote:
> On 4/7/2012 9:40 AM, De-Jian Zhao wrote:
>> Dear all,
>>
>> I noticed that there is a command - rpm - under Cygwin 1.7. Does that
>> mean RPM packages can be installed into Cygwin?
>>
>> I tried to install ncbi-blast-2.2.26+-3.i686.rpm (see:
>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ) into
>> Cygwin 1.7.13 with the command "install -i
>> ncbi-blast-2.2.26+-3.i686.rpm". However, error message appeared as
>> below. I tried to search for the missing libs using the setup.exe of
>> Cygwin. It seems that some of them were not present, such as libc.so.6,
>> libdl.so.2, libm.so.6, libnsl.so.1, and libz.so.1. Where can I get these
>> libs? Thanks!
>>
>> $ rpm -i ncbi-blast-2.2.26+-3.i686.rpm
>> error: Failed dependencies:
>> /usr/bin/perl is needed by ncbi-blast-2.2.26+-3
>> libbz2.so.1 is needed by ncbi-blast-2.2.26+-3
>> libc.so.6 is needed by ncbi-blast-2.2.26+-3
> {cut]
>>
>>
> ...isn't it?
>
> from cygwin website (first page):
>
> Cygwin is not:
>
> -    a way to run native Linux apps on Windows. You must rebuild your 
> application
>      from source if you want it to run on Windows.
> -    a way to magically make native Windows apps aware of UNIX® 
> functionality like
>      signals, ptys, etc. Again, you need to build your apps from 
> source if you want
>      to take advantage of Cygwin functionality.
>
> Regards
> Marco
Thanks, Marco. I was not trying to run a native linux apps, and instead 
tried to rebuild the app from source. The BLAST software provides the 
Build.sh and Check.sh scripts under the dirctory of 
ncbi-blast-2.2.26+-src.tar\ncbi-blast-2.2.26+-src\c++\compilers\cygwin\. 
So I think it is possible to run the software under cygwin. However, the 
compilation stopped at "checking for python", even if python was 
installed. That's to say, I installed the latest python and the 
compilation could find it, but the compilation tried to search for 
python2.3 and 2.4 further, and stopped when searching for 2.4.

What I am concern is that whether the i686.rpm indicates it is prepared 
for cygwin. As you know, when you run "uname -smo" , you can get 
something like this "CYGWIN_NT-5.1 i686 Cygwin". I think the package 
ncbi-blast-2.2.26+-3.i686.rpm is for Cygwin. Is that right? Has anyone 
ever succeeded in installing a RPM package into cygwin using "rpm -i *rpm"?

Regards
Dejian

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Re: Can RPM packages be installed into Cygwin?

[Csaba Raduly]

Hi,

On Sun, Apr 8, 2012 at 6:10 AM, De-Jian Zhao  wrote:
> What I am concern is that whether the i686.rpm indicates it is prepared for
> cygwin. As you know, when you run "uname -smo" , you can get something like
> this "CYGWIN_NT-5.1 i686 Cygwin". I think the package
> ncbi-blast-2.2.26+-3.i686.rpm is for Cygwin. Is that right? Has anyone ever
> succeeded in installing a RPM package into cygwin using "rpm -i *rpm"?

It is highly unlikely that any *86.rpm is for Cygwin. Cygwin is not
the only Unix-like environment that runs on Intel processors :)
The binaries are probably for some Linux version.

Csaba
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Re: Can RPM packages be installed into Cygwin?

[marco atzeri]

On 4/8/2012 5:10 AM, De-Jian Zhao wrote:
> On 2012-4-7 16:12, marco atzeri wrote:

> Thanks, Marco. I was not trying to run a native linux apps, and instead
> tried to rebuild the app from source. The BLAST software provides the
> Build.sh and Check.sh scripts under the dirctory of
> ncbi-blast-2.2.26+-src.tar\ncbi-blast-2.2.26+-src\c++\compilers\cygwin\.
> So I think it is possible to run the software under cygwin. However, the
> compilation stopped at "checking for python", even if python was
> installed. That's to say, I installed the latest python and the
> compilation could find it, but the compilation tried to search for
> python2.3 and 2.4 further, and stopped when searching for 2.4.
>
> What I am concern is that whether the i686.rpm indicates it is prepared
> for cygwin. As you know, when you run "uname -smo" , you can get
> something like this "CYGWIN_NT-5.1 i686 Cygwin". I think the package
> ncbi-blast-2.2.26+-3.i686.rpm is for Cygwin. Is that right? Has anyone
> ever succeeded in installing a RPM package into cygwin using "rpm -i *rpm"?
>
> Regards
> Dejian


i686.rpm is not the source package, is the binary for linux on 686 
processor.
On cygwin we do not use rpm for building packages so the source rpm
file will unlikely work.

The source for all platforms is

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.26+-src.tar.gz



Regards
Marco




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Re: Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

On 2012-4-8 14:47, marco atzeri wrote:
> On 4/8/2012 5:10 AM, De-Jian Zhao wrote:
>> On 2012-4-7 16:12, marco atzeri wrote:
>
>> Thanks, Marco. I was not trying to run a native linux apps, and instead
>> tried to rebuild the app from source. The BLAST software provides the
>> Build.sh and Check.sh scripts under the dirctory of
>> ncbi-blast-2.2.26+-src.tar\ncbi-blast-2.2.26+-src\c++\compilers\cygwin\.
>> So I think it is possible to run the software under cygwin. However, the
>> compilation stopped at "checking for python", even if python was
>> installed. That's to say, I installed the latest python and the
>> compilation could find it, but the compilation tried to search for
>> python2.3 and 2.4 further, and stopped when searching for 2.4.
>>
>> What I am concern is that whether the i686.rpm indicates it is prepared
>> for cygwin. As you know, when you run "uname -smo" , you can get
>> something like this "CYGWIN_NT-5.1 i686 Cygwin". I think the package
>> ncbi-blast-2.2.26+-3.i686.rpm is for Cygwin. Is that right? Has anyone
>> ever succeeded in installing a RPM package into cygwin using "rpm -i 
>> *rpm"?
>>
>> Regards
>> Dejian
>
>
> i686.rpm is not the source package, is the binary for linux on 686 
> processor.
> On cygwin we do not use rpm for building packages so the source rpm
> file will unlikely work.
>
> The source for all platforms is
>
> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.26+-src.tar.gz 
>
>
>
>
> Regards
> Marco
>
Thank you, Marco. I tried that version. Unfortunately, the compilation 
always stopped at "checking python" even after python was installed. It 
seems to me that it is a tough work to rebuild a software from the 
source code under Cygwin. The dependency is hard to satisfy.

I am curious about the utility rpm under Cygwin environment. When 
running the setup.exe, I noticed that there is a rpm packge. (Search for 
"rpm" at the stage of "Select Packages" when running setup.exe, you can 
find the package under "Utils Default".) Then what is it for?

Regards,
Dejian

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Re: Can RPM packages be installed into Cygwin?

[Warren Young]

On 4/9/2012 9:12 AM, De-Jian Zhao wrote:
> the compilation
> always stopped at "checking python" even after python was installed.

My wild guess based on no personal experience with BLAST+ is that there 
is some linkage error here.  I'd have to try it myself (not interested) 
or examine the config.log file (still not interested) to figure out if 
this guess is correct.

I'd bet there are more Cygwin-using BLAST+ users on the BLAST+ mailing 
list than on the Cygwin list, so you'd have a better chance of getting a 
solution by sending the config.log file to that list than continuing to 
pursue this problem here.

Instead of trying to start with RPM, I'd recommend figuring out how to 
build BLAST+ to build from source first.  You need that experience to 
help you build binary packages.

I think you'll have an easier time learning to build a native Cygwin 
package than trying to get the .src.rpm file to rebuild on Cygwin:

	http://cygwin.com/setup.html

That page gives several methods for building Cygwin packages.  I'd 
recommend going with the Cygport option.  Cygport does fewer things than 
RPM, so building .cygport files is easier than building RPM .spec files. 
  (In Cygwin, much of the rest of what RPM does lives in setup.exe and 
cygcheck.exe.)

I doubt there's enough value in the existing BLAST+ .spec file to make 
it an easier path for you than building a .cygport file from scratch.

> Then what is [the rpm package] for?

It is for people who wish to build a secondary packaging system on top 
of Cygwin's native system.

It doesn't magically port Linux RPM packages over for you.  You still 
have to do that work yourself.  And, you have to do that work without 
having the benefit of an ecosystem of existing RPM binary packages, upon 
which that BLAST+ .spec file probably depends.

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Re: Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

  It seems that the compilation under Cygwin is more complicated than 
expected.
Thank you for your explanation, Warren.

On 2012-4-10 8:49, Warren Young wrote:
> On 4/9/2012 9:12 AM, De-Jian Zhao wrote:
>> the compilation
>> always stopped at "checking python" even after python was installed.
>
> My wild guess based on no personal experience with BLAST+ is that 
> there is some linkage error here.  I'd have to try it myself (not 
> interested) or examine the config.log file (still not interested) to 
> figure out if this guess is correct.
>
> I'd bet there are more Cygwin-using BLAST+ users on the BLAST+ mailing 
> list than on the Cygwin list, so you'd have a better chance of getting 
> a solution by sending the config.log file to that list than continuing 
> to pursue this problem here.
>
> Instead of trying to start with RPM, I'd recommend figuring out how to 
> build BLAST+ to build from source first.  You need that experience to 
> help you build binary packages.
>
> I think you'll have an easier time learning to build a native Cygwin 
> package than trying to get the .src.rpm file to rebuild on Cygwin:
>
>     http://cygwin.com/setup.html
>
> That page gives several methods for building Cygwin packages.  I'd 
> recommend going with the Cygport option.  Cygport does fewer things 
> than RPM, so building .cygport files is easier than building RPM .spec 
> files.  (In Cygwin, much of the rest of what RPM does lives in 
> setup.exe and cygcheck.exe.)
>
> I doubt there's enough value in the existing BLAST+ .spec file to make 
> it an easier path for you than building a .cygport file from scratch.
>
>> Then what is [the rpm package] for?
>
> It is for people who wish to build a secondary packaging system on top 
> of Cygwin's native system.
>
> It doesn't magically port Linux RPM packages over for you.  You still 
> have to do that work yourself.  And, you have to do that work without 
> having the benefit of an ecosystem of existing RPM binary packages, 
> upon which that BLAST+ .spec file probably depends.
>

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Re: Can RPM packages be installed into Cygwin?

[Christopher Faylor]

On Tue, Apr 10, 2012 at 02:03:29PM +0800, De-Jian Zhao wrote:
>It seems that the compilation under Cygwin is more complicated than
>expected.

Sometimes it is, especially when you are not quite sure what you're
doing, and the upstream project has made regrettable decisions about
compiling for Cygwin.

cgf

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Re: Can RPM packages be installed into Cygwin?

[Linda Walsh]

De-Jian Zhao wrote:

> Dear all,
> 
> I noticed that there is a command - rpm - under Cygwin 1.7. Does that 
> mean RPM packages can be installed into Cygwin?
> 
> I tried to install ncbi-blast-2.2.26+-3.i686.rpm (see: 
> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ) into 
> Cygwin 1.7.13 with the command "install -i 
> ncbi-blast-2.2.26+-3.i686.rpm". However, error message appeared as 
> below. libc.so.6, 
> libdl.so.2,  libm.so.6,  libnsl.so.1, and  libz.so.1. Where can I get 
> these libs? Thanks!
> 
> $ rpm -i ncbi-blast-2.2.26+-3.i686.rpm
> error: Failed dependencies:
>         /usr/bin/perl is needed by ncbi-blast-2.2.26+-3
>         libbz2.so.1 is needed by ncbi-blast-2.2.26+-3
>         libc.so.6 is needed by ncbi-blast-2.2.26+-3
>         libc.so.6(GLIBC_2.1.3) is needed by ncbi-blast-2.2.26+-3
>         libc.so.6(GLIBC_2.2) is needed by ncbi-blast-2.2.26+-3
>         libc.so.6(GLIBC_2.3) is needed by ncbi-blast-2.2.26+-3

.....
On Tue, Apr 10, 2012 at 02:03:29PM +0800, De-Jian Zhao wrote:

 > It seems that the compilation under Cygwin is more complicated than
 > expected.
==========================================================

This has nothing to do with cygwin.

It is 'rpm' looking for installed dependencies in the rpm database.

Since everything was installed with 'setup.exe' which keeps it's own
'database', rpm thinks nothing is installed.

You need to make sure the versions required by the rpm are installed by setup,
then you can build from a ncbi-blast-2.2.26+-3.src.rpm
                                                ^^^

The i686.rpm package is prebuilt for "some" platform (you would have to know
which from the download -- i.e. one built for suse won't necessarily run on 
redhat, or ubuntu...  or other combinations.   Ones that do will be statically
built and will be usable on some range of OS-versions of some particular OS.
Since rpm is a linux thing, it would be built for the linux OS... so 
double-screw.  Wrong OS, wrong executable format...etc...   look for a 
corresponding .src. rpm, OR as someone else already suggested, look for the
'tar' that the is included in the ".src".  -- in fact, if you have the .src.,
usually the .tar. file they build from is packed into it (then patches and OS
specific stuff is applied), so you can often just take the tar from your src.rpm
and move it to cygwin, and run it directly if it has a "configure" script.

it might also have something like "bootstrap.sh" (or bootstrap something) that 
will produce a configure script -- that will usually allow you to build an 
executable that will work on your platform (in this case cygwin) -- but you
will still have to have _needed_ dependencies installed (like development 
packages from cygwin for some of the above).

All of those packages may not be needed -- dependencies are often based
on what options you select in configure (configure --help tells you all it's 
options).  Sometimes you don't need all the options the 'default' rpm builds
with making life simpler.

Compilation, period, other than on the system the package was designed for is
never completely trivial, but configure makes it nearly so if it is used --
most packages these days have such a script -- rpm packages just have pre-built
some pre-configured image for distribution -- may not be optimal for your needs
nor is it likely to be optimized for your machine.

Hope this was of some help.
Good luck!

Linda


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Re: Can RPM packages be installed into Cygwin?

[Christopher Faylor]

On Mon, Apr 16, 2012 at 10:58:03PM -0700, Linda Walsh wrote:
>De-Jian Zhao wrote:
>
>> Dear all,
>> 
>> I noticed that there is a command - rpm - under Cygwin 1.7. Does that 
>> mean RPM packages can be installed into Cygwin?
>> 
>> I tried to install ncbi-blast-2.2.26+-3.i686.rpm (see: 
>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ) into 
>> Cygwin 1.7.13 with the command "install -i 
>> ncbi-blast-2.2.26+-3.i686.rpm". However, error message appeared as 
>> below. libc.so.6, 
>> libdl.so.2,  libm.so.6,  libnsl.so.1, and  libz.so.1. Where can I get 
>> these libs? Thanks!
>> 
>> $ rpm -i ncbi-blast-2.2.26+-3.i686.rpm
>> error: Failed dependencies:
>>         /usr/bin/perl is needed by ncbi-blast-2.2.26+-3
>>         libbz2.so.1 is needed by ncbi-blast-2.2.26+-3
>>         libc.so.6 is needed by ncbi-blast-2.2.26+-3
>>         libc.so.6(GLIBC_2.1.3) is needed by ncbi-blast-2.2.26+-3
>>         libc.so.6(GLIBC_2.2) is needed by ncbi-blast-2.2.26+-3
>>         libc.so.6(GLIBC_2.3) is needed by ncbi-blast-2.2.26+-3
>
>.....
>On Tue, Apr 10, 2012 at 02:03:29PM +0800, De-Jian Zhao wrote:
>
> > It seems that the compilation under Cygwin is more complicated than
> > expected.
>==========================================================
>
>This has nothing to do with cygwin.

Please don't resurrect old messages.  This was all dealt with six days
ago.

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Re: Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

On 2012-4-17 13:58, Linda Walsh wrote:
> De-Jian Zhao wrote:
>
>> Dear all,
>>
>> I noticed that there is a command - rpm - under Cygwin 1.7. Does that 
>> mean RPM packages can be installed into Cygwin?
>>
>> I tried to install ncbi-blast-2.2.26+-3.i686.rpm (see: 
>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ) into 
>> Cygwin 1.7.13 with the command "install -i 
>> ncbi-blast-2.2.26+-3.i686.rpm". However, error message appeared as 
>> below. libc.so.6, libdl.so.2,  libm.so.6,  libnsl.so.1, and  
>> libz.so.1. Where can I get these libs? Thanks!
>>
>> $ rpm -i ncbi-blast-2.2.26+-3.i686.rpm
>> error: Failed dependencies:
>>         /usr/bin/perl is needed by ncbi-blast-2.2.26+-3
>>         libbz2.so.1 is needed by ncbi-blast-2.2.26+-3
>>         libc.so.6 is needed by ncbi-blast-2.2.26+-3
>>         libc.so.6(GLIBC_2.1.3) is needed by ncbi-blast-2.2.26+-3
>>         libc.so.6(GLIBC_2.2) is needed by ncbi-blast-2.2.26+-3
>>         libc.so.6(GLIBC_2.3) is needed by ncbi-blast-2.2.26+-3
>
> .....
> On Tue, Apr 10, 2012 at 02:03:29PM +0800, De-Jian Zhao wrote:
>
> > It seems that the compilation under Cygwin is more complicated than
> > expected.
> ==========================================================
>
> This has nothing to do with cygwin.
>
> It is 'rpm' looking for installed dependencies in the rpm database.
>
> Since everything was installed with 'setup.exe' which keeps it's own
> 'database', rpm thinks nothing is installed.
>
> You need to make sure the versions required by the rpm are installed 
> by setup,
> then you can build from a ncbi-blast-2.2.26+-3.src.rpm
>                                                ^^^
>
> The i686.rpm package is prebuilt for "some" platform (you would have 
> to know
> which from the download -- i.e. one built for suse won't necessarily 
> run on redhat, or ubuntu...  or other combinations.   Ones that do 
> will be statically
> built and will be usable on some range of OS-versions of some 
> particular OS.
> Since rpm is a linux thing, it would be built for the linux OS... so 
> double-screw.  Wrong OS, wrong executable format...etc...   look for a 
> corresponding .src. rpm, OR as someone else already suggested, look 
> for the
> 'tar' that the is included in the ".src".  -- in fact, if you have the 
> .src.,
> usually the .tar. file they build from is packed into it (then patches 
> and OS
> specific stuff is applied), so you can often just take the tar from 
> your src.rpm
> and move it to cygwin, and run it directly if it has a "configure" 
> script.
>
> it might also have something like "bootstrap.sh" (or bootstrap 
> something) that will produce a configure script -- that will usually 
> allow you to build an executable that will work on your platform (in 
> this case cygwin) -- but you
> will still have to have _needed_ dependencies installed (like 
> development packages from cygwin for some of the above).
>
> All of those packages may not be needed -- dependencies are often based
> on what options you select in configure (configure --help tells you 
> all it's options).  Sometimes you don't need all the options the 
> 'default' rpm builds
> with making life simpler.
>
> Compilation, period, other than on the system the package was designed 
> for is
> never completely trivial, but configure makes it nearly so if it is 
> used --
> most packages these days have such a script -- rpm packages just have 
> pre-built
> some pre-configured image for distribution -- may not be optimal for 
> your needs
> nor is it likely to be optimized for your machine.
>
> Hope this was of some help.
> Good luck!
>
> Linda
>
>

Thank you, Linda. When I saw the error message after installing some 
packages to satisfy the dependencies, I was wondering why the rpm 
package still complained about the already installed packages. I was not 
aware that cygwin and rpm were not sharing the 'database'. Thank you for 
making it clear to me.I will try the src.rpm when I am free.

DJ

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Re: Can RPM packages be installed into Cygwin?

[Christopher Faylor]

On Wed, Apr 18, 2012 at 09:13:20PM +0800, De-Jian Zhao wrote:
>On 2012-4-17 13:58, Linda Walsh wrote:
>>[snip]
>Thank you, Linda.  When I saw the error message after installing some
>packages to satisfy the dependencies, I was wondering why the rpm
>package still complained about the already installed packages.  I was
>not aware that cygwin and rpm were not sharing the 'database'.  Thank
>you for making it clear to me.I will try the src.rpm when I am free.

So with all of the back and forth about this, you never realized that
Cygwin's setup.exe doesn't use RPM?  Wow.  Wasn't the fact that there
are no .rpm files in the distribution a big enough clue?

cgf

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Re: Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

On 2012-4-18 22:03, Christopher Faylor wrote:
> On Wed, Apr 18, 2012 at 09:13:20PM +0800, De-Jian Zhao wrote:
>> On 2012-4-17 13:58, Linda Walsh wrote:
>>> [snip]
>> Thank you, Linda.  When I saw the error message after installing some
>> packages to satisfy the dependencies, I was wondering why the rpm
>> package still complained about the already installed packages.  I was
>> not aware that cygwin and rpm were not sharing the 'database'.  Thank
>> you for making it clear to me.I will try the src.rpm when I am free.
> So with all of the back and forth about this, you never realized that
> Cygwin's setup.exe doesn't use RPM?  Wow.  Wasn't the fact that there
> are no .rpm files in the distribution a big enough clue?
>
> cgf

I never expect setup.exe will use rpm packages. There is a rpm command 
in Cygwin. I just thought it could be used to install a rpm package.

The rpm package complained about dependencies during installation. I did 
think that the dependency could be solved by installing proper packages 
through setup.exe. But after installing some libraries through 
setup.exe, the rpm package still complained the same as before. It 
seemed that the rpm package did not see the installed libraries at all.

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Re: Can RPM packages be installed into Cygwin?

[Linda Walsh]

De-Jian Zhao wrote:

> 
> Thank you, Linda. When I saw the error message after installing some 
> packages to satisfy the dependencies, I was wondering why the rpm 
> package still complained about the already installed packages. I was not 
> aware that cygwin and rpm were not sharing the 'database'. Thank you for 
> making it clear to me.I will try the src.rpm when I am free.

---
	Note:
	The src.rpm will likely look in the rpm database for it's
pre-reqs as well.
	you will need to look inside it (install the src.rpm, and look
in the /usr/src/packages/specs dir for <package>.spec>) -- and you will see 
lines like: (example from suse samba package):

BuildRequires:  cups-devel e2fsprogs-devel fam-devel libacl-devel pam-devel 
popt-devel python-devel readline-devel
%if 0%{?suse_version}
BuildRequires:  cracklib-devel openldap2-devel
%endif
%if 0%{?suse_version} > 1030
BuildRequires:  gdbm-devel pwdutils
%endif
%if 0%{?suse_version} > 930
BuildRequires:  krb5-devel libiniparser-devel libnscd-devel
%endif
....
(there's a bunch more .. the BuildRequires lines -- will refer to
DISTRO-specific package names (if that was built for Redhat, will refer
to redhat's package names).

The "if" statements are all about configure the same "spec" file for different
conditions... if you wanted to make things complex (I wouldn't), you could
build all the packages it needs and put in an if statement that would be true
for cygwin (would be alot of work!)

Or. look at the minimum set of packages you will need and make sure they
are installed from cygwin,
and comment out all those build-require lines and -- try it.. cross fingers.

But it will then likely be built for whatever DISTRO's specific file layout
which may not match cygwin's.

Safest -- after you install src.rpm, look in /usr/src/packages/SOURCES/ for
<name of your package>.tar.[bz2,gz] -- that will be the original tar package
-- prior to any DISTRO specific changes, that you will want.

Unpack that to a dir and hope it is setup with the configure route -- or figure
out what it needs to build (make...blah).

I have taken suse src rpms and direct ported them to cygwin -- but I had
to disable all the pre-requisite checking at build and install time, due to
the missing rpm database -- but the program was a *simple one*, and it worked.
So it is possible.   The more complex the program, the more likely it will
take more work to port...but sometimes you get lucky and the developer did
a good job setting up a configure script that will work with cygwin...

It is a pain -- you will be porting the source to cygwin -- but it it is worth 
it to you, you can get it done.  (But you really have to want it!) ;-)




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Re: Can RPM packages be installed into Cygwin?

[Christopher Faylor]

On Thu, Apr 19, 2012 at 12:05:38AM +0800, De-Jian Zhao wrote:
>On 2012-4-18 22:03, Christopher Faylor wrote:
>> On Wed, Apr 18, 2012 at 09:13:20PM +0800, De-Jian Zhao wrote:
>>> On 2012-4-17 13:58, Linda Walsh wrote:
>>>> [snip]
>>> Thank you, Linda.  When I saw the error message after installing some
>>> packages to satisfy the dependencies, I was wondering why the rpm
>>> package still complained about the already installed packages.  I was
>>> not aware that cygwin and rpm were not sharing the 'database'.  Thank
>>> you for making it clear to me.I will try the src.rpm when I am free.
>>
>> So with all of the back and forth about this, you never realized that
>> Cygwin's setup.exe doesn't use RPM?  Wow.  Wasn't the fact that there
>> are no .rpm files in the distribution a big enough clue?
>
>I never expect setup.exe will use rpm packages. There is a rpm command 
>in Cygwin. I just thought it could be used to install a rpm package.

And, although it is a very old, basically-unmaintained package, it can
be used to install rpm packages.

>The rpm package complained about dependencies during installation. I did 
>think that the dependency could be solved by installing proper packages 
>through setup.exe.

>But after installing some libraries through setup.exe, the rpm package
>still complained the same as before.  It seemed that the rpm package
>did not see the installed libraries at all.

I don't know if you are getting this or not but, yes, you can install
cygwin packages which would allow you to satisfy the needs for building
an rpm package.  That doesn't mean that rpm would magically know about
it since rpm maintains its own package database which obviously is not
updated by setup.exe.  So, while the programs you need to build an
rpm package may be available, rpm does not know this.  The fact that
we use setup.exe and "cygcheck" to query our packages should be a
huge clue that setup.exe does not know anything about rpm.

The --nodeps option to rpm will silence the dependency warnings but
it won't fix real problems if required packages are missing.

rpm is basically a curiosity on Cygwin.  It really isn't that useful.
If you want to build Cygwin packages, you should be investigating
cygport.

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Re: Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

On 2012-4-19 0:58, Linda Walsh wrote:
> De-Jian Zhao wrote:
>
>>
>> Thank you, Linda. When I saw the error message after installing some 
>> packages to satisfy the dependencies, I was wondering why the rpm 
>> package still complained about the already installed packages. I was 
>> not aware that cygwin and rpm were not sharing the 'database'. Thank 
>> you for making it clear to me.I will try the src.rpm when I am free.
>
> ---
>     Note:
>     The src.rpm will likely look in the rpm database for it's
> pre-reqs as well.
>     you will need to look inside it (install the src.rpm, and look
> in the /usr/src/packages/specs dir for <package>.spec>) -- and you 
> will see lines like: (example from suse samba package):
>
> BuildRequires:  cups-devel e2fsprogs-devel fam-devel libacl-devel 
> pam-devel popt-devel python-devel readline-devel
> %if 0%{?suse_version}
> BuildRequires:  cracklib-devel openldap2-devel
> %endif
> %if 0%{?suse_version} > 1030
> BuildRequires:  gdbm-devel pwdutils
> %endif
> %if 0%{?suse_version} > 930
> BuildRequires:  krb5-devel libiniparser-devel libnscd-devel
> %endif
> ....
> (there's a bunch more .. the BuildRequires lines -- will refer to
> DISTRO-specific package names (if that was built for Redhat, will refer
> to redhat's package names).
>
> The "if" statements are all about configure the same "spec" file for 
> different
> conditions... if you wanted to make things complex (I wouldn't), you 
> could
> build all the packages it needs and put in an if statement that would 
> be true
> for cygwin (would be alot of work!)
>
> Or. look at the minimum set of packages you will need and make sure they
> are installed from cygwin,
> and comment out all those build-require lines and -- try it.. cross 
> fingers.
>
> But it will then likely be built for whatever DISTRO's specific file 
> layout
> which may not match cygwin's.
>
> Safest -- after you install src.rpm, look in 
> /usr/src/packages/SOURCES/ for
> <name of your package>.tar.[bz2,gz] -- that will be the original tar 
> package
> -- prior to any DISTRO specific changes, that you will want.
>
> Unpack that to a dir and hope it is setup with the configure route -- 
> or figure
> out what it needs to build (make...blah).
>
> I have taken suse src rpms and direct ported them to cygwin -- but I had
> to disable all the pre-requisite checking at build and install time, 
> due to
> the missing rpm database -- but the program was a *simple one*, and it 
> worked.
> So it is possible.   The more complex the program, the more likely it 
> will
> take more work to port...but sometimes you get lucky and the developer 
> did
> a good job setting up a configure script that will work with cygwin...
>
> It is a pain -- you will be porting the source to cygwin -- but it it 
> is worth it to you, you can get it done.  (But you really have to want 
> it!) ;-)
>

Hi, Linda. Thank you for your detailed explanation. The "spec" file 
seems different from your description. There is no explicit 
BuildRequires statement. There is no explicit statement of packages 
required. It is as follows:

====Star ncbi-blast.spec===

Name:        ncbi-blast
Version:     2.2.26+
Release:     3
Source0:     %{name}-%{version}.tgz
Summary:     NCBI BLAST finds regions of similarity between biological 
sequences.
Exclusiveos: linux
Group:       NCBI/BLAST
License:     Public Domain
BuildArch:   i686 x86_64
BuildRoot:   /var/tmp/%{name}-buildroot
Prefix:      /usr

%description
The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of
local similarity between sequences. The program compares nucleotide or
protein sequences to sequence databases and calculates the statistical
significance of matches. BLAST can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.

%prep
%setup -q

%build
./configure
cd c++/*/build
%__make -f Makefile.flat

%install
%__mkdir_p $RPM_BUILD_ROOT/%_bindir
cd c++/*/bin
%__install -m755 blastp blastn blastx tblastn tblastx psiblast rpsblast 
rpstblastn blast_formatter deltablast makembindex segmasker dustmasker 
windowmasker makeblastdb makeprofiledb blastdbcmd blastdb_aliastool 
convert2blastmask blastdbcheck legacy_blast.pl update_blastdb.pl 
$RPM_BUILD_ROOT/%_bindir

%clean
rm -rf $RPM_BUILD_ROOT

%files
%defattr(-,root,root)
%_bindir/*

%changelog
* Mon Jul 21 2008 Christiam Camacho <camacho@ncbi.nlm.nih.gov>
- See ChangeLog file

===End ncbi-blast.spec===



There is a file ncbi-blast-2.2.26+.tgz under the directory SOURCES. 
There are two files, or build.sh and check.sh, in the directory 
ncbi-blast-2.2.26+\c++\compilers\cygwin\, which is similar to the 
package ncbi-blast-2.2.26+-src.tar.gz. I was stuck with "checking for 
python" when compiling ncbi-blast-2.2.26+-src.tar.gz.


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Re: Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

On 2012-4-19 1:08, Christopher Faylor wrote:
> On Thu, Apr 19, 2012 at 12:05:38AM +0800, De-Jian Zhao wrote:
>> On 2012-4-18 22:03, Christopher Faylor wrote:
>>> On Wed, Apr 18, 2012 at 09:13:20PM +0800, De-Jian Zhao wrote:
>>>> On 2012-4-17 13:58, Linda Walsh wrote:
>>>>> [snip]
>>>> Thank you, Linda.  When I saw the error message after installing some
>>>> packages to satisfy the dependencies, I was wondering why the rpm
>>>> package still complained about the already installed packages.  I was
>>>> not aware that cygwin and rpm were not sharing the 'database'.  Thank
>>>> you for making it clear to me.I will try the src.rpm when I am free.
>>> So with all of the back and forth about this, you never realized that
>>> Cygwin's setup.exe doesn't use RPM?  Wow.  Wasn't the fact that there
>>> are no .rpm files in the distribution a big enough clue?
>> I never expect setup.exe will use rpm packages. There is a rpm command
>> in Cygwin. I just thought it could be used to install a rpm package.
> And, although it is a very old, basically-unmaintained package, it can
> be used to install rpm packages.
>
>> The rpm package complained about dependencies during installation. I did
>> think that the dependency could be solved by installing proper packages
>> through setup.exe.
>> But after installing some libraries through setup.exe, the rpm package
>> still complained the same as before.  It seemed that the rpm package
>> did not see the installed libraries at all.
> I don't know if you are getting this or not but, yes, you can install
> cygwin packages which would allow you to satisfy the needs for building
> an rpm package.  That doesn't mean that rpm would magically know about
> it since rpm maintains its own package database which obviously is not
> updated by setup.exe.  So, while the programs you need to build an
> rpm package may be available, rpm does not know this.  The fact that
> we use setup.exe and "cygcheck" to query our packages should be a
> huge clue that setup.exe does not know anything about rpm.
>
> The --nodeps option to rpm will silence the dependency warnings but
> it won't fix real problems if required packages are missing.
>
> rpm is basically a curiosity on Cygwin.  It really isn't that useful.
> If you want to build Cygwin packages, you should be investigating
> cygport.
>
>

Thank you, Christopher. Is there a way to export the package info or lib 
info of setup.exe to rpm? If they can share information, the problem 
will be easily solved.

Besides, I tried --nodeps option with src.rpm. It requires root 
privilege (see below). However, "sudo rpm" and "su root" both failed to 
work. Any way to fix it? Does Cygwin has a root user?
Administrator@acer /cygdrive/d/Blast/source
$ rpm --nodeps --install ncbi-blast-2.2.26+-3.src.rpm
warning: user coremake does not exist - using root
warning: group cppcore does not exist - using root
warning: user coremake does not exist - using root
warning: group cppcore does not exist - using root

As to cygport, it seems that a *.cygport file is required. How to get 
the file?
$ cygport ncbi-blast-2.2.26+-3.src.rpm install
*** ERROR: ncbi-blast-2.2.26+-3.src.rpm.cygport not found.
Administrator@acer /cygdrive/d/Blast/source
$ cygport cbi-blast-2.2.26+-src.tar.gz install
*** ERROR: cbi-blast-2.2.26+-src.tar.gz.cygport not found.

DJ

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Re: Can RPM packages be installed into Cygwin?

[Earnie Boyd]

On Wed, Apr 18, 2012 at 2:21 PM, De-Jian Zhao wrote:
>
> Thank you, Christopher. Is there a way to export the package info or lib
> info of setup.exe to rpm? If they can share information, the problem will be
> easily solved.
>

You can always read the source code to determine how to read the
package info of setup.exe.

> Besides, I tried --nodeps option with src.rpm. It requires root privilege
> (see below). However, "sudo rpm" and "su root" both failed to work. Any way
> to fix it? Does Cygwin has a root user?

It would be the Windows administrator user.  You probably need to
execute mkpasswd.  See http://cygwin.com/faq/ and search for passwd on
the page.

-- 
Earnie
-- https://sites.google.com/site/earnieboyd

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Re: Can RPM packages be installed into Cygwin?

[Larry Hall (Cygwin)]

On 4/18/2012 2:30 PM, Earnie Boyd wrote:
> On Wed, Apr 18, 2012 at 2:21 PM, De-Jian Zhao wrote:
>>
>> Thank you, Christopher. Is there a way to export the package info or lib
>> info of setup.exe to rpm? If they can share information, the problem will be
>> easily solved.
>>
>
> You can always read the source code to determine how to read the
> package info of setup.exe.

Or in other words, there is nothing that currently exists that translates
setup's view of this information to RPMs or vice-versa.

>> Besides, I tried --nodeps option with src.rpm. It requires root privilege
>> (see below). However, "sudo rpm" and "su root" both failed to work. Any way
>> to fix it? Does Cygwin has a root user?
>
> It would be the Windows administrator user.  You probably need to
> execute mkpasswd.  See http://cygwin.com/faq/ and search for passwd on
> the page.

Actually, that's not 100% true, though mapping "root" to the Administrator's
SID in the '/etc/passwd' file might work in this case.  'mkpasswd' won't
generate a 'root' user by default.  In any case, I'd ask first why DJ
thinks that root is actually required.  I don't see anything in the output
that says this.



-- 
Larry

_____________________________________________________________________

A: Yes.
 > Q: Are you sure?
 >> A: Because it reverses the logical flow of conversation.
 >>> Q: Why is top posting annoying in email?

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Re: Can RPM packages be installed into Cygwin?

[Yaakov (Cygwin/X)]

On 2012-04-18 13:21, De-Jian Zhao wrote:
> As to cygport, it seems that a *.cygport file is required. How to get
> the file?

You have to write one.  API documentation is included in the cygport 
manual, and Ports git has thousands of examples to learn from.


Yaakov

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Re: Can RPM packages be installed into Cygwin?

[Warren Young]

On 4/18/2012 12:21 PM, De-Jian Zhao wrote:
> Is there a way to export the package info or lib
> info of setup.exe to rpm? If they can share information, the problem
> will be easily solved.

Big "if".

I said it before, but a .src.rpm built for one Linux distribution 
typically will not just recompile as-is on another Linux.  Expecting 
effortless portability to an entirely different platform like Cygwin is 
a pipe dream.

You seem to be envisioning a world where the RPM spec file says it 
requires libfoo-1.2.3.so or whatever, and that someone has ported that 
to Cygwin.  Then all you'd need to do is change RPM so it knows how to 
mung file names to cygfoo-1.2.3.dll or whatever.

That *could* happen.

What actually happens more commonly is:

- The Fedora spec file says it depends on the foo-devel package, which 
contains the .so file in question.

- The SuSE spec file says it depends on the foo-shared-lib package 
instead, because that's what the same package is called there.

- The Repoforge spec file depends on the platform spec file, but also on 
a passel of other infrastructure that has no direct correspondence to 
anything else, and without it it won't even rebuild on supported platforms.

- The third-party spec file which was built to support the first-party 
foo package from the upstream vendor (as opposed to the version in the 
distro) says it depends on the first-party foo-community-shared package.

So, which one should this mythical Cygwin .pkg -> RPM DB tool convert 
the dependencies to?

The first scenario above also ignores versioning issues.

This mythical automatic package porting tool you imagine cannot be 
magicked into existence with a "But if you just..." observation.  There 
is no "just".  It would probably take more work to build the automatic 
dependency translation tool than to just manually port everything.

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Re: Can RPM packages be installed into Cygwin?

[Linda Walsh]

De-Jian Zhao wrote:

> Hi, Linda. Thank you for your detailed explanation. The "spec" file 
> seems different from your description. There is no explicit 
> BuildRequires statement. There is no explicit statement of packages 
> required. It is as follows:

----
	The one I included was definitely a more complicated one.

Most OLDER src BUILD spec files did NOT include a list of what they
needed to build -- so you wouldn't see any BuildRequires -- in them...

A major improvement, IMO -- since before, you could run and run builds
and have them fail due to something missing... and it woudl take
forever to try to figure it out, or worse -- what package the referennce
was in --

The cygwin build package was still at that level last time I tried... Never
could figure out all the prereqs, so it always failed on my machine...
sigh.

(only made attempts about 3 times spaced about a year or more apart each...)..

There's a load of difference between those who say it is easy (when they know
they solution), vs. out of 100 choices, if you don't know they right one --
it's hard -- multiply that by more choices and products and the solution becomes
NP-hard.




> ./configure
> cd c++/*/build
> %__make -f Makefile.flat

----
The above is the part you want - it uses configure to build itself -- so ideally
you can just unpack the tar (read the build.sh and see if it does anything
special (sets ENV vars or uses special options to configure), then do the 
configure.  When done, you should be able to cd to 'somedir' (usually the
top level dir -- looks like they are only building part of the product).
and usually just run 'make'
Again -- they seem to be using a custom 'Makefile.flat', instead of the regular
make, so you might want to look at the makefile configure generates and 
Makefile.flat and see what's different and 'why' they did it that way (maybe 
tried to make it more portable on different architectures..?  guessing)...


> 
> %install
> %__mkdir_p $RPM_BUILD_ROOT/%_bindir
> cd c++/*/bin
> %__install -m755 blastp blastn blastx tblastn tblastx psiblast rpsblast 
> rpstblastn blast_formatter deltablast makembindex segmasker dustmasker 
> windowmasker makeblastdb makeprofiledb blastdbcmd blastdb_aliastool 
> convert2blastmask blastdbcheck legacy_blast.pl update_blastdb.pl 
> $RPM_BUILD_ROOT/%_bindir

----
You likely won't need this -- if you tell configure where your bind dir is
(remember ./configure --help, will tell you how to set options for where you
want things to go -- can always make a best guess and see if it works, if not,
try again (I've made many more wrong choices than right ones -- but I just try 
not to stop until I find the right one (or at least one that's good enough for 
me!)...
though to install, usually after you 'make', you need to do a 'make install'

-


> 
> 
> There is a file ncbi-blast-2.2.26+.tgz under the directory SOURCES. 
> There are two files, or build.sh and check.sh, in the directory 
> ncbi-blast-2.2.26+\c++\compilers\cygwin\, which is similar to the 
> package ncbi-blast-2.2.26+-src.tar.gz. I was stuck with "checking for 
> python" when compiling ncbi-blast-2.2.26+-src.tar.gz.

----
	Well, then they are doing something similar to what rpm does...
I assume you mean when you did the configure/make manually or are you still
trying it through rpm?... rpm has those problems I mentioned earlier.
Does the package you are using use python that you know of?

Might look through the makefile and see what it does with python -- find out 
where that message is comming from (process explorer/process monitor (both from
sysinternals (part of microsoft).. are free). they can help you identify what 
processes are running and such.

also .. don't forget cygwin's 'strace -ff fffff'    If you start your make
with strace, you'll get lots of output, but it should 'hang'  (or be going in 
loops) pretty close to where you are seeing that message!)...

If fact, when that message comes out, us 'ps' to see what is running and
use strace to attach to the running process and see what the bleep it is 
doing.....   Work on tracking it back to what script is beign called and see
if you need it.  if not-- nix it some way (exit 0 as 1st line works!)...;-)

Welcome to the world of porting...

A real pain when all you wanted to do was calculate "2+2"... ;-)



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Re: Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

On 2012-4-19 7:09, Buchbinder, Barry (NIH/NIAID) [E] wrote:
> De-Jian,
>
> Hello.  It's me again.
>
> I suspect that just writing wrapper scripts would be faster than playing
> with RPMs and/or trying to compile blast yourself.
>
> As I understand it, blast programs are all command-line.  I think
> that the easiest thing would be to just use the Windows version
> supplied by NCBI and write wrapper scripts that will convert cygwin's
> POSIX paths to Windows paths.  You might have to experiment to see if
> you also need to convert file formats from \n to \r\n line endings.
>
> See
>    $ man cygpath
>    $ man dos2unix
>    $ man unix2dos
>
> Luc Hermitte's cyg-wrapper.sh might be all you need.
>    http://hermitte.free.fr/cygwin/#Win32
> Example (using vim):
>    http://vim.wikia.com/wiki/Running_the_win32-version_of_Vim_from_cygwin
> I've never used cyg-wrapper.sh, so this suggestion is "theoretical" and
> not based on my personal experience.
>
> Related:
>    http://www.ncbi.nlm.nih.gov/books/NBK1762/
>    http://www.ncbi.nlm.nih.gov/books/NBK52637/
>
> Good luck,
>
> - Barry
>    Disclaimer: Statements made herein are not made on behalf of NIAID.
>    Disclaimer: Please see http://cygwin.com/ml/cygwin/2012-04/msg00247.html
>                for other disclaimers and statements concerning the limited
>                reliability of my advice on this topic.
>

Hi,Barry. Thank you for your suggestion. Actually I am using the windows 
version of BLAST these days. The only inconvenience is that windows 
version of blast does not recognize the linux-like paths, as mentioned 
in my previous replies.

Now, it is solved after reading your reply. I was inspired by the notion 
of "convert cygwin's POSIX paths to Windows paths". I tried to convert 
the path into windows path using "cygpath -w" and it works smoothly. An 
example command line is as below:

blastall -p blastn -i nt.fas -d $(cygpath -w genome.db) -o test.out -m 8

I have modified the PATH variable so as to the blast programs could be 
automatically identified. genome.db is a soft link to the target 
database under the working directory. blastall can not interpret the 
soft link; but after translating the path using $(cygpath -w genome.db), 
it works perfectly.

Furthermore, there is in fact no need to create the linux-style soft 
link. I added a variable DB to store the windows-style path of the 
database and this makes a more simple solution.

DB="D:\Blast\blast-2.2.13\db\genome\genome.db"
blastall -p blastn -i nt.fas -d $DB -o test.out -m 8

Up to now, the problem is solved. Thanks to all that participated in the 
discussion. I should have make it clear that I just want to use the 
blast program under Cygwin. The efforts were diverted into two 
directions. One was to compile the program from source code. Many people 
contributed their ideas and the discussion deepened my understanding of 
Cygwin. The other was to use the windows version. The problem of 
different styles of paths was settled today. Thanks to all for your help.

Best regards,
DJ


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RE: Can RPM packages be installed into Cygwin?

[Buchbinder, Barry (NIH/NIAID) [E]]

De-Jian,

Hello.  It's me again.

I suspect that just writing wrapper scripts would be faster than playing
with RPMs and/or trying to compile blast yourself.

As I understand it, blast programs are all command-line.  I think
that the easiest thing would be to just use the Windows version
supplied by NCBI and write wrapper scripts that will convert cygwin's
POSIX paths to Windows paths.  You might have to experiment to see if
you also need to convert file formats from \n to \r\n line endings.

See
  $ man cygpath
  $ man dos2unix
  $ man unix2dos

Luc Hermitte's cyg-wrapper.sh might be all you need.
  http://hermitte.free.fr/cygwin/#Win32
Example (using vim):
  http://vim.wikia.com/wiki/Running_the_win32-version_of_Vim_from_cygwin
I've never used cyg-wrapper.sh, so this suggestion is "theoretical" and
not based on my personal experience.

Related:
  http://www.ncbi.nlm.nih.gov/books/NBK1762/
  http://www.ncbi.nlm.nih.gov/books/NBK52637/

Good luck,

- Barry
  Disclaimer: Statements made herein are not made on behalf of NIAID.
  Disclaimer: Please see http://cygwin.com/ml/cygwin/2012-04/msg00247.html
              for other disclaimers and statements concerning the limited
              reliability of my advice on this topic.

Re: Can RPM packages be installed into Cygwin?

[Warren Young]

On 4/9/2012 11:48 PM, De-Jian Zhao wrote:
> I wrote to the help desk of NCBI Blast+. They have no guidelines
> for Cygwin users and also suggested the windows version.

It sounds like the Cygwin port is abandoned, then.  You should consider 
adopting it.

Yes, it's a fair bit of work, and I wouldn't be surprised if you 
initially don't have the skill to figure out everything about reviving 
this port.  However, the best way to learn is to try and do something.

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Re: Can RPM packages be installed into Cygwin?

[De-Jian Zhao]

On 2012-4-10 8:30, Buchbinder, Barry (NIH/NIAID) [E] wrote:
> De-Jian Zhao sent the following at Monday, April 09, 2012 11:12 AM
>>> On 4/8/2012 5:10 AM, De-Jian Zhao wrote:
>>>> On 2012-4-7 16:12, marco atzeri wrote:
>>>> Thanks, Marco. I was not trying to run a native linux apps, and instead
>>>> tried to rebuild the app from source. The BLAST software provides the
>>>> Build.sh and Check.sh scripts under the directory of
>>>> ncbi-blast-2.2.26+-src.tar\ncbi-blast-2.2.26+-src\c++\compilers\cygwin\.
>>>> So I think it is possible to run the software under cygwin. However, the
>>>> compilation stopped at "checking for python", even if python was
>>>> installed. That's to say, I installed the latest python and the
>>>> compilation could find it, but the compilation tried to search for
>>>> python2.3 and 2.4 further, and stopped when searching for 2.4.
>>>>
>>>> What I am concern is that whether the i686.rpm indicates it is prepared
>>>> for cygwin. As you know, when you run "uname -smo", you can get
>>>> something like this "CYGWIN_NT-5.1 i686 Cygwin". I think the package
>>>> ncbi-blast-2.2.26+-3.i686.rpm is for Cygwin. Is that right? Has anyone
>>>> ever succeeded in installing a RPM package into cygwin using "rpm -i
>>>> *rpm"?
>>>>
>>> i686.rpm is not the source package, is the binary for linux on 686
>>> processor.
>>> On cygwin we do not use rpm for building packages so the source rpm
>>> file will unlikely work.
>>>
>>> The source for all platforms is
>>>
>>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.26+-src.tar.gz
>>>
>> On 2012-4-8 14:47, marco atzeri wrote: Thank you, Marco. I tried that
>> version. Unfortunately, the compilation always stopped at "checking
>> python" even after python was installed. It seems to me that it is a
>> tough work to rebuild a software from the source code under Cygwin. The
>> dependency is hard to satisfy.
>>
>> I am curious about the utility rpm under Cygwin environment. When
>> running the setup.exe, I noticed that there is a rpm package. (Search for
>> "rpm" at the stage of "Select Packages" when running setup.exe, you can
>> find the package under "Utils Default".) Then what is it for?
> Looking at the blast directory, they have a source rpm.  Perhaps some source
> code is only available as an rpm?
>
> For what it is worth, I tried compiling and it seemed to compile OK when I
> used "./configure --without-boost" (recommended by make after a simple
> "./configure".  "make check" passed two of three tests.  YMMV.  As I did not
> install any dependencies, maybe you could do better.
>
> Also, I noted that ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
> contains some windows binaries.  You might consider using them as native
> binaries usually run faster than cygwin binaries.
>
> Also, note that there is a folder ncbi-blast-2.2.26+-src/c++/compilers/cygwin.
> I didn't notice it until after I tried compiling.  You might try to figure out
> whether the scripts there help you compile blast.
>
> IMPORTANT: I'm not a programmer, I don't work at NCBI, I have no experience in
> bioinformatics and have certainly never used BLAST.  DO NOT assume that I know
> anything about this more than what I reported above.  I was intrigued and did
> an experiment - that is all.
>
> Good luck.
>
> - Barry
>    Disclaimer: Statements made herein are not made on behalf of NIAID.
>    Disclaimer: Statements made herein are not made on behalf of NCBI.
>    Disclaimer: Statements made herein are not made on behalf of NLM.
>    Disclaimer: Statements made herein are not made on behalf of NIH.
>    Disclaimer: Statements made herein are not made on behalf of PHS.
>    Disclaimer: Statements made herein are not made on behalf of DHHS.
>

Thank you, Barry. I tried the file c++/compilers/cygwin/build.sh but 
failed. I wrote to the help desk of NCBI Blast+. They have no guidelines 
for Cygwin users and also suggested the windows version. Actually, I am 
using the windows version now. The only shortcoming is that the windows 
binaries do not recognize the linux-like Cygwin path, so the soft links 
to the blast databases become invalid. I have to change to the directory 
of the Blast database every time I want to run blast search. Anyway, it 
works although a bit inconvenient. Thanks again for your help.

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RE: Can RPM packages be installed into Cygwin?

[Buchbinder, Barry (NIH/NIAID) [E]]

De-Jian Zhao sent the following at Monday, April 09, 2012 11:12 AM
>> On 4/8/2012 5:10 AM, De-Jian Zhao wrote:
>>> On 2012-4-7 16:12, marco atzeri wrote:
>>
>>> Thanks, Marco. I was not trying to run a native linux apps, and instead
>>> tried to rebuild the app from source. The BLAST software provides the
>>> Build.sh and Check.sh scripts under the directory of
>>> ncbi-blast-2.2.26+-src.tar\ncbi-blast-2.2.26+-src\c++\compilers\cygwin\.
>>> So I think it is possible to run the software under cygwin. However, the
>>> compilation stopped at "checking for python", even if python was
>>> installed. That's to say, I installed the latest python and the
>>> compilation could find it, but the compilation tried to search for
>>> python2.3 and 2.4 further, and stopped when searching for 2.4.
>>>
>>> What I am concern is that whether the i686.rpm indicates it is prepared
>>> for cygwin. As you know, when you run "uname -smo", you can get
>>> something like this "CYGWIN_NT-5.1 i686 Cygwin". I think the package
>>> ncbi-blast-2.2.26+-3.i686.rpm is for Cygwin. Is that right? Has anyone
>>> ever succeeded in installing a RPM package into cygwin using "rpm -i
>>> *rpm"?
>>>
>> i686.rpm is not the source package, is the binary for linux on 686
>> processor.
>> On cygwin we do not use rpm for building packages so the source rpm
>> file will unlikely work.
>>
>> The source for all platforms is
>>
>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.26+-src.tar.gz
>>
>On 2012-4-8 14:47, marco atzeri wrote: Thank you, Marco. I tried that
>version. Unfortunately, the compilation always stopped at "checking
>python" even after python was installed. It seems to me that it is a
>tough work to rebuild a software from the source code under Cygwin. The
>dependency is hard to satisfy.
>
>I am curious about the utility rpm under Cygwin environment. When
>running the setup.exe, I noticed that there is a rpm package. (Search for
>"rpm" at the stage of "Select Packages" when running setup.exe, you can
>find the package under "Utils Default".) Then what is it for?

Looking at the blast directory, they have a source rpm.  Perhaps some source
code is only available as an rpm?

For what it is worth, I tried compiling and it seemed to compile OK when I
used "./configure --without-boost" (recommended by make after a simple
"./configure".  "make check" passed two of three tests.  YMMV.  As I did not
install any dependencies, maybe you could do better.

Also, I noted that ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
contains some windows binaries.  You might consider using them as native
binaries usually run faster than cygwin binaries.

Also, note that there is a folder ncbi-blast-2.2.26+-src/c++/compilers/cygwin.
I didn't notice it until after I tried compiling.  You might try to figure out
whether the scripts there help you compile blast.

IMPORTANT: I'm not a programmer, I don't work at NCBI, I have no experience in
bioinformatics and have certainly never used BLAST.  DO NOT assume that I know
anything about this more than what I reported above.  I was intrigued and did
an experiment - that is all.

Good luck.

- Barry
  Disclaimer: Statements made herein are not made on behalf of NIAID.
  Disclaimer: Statements made herein are not made on behalf of NCBI.
  Disclaimer: Statements made herein are not made on behalf of NLM.
  Disclaimer: Statements made herein are not made on behalf of NIH.
  Disclaimer: Statements made herein are not made on behalf of PHS.
  Disclaimer: Statements made herein are not made on behalf of DHHS.

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