Allow control over compile commands and add staged install targets to Makefile

These changes are more extensive than the previous pull requests.
I added example install and install-strip targets to facilitate the creation of packages such as
Debian packages, FreeBSD ports, MacPorts, etc.  With a Makefile like this, creating the package manager framework will be trivial.  ( They supply variables like CXX by default. )
Default behavior of the Makefile should still be the same.

Thanks for all of these. What are you up to?

We have a researcher who wants to use dDocent, hence freebayes, hence
vcflib.  I'm building packages for deploying it on our CentOS and
FreeBSD systems, including some large clusters and grids:
http://uwm.edu/hpc/specifications-3/
Thanks for the quick response to all of these.  It's great to be able to
push patches upstream immediately rather than have them accumulate in
the package frameworks...
On 11/17/15 15:27, Erik Garrison wrote:

Thanks for all of these. What are you up to?
—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157512672.

--
   Jason W. Bacon
<EMAIL_ADDRESS>
   If a problem can be solved,
   there's no need to worry.

   If it cannot be solved, then
   worrying will do no good.

If I've learned anything it is that one shouldn't let patches wait for
merging. The help is very welcome, and what you have changed looks
completely sensible so I've quickly merged things.
Are you interested in setting freebayes up for deployment in a package
manager, and if so how can I help?
On Nov 17, 2015 10:44 PM, "outpaddling"<EMAIL_ADDRESS>wrote:

We have a researcher who wants to use dDocent, hence freebayes, hence
vcflib. I'm building packages for deploying it on our CentOS and
FreeBSD systems, including some large clusters and grids:
http://uwm.edu/hpc/specifications-3/
Thanks for the quick response to all of these. It's great to be able to
push patches upstream immediately rather than have them accumulate in
the package frameworks...
On 11/17/15 15:27, Erik Garrison wrote:

Thanks for all of these. What are you up to?
—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157512672.

--
Jason W. Bacon
<EMAIL_ADDRESS>
If a problem can be solved,
there's no need to worry.

If it cannot be solved, then
worrying will do no good.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157518570.

Yes, we're working our way up to dDocent from the leaf nodes.
Thanks for the offer to help.  The patches I've submitted already are
pretty indicative of what makes packaging easy.
Providing install and install-strip targets in the Makefile and letting
the package manager specify compilers and non-essential flags makes
things really easy.
For example, here's the entire FreeBSD port Makefile for fastahack:
Created by: Jason Bacon<EMAIL_ADDRESS>$FreeBSD$
PORTNAME=       fastahack
PORTVERSION=    6846daed076983105b87e24d2be913b094c4ea12
CATEGORIES=     biology
MAINTAINER=<EMAIL_ADDRESS>COMMENT=        Utilities for indexing and sequence extraction from
FASTA files
USE_GITHUB=     yes
GH_ACCOUNT=     outpaddling
GH_TAGNAME=     ${PORTVERSION}
INSTALL_TARGET= install-strip
PLIST_FILES=    bin/fastahack
.include <bsd.port.mk>
A Debian package or MacPort would be about as simple.  They all look for
the same standards upstream.
The vcflib port will be a little more challenging, since it depends on
submodules that it looks for in child directories. I'll have to tweak it
and the submodule ports so that it can find the objects it needs under
the install prefix instead.  Shouldn't be too difficult, but I don't
want to break the integrated build system you have now, so I'm going
about this one very carefully.
I assume your intent is to have all of these built and installed
separately at some point, since created separate repos for all of them.
Either way, most package managers almost require it.
I'll keep sending pull requests, but they'll be more interesting from
here on.
Thanks much,
 Jason

On 11/17/15 15:46, Erik Garrison wrote:

If I've learned anything it is that one shouldn't let patches wait for
merging. The help is very welcome, and what you have changed looks
completely sensible so I've quickly merged things.
Are you interested in setting freebayes up for deployment in a package
manager, and if so how can I help?
On Nov 17, 2015 10:44 PM, "outpaddling"<EMAIL_ADDRESS>wrote:

We have a researcher who wants to use dDocent, hence freebayes, hence
vcflib. I'm building packages for deploying it on our CentOS and
FreeBSD systems, including some large clusters and grids:
http://uwm.edu/hpc/specifications-3/
Thanks for the quick response to all of these. It's great to be able to
push patches upstream immediately rather than have them accumulate in
the package frameworks...
On 11/17/15 15:27, Erik Garrison wrote:

Thanks for all of these. What are you up to?
—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157512672.

--
Jason W. Bacon
<EMAIL_ADDRESS>
If a problem can be solved,
there's no need to worry.

If it cannot be solved, then
worrying will do no good.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157518570.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157519234.

--
   Jason W. Bacon
<EMAIL_ADDRESS>
   If a problem can be solved,
   there's no need to worry.

   If it cannot be solved, then
   worrying will do no good.

@edawson has just put a ton of work into this. Things are still in flux but
the ultimate goal is easier builds and matching packaging requirements. In
our case the target is vg rather than freebayes, which should also be
restructured to match what he's done there.
On Nov 17, 2015 11:08 PM, "outpaddling"<EMAIL_ADDRESS>wrote:

Yes, we're working our way up to dDocent from the leaf nodes.
Thanks for the offer to help. The patches I've submitted already are
pretty indicative of what makes packaging easy.
Providing install and install-strip targets in the Makefile and letting
the package manager specify compilers and non-essential flags makes
things really easy.
For example, here's the entire FreeBSD port Makefile for fastahack:
Created by: Jason Bacon<EMAIL_ADDRESS>$FreeBSD$
PORTNAME= fastahack
PORTVERSION= 6846daed076983105b87e24d2be913b094c4ea12
CATEGORIES= biology
MAINTAINER=<EMAIL_ADDRESS>COMMENT= Utilities for indexing and sequence extraction from
FASTA files
USE_GITHUB= yes
GH_ACCOUNT= outpaddling
GH_TAGNAME= ${PORTVERSION}
INSTALL_TARGET= install-strip
PLIST_FILES= bin/fastahack
.include <bsd.port.mk>
A Debian package or MacPort would be about as simple. They all look for
the same standards upstream.
The vcflib port will be a little more challenging, since it depends on
submodules that it looks for in child directories. I'll have to tweak it
and the submodule ports so that it can find the objects it needs under
the install prefix instead. Shouldn't be too difficult, but I don't
want to break the integrated build system you have now, so I'm going
about this one very carefully.
I assume your intent is to have all of these built and installed
separately at some point, since created separate repos for all of them.
Either way, most package managers almost require it.
I'll keep sending pull requests, but they'll be more interesting from
here on.
Thanks much,
Jason
On 11/17/15 15:46, Erik Garrison wrote:

If I've learned anything it is that one shouldn't let patches wait for
merging. The help is very welcome, and what you have changed looks
completely sensible so I've quickly merged things.
Are you interested in setting freebayes up for deployment in a package
manager, and if so how can I help?
On Nov 17, 2015 10:44 PM, "outpaddling"<EMAIL_ADDRESS>wrote:

We have a researcher who wants to use dDocent, hence freebayes, hence
vcflib. I'm building packages for deploying it on our CentOS and
FreeBSD systems, including some large clusters and grids:
http://uwm.edu/hpc/specifications-3/
Thanks for the quick response to all of these. It's great to be able to
push patches upstream immediately rather than have them accumulate in
the package frameworks...
On 11/17/15 15:27, Erik Garrison wrote:

Thanks for all of these. What are you up to?
—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157512672.

--
Jason W. Bacon
<EMAIL_ADDRESS>
If a problem can be solved,
there's no need to worry.

If it cannot be solved, then
worrying will do no good.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157518570.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157519234.

--
Jason W. Bacon
<EMAIL_ADDRESS>
If a problem can be solved,
there's no need to worry.

If it cannot be solved, then
worrying will do no good.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157524566.

What would be most helpful as the next step, I think, would be building
a library for each submodule instead of pulling object files from the
submodule directories.  Package managers generally don't allow
installing loose object files.
I just pushed some changes to my vcflib and smithwaterman forks that
demonstrate how I would go about it.
Following these changes, a package manager would install smithwaterman
as a build dependency for vcflib, and then simply supply the SW_PATH
variable, so that the vcflib Makefile knows where to find libsw.a (and
headers if needed).
The integrated build system still works with these changes, and it will
be much easier to package vcflib this way.
Let me know how you like this approach.  I can easily do the same with
the other submodules.
Thanks,
 Jason

On 11/17/15 16:24, Erik Garrison wrote:

@edawson has just put a ton of work into this. Things are still in
flux but
the ultimate goal is easier builds and matching packaging requirements. In
our case the target is vg rather than freebayes, which should also be
restructured to match what he's done there.
On Nov 17, 2015 11:08 PM, "outpaddling"<EMAIL_ADDRESS>wrote:

Yes, we're working our way up to dDocent from the leaf nodes.
Thanks for the offer to help. The patches I've submitted already are
pretty indicative of what makes packaging easy.
Providing install and install-strip targets in the Makefile and letting
the package manager specify compilers and non-essential flags makes
things really easy.
For example, here's the entire FreeBSD port Makefile for fastahack:
Created by: Jason Bacon<EMAIL_ADDRESS>$FreeBSD$
PORTNAME= fastahack
PORTVERSION= 6846daed076983105b87e24d2be913b094c4ea12
CATEGORIES= biology
MAINTAINER=<EMAIL_ADDRESS>COMMENT= Utilities for indexing and sequence extraction from
FASTA files
USE_GITHUB= yes
GH_ACCOUNT= outpaddling
GH_TAGNAME= ${PORTVERSION}
INSTALL_TARGET= install-strip
PLIST_FILES= bin/fastahack
.include <bsd.port.mk>
A Debian package or MacPort would be about as simple. They all look for
the same standards upstream.
The vcflib port will be a little more challenging, since it depends on
submodules that it looks for in child directories. I'll have to tweak it
and the submodule ports so that it can find the objects it needs under
the install prefix instead. Shouldn't be too difficult, but I don't
want to break the integrated build system you have now, so I'm going
about this one very carefully.
I assume your intent is to have all of these built and installed
separately at some point, since created separate repos for all of them.
Either way, most package managers almost require it.
I'll keep sending pull requests, but they'll be more interesting from
here on.
Thanks much,
Jason
On 11/17/15 15:46, Erik Garrison wrote:

If I've learned anything it is that one shouldn't let patches wait for
merging. The help is very welcome, and what you have changed looks
completely sensible so I've quickly merged things.
Are you interested in setting freebayes up for deployment in a package
manager, and if so how can I help?
On Nov 17, 2015 10:44 PM, "outpaddling"<EMAIL_ADDRESS>wrote:

We have a researcher who wants to use dDocent, hence freebayes,
hence
vcflib. I'm building packages for deploying it on our CentOS and
FreeBSD systems, including some large clusters and grids:
http://uwm.edu/hpc/specifications-3/
Thanks for the quick response to all of these. It's great to be
able to
push patches upstream immediately rather than have them
accumulate in
the package frameworks...
On 11/17/15 15:27, Erik Garrison wrote:

Thanks for all of these. What are you up to?
—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157512672.

--
Jason W. Bacon
<EMAIL_ADDRESS>
If a problem can be solved,
there's no need to worry.

If it cannot be solved, then
worrying will do no good.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157518570.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157519234.

--
Jason W. Bacon
<EMAIL_ADDRESS>
If a problem can be solved,
there's no need to worry.

If it cannot be solved, then
worrying will do no good.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157524566.

—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157529662.

--
   Jason W. Bacon
<EMAIL_ADDRESS>
   If a problem can be solved,
   there's no need to worry.

   If it cannot be solved, then
   worrying will do no good.

This is awesome, Jason! The object file shuffling was a first pass on my part - packaging things as a library is a much better solution. It seems to me that building statically with libs versus the current approach of building with object files should produce equivalent libs/binaries for local builds like we use in VG.
@ekg We should probably consider doing this porting process on vg for Debian/Centos/RHEL in the far future. It would help out a bunch of sysadmins.

Cool, I'll add libs to the other submodules ASAP and submit pull requests.
FYI, my work-in-progress FreeBSD ports are here:
 https://github.com/outpaddling/freebsd-ports-wip

I never done a Debian package, but they should be very similar.
For CentOS/RHEL, we use Pkgsrc.   It's a bigger, newer collection than
Yum's, so I use it for most of our open source builds.
As soon as we get our users running dDocent on our FreeBSD test
machines, I'll begin converting everything to Pkgsrc for our CentOS
clusters.  These will be available in pkgsrc-wip immediately:
 http://pkgsrc.org/wip/

I also developed a new tool that automatically converts most of a
FreeBSD port to a Pkgsrc package.  It's in pkgsrc-wip/fbsd2pkg. FreeBSD
ports has a huge collection, comparable to Debian packages, so I can
usually get people up and running very quickly and leverage a lot of
other people's work when creating Pkgsrc packages.
Cheers,
 Jason

On 11/18/15 03:54, Eric T. Dawson wrote:

This is awesome, Jason! The object file shuffling was a first pass on
my part - packaging things as a library is a much better solution. It
seems to me that building statically with libs versus the current
approach of building with object files should produce equivalent
libs/binaries for local builds like we use in VG.
@ekg https://github.com/ekg We should probably consider doing this
porting process on vg for Debian/Centos/RHEL in the far future. It
would help out a bunch of sysadmins.
—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157661576.

--
   Jason W. Bacon
<EMAIL_ADDRESS>
   If a problem can be solved,
   there's no need to worry.

   If it cannot be solved, then
   worrying will do no good.

I've gotten everything into a pretty good working state now.  For
vcflib, I decided to create a separate Makefile for building against
external libraries.  I don't think there's a clean way to implement both
approaches in a single Makefile.
I did break out some of the common code to Makefile.common to save grunt
work on future updates.  We can push a few more things into it as well:
it's just a first draft at this point.
I'll do pull requests one at a time starting with the simplest
submodules.  I would suggest thoroughly testing each one before we do
the next, in case I broke anything.
Cheers,
 Jason

On 11/18/15 03:54, Eric T. Dawson wrote:

This is awesome, Jason! The object file shuffling was a first pass on
my part - packaging things as a library is a much better solution. It
seems to me that building statically with libs versus the current
approach of building with object files should produce equivalent
libs/binaries for local builds like we use in VG.
@ekg https://github.com/ekg We should probably consider doing this
porting process on vg for Debian/Centos/RHEL in the far future. It
would help out a bunch of sysadmins.
—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157661576.

--
   Jason W. Bacon
<EMAIL_ADDRESS>
   If a problem can be solved,
   there's no need to worry.

   If it cannot be solved, then
   worrying will do no good.

Hey guys,
I finished the FreeBSD ports for freebayes and all its dependencies.
You can view the port frameworks here if you're interested:
 https://github.com/outpaddling/freebsd-ports-wip

I'm now working on converting them to pkgsrc for our CentOS 6 clusters
(this part is pretty quick and easy once we have working FreeBSD ports).
FYI, I got a bunch of warnings with clang that gcc may have been silent
about.  Some of them look like they might be real bugs, e.g.:
src/vcfgenosummarize.cpp:14:30: warning: result of comparison against a
string literal is unspecified (use strncmp instead) [-Wstring-compare]
if (argc > 1 && (argv[1] == "-h" || argv[1] == "--help")) {
^  ~~~~
I attached output from the build.  Just "grep warning log" to see all
the issues like the one above.
BTW, what platform(s) do you develop and test on?
Cheers,
 Jason

On 11/18/15 03:54, Eric T. Dawson wrote:

This is awesome, Jason! The object file shuffling was a first pass on
my part - packaging things as a library is a much better solution. It
seems to me that building statically with libs versus the current
approach of building with object files should produce equivalent
libs/binaries for local builds like we use in VG.
@ekg https://github.com/ekg We should probably consider doing this
porting process on vg for Debian/Centos/RHEL in the far future. It
would help out a bunch of sysadmins.
—
Reply to this email directly or view it on GitHub
https://github.com/ekg/fastahack/pull/9#issuecomment-157661576.

--
   Jason W. Bacon
<EMAIL_ADDRESS>
   If a problem can be solved,
   there's no need to worry.

   If it cannot be solved, then
   worrying will do no good.

Updating database digests format: ... done
Checking integrity... done (0 conflicting)
Deinstallation has been requested for the following 10 packages (of 0 packages in the universe):
Installed packages to be REMOVED:
tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7
smithwaterman-8e667291798b785d698f0875e58da2710d740567
fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155
filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849
fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47
multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35
intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23
bamtools-2.4.0
vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
The operation will free 27 MiB.
[1/10] Deinstalling freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc...
[1/10] Deleting files for freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc: ..... done
[2/10] Deinstalling vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73...
[2/10] Deleting files for vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73: .......... done
[3/10] Deinstalling tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7...
[3/10] Deleting files for tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7: .... done
[4/10] Deinstalling smithwaterman-8e667291798b785d698f0875e58da2710d740567...
[4/10] Deleting files for smithwaterman-8e667291798b785d698f0875e58da2710d740567: .......... done
[5/10] Deinstalling fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155...
[5/10] Deleting files for fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155: ....... done
[6/10] Deinstalling filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849...
[6/10] Deleting files for filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849: ...... done
[7/10] Deinstalling fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47...
[7/10] Deleting files for fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47: ..... done
[8/10] Deinstalling multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35...
[8/10] Deleting files for multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35: ......... done
[9/10] Deinstalling intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23...
[9/10] Deleting files for intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23: ..... done
[10/10] Deinstalling bamtools-2.4.0...
[10/10] Deleting files for bamtools-2.4.0: .......... done
Updating '.':
At revision 1236.
===>  Deinstalling for update-wip-ports
===>   Deinstalling update-wip-ports-0.1
Checking integrity... done (0 conflicting)
Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
Installed packages to be REMOVED:
update-wip-ports-0.1
The operation will free 3 KiB.
[1/1] Deinstalling update-wip-ports-0.1...
[1/1] Deleting files for update-wip-ports-0.1: ... done
===>  Cleaning for update-wip-ports-0.1
===>  Deleting distfiles for update-wip-ports-0.1
===>   update-wip-ports-0.1 depends on file: /usr/local/sbin/pkg - found
=> update-wip-ports-0.1.tar.xz doesn't seem to exist in /usr/ports/distfiles/.
=> Attempting to fetch http://acadix.biz/Ports/distfiles/update-wip-ports-0.1.tar.xz
update-wip-ports-0.1.tar.xz                              0  B    0  Bps
===> Fetching all distfiles required by update-wip-ports-0.1 for building
===>  Extracting for update-wip-ports-0.1
=> SHA256 Checksum OK for update-wip-ports-0.1.tar.xz.
===>  Patching for update-wip-ports-0.1
===>  Configuring for update-wip-ports-0.1
===>  Staging for update-wip-ports-0.1
===>   update-wip-ports-0.1 depends on executable: svn - found
===>   Generating temporary packing list
install  -m 555 /usr/wip/ports-mgmt/update-wip-ports/work/update-wip-ports-0.1/update-wip-ports /usr/wip/ports-mgmt/update-wip-ports/work/stage/usr/local/bin
install  -m 555 /usr/wip/ports-mgmt/update-wip-ports/work/update-wip-ports-0.1/reinstall-wip-port /usr/wip/ports-mgmt/update-wip-ports/work/stage/usr/local/bin
install  -m 444 /usr/wip/ports-mgmt/update-wip-ports/work/update-wip-ports-0.1/update-wip-ports.1 /usr/wip/ports-mgmt/update-wip-ports/work/stage/usr/local/man/man1
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
===>  Installing for update-wip-ports-0.1
===>   Registering installation for update-wip-ports-0.1
Installing update-wip-ports-0.1...
===>  Cleaning for update-wip-ports-0.1
===>  Deleting distfiles for update-wip-ports-0.1

You can now install any of the ports added above using:
cd /usr/wip//
make install

===>  Cleaning for freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
===>  Deleting distfiles for freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
===>  Deinstalling for freebayes
===>   freebayes not installed, skipping
===>  Cleaning for freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
===> No user-specified options configured for freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
===>  License MIT accepted by the user
===>   freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc depends on file: /usr/local/sbin/pkg - found
=> outpaddling-freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc_GH0.tar.gz doesn't seem to exist in /usr/ports/distfiles/.
=> Attempting to fetch https://codeload.github.com/outpaddling/freebayes/tar.gz/bf31341be12fa616fe1e43c8aef7a04108f7bfdc?dummy=/outpaddling-freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc_GH0.tar.gz
outpaddling-freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc_           0  B    0  Bps
===> Fetching all distfiles required by freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc for building
===>  Extracting for freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
=> SHA256 Checksum OK for outpaddling-freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc_GH0.tar.gz.
===>  Patching for freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
===>   freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc depends on file: /usr/local/include/intervaltree/IntervalTree.h - not found
===>  License MIT accepted by the user
===>   intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23 for building
===>  Extracting for intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23
=> SHA256 Checksum OK for ekg-intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23_GH0.tar.gz.
===>  Patching for intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23
===>  Configuring for intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23
===>  Building for intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23
--- interval_tree_test ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing   interval_tree_test.cpp -std=c++0x -o interval_tree_test
===>  Staging for intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23
===>   Generating temporary packing list
mkdir -p /usr/wip/math/intervaltree/work/stage/usr/local/bin
mkdir -p /usr/wip/math/intervaltree/work/stage/usr/local/include/intervaltree
install interval_tree_test /usr/wip/math/intervaltree/work/stage/usr/local/bin
install IntervalTree.h /usr/wip/math/intervaltree/work/stage/usr/local/include/intervaltree
strip /usr/wip/math/intervaltree/work/stage/usr/local/bin/interval_tree_test
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
===>  Installing for intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23
===>   Registering installation for intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23 as automatic
Installing intervaltree-49a0e290efaaa760e0b03e52ca18ac03e7582f23...
===>   freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc depends on file: /usr/local/include/intervaltree/IntervalTree.h - found
===>   Returning to build of freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
===>   freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc depends on file: /usr/local/include/multichoose/multichoose.h - not found
===>  License MIT accepted by the user
===>   multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35 for building
===>  Extracting for multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35
=> SHA256 Checksum OK for outpaddling-multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35_GH0.tar.gz.
===>  Patching for multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35
===>  Configuring for multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35
===>  Building for multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35
--- multichoose ---
--- cmultichoose ---
--- multichoose ---
c++ multichoose.cpp -o multichoose
--- cmultichoose ---
cc multichoose.c -o cmultichoose
--- multipermute ---
c++ multipermute.cpp -o multipermute
===>  Staging for multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35
===>   Generating temporary packing list
mkdir -p /usr/wip/math/multichoose/work/stage/usr/local/bin
mkdir -p /usr/wip/math/multichoose/work/stage/usr/local/include/multichoose
install multichoose cmultichoose multipermute /usr/wip/math/multichoose/work/stage/usr/local/bin
install *.py /usr/wip/math/multichoose/work/stage/usr/local/bin
install *.h /usr/wip/math/multichoose/work/stage/usr/local/include/multichoose
strip /usr/wip/math/multichoose/work/stage/usr/local/bin/*e
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
===>  Installing for multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35
===>   Registering installation for multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35 as automatic
Installing multichoose-a35c94abd1b312fdcc10455f90b6e527c271bb35...
===>   freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc depends on file: /usr/local/include/multichoose/multichoose.h - found
===>   Returning to build of freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
===>   freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc depends on executable: gmake - found
===>   freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc depends on shared library: libbamtools.so - not found
===>  License MIT accepted by the user
===>   bamtools-2.4.0 depends on file: /usr/local/sbin/pkg - found
=> pezmaster31-bamtools-2.4.0-v2.4.0_GH0.tar.gz doesn't seem to exist in /usr/ports/distfiles/.
=> Attempting to fetch https://codeload.github.com/pezmaster31/bamtools/tar.gz/v2.4.0?dummy=/pezmaster31-bamtools-2.4.0-v2.4.0_GH0.tar.gz
fetch: https://codeload.github.com/pezmaster31/bamtools/tar.gz/v2.4.0?dummy=/pezmaster31-bamtools-2.4.0-v2.4.0_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/pezmaster31/bamtools/tar.gz/v2.4.0?dummy=/pezmaster31-bamtools-2.4.0-v2.4.0_GH0.tar.gz: size of remote file is not known
pezmaster31-bamtools-2.4.0-v2.4.0_GH0.tar.gz             0  B    0  Bps
===> Fetching all distfiles required by bamtools-2.4.0 for building
===>  Extracting for bamtools-2.4.0
=> SHA256 Checksum OK for pezmaster31-bamtools-2.4.0-v2.4.0_GH0.tar.gz.
===>  Patching for bamtools-2.4.0
===>  Applying FreeBSD patches for bamtools-2.4.0
/usr/bin/sed -i.bak -e 's|lib/bamtools|lib|g'  work/bamtools-2.4.0/src/api/CMakeLists.txt
===>   bamtools-2.4.0 depends on file: /usr/local/bin/cmake - found
===>  Configuring for bamtools-2.4.0
===>  Performing out-of-source build
/bin/mkdir -p /usr/wip/biology/bamtools/work/.build
-- The C compiler identification is Clang 3.4.1
-- The CXX compiler identification is Clang 3.4.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_CXX_FLAGS_DEBUG
CMAKE_C_FLAGS_DEBUG
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
LIB_DIR
THREADS_HAVE_PTHREAD_ARG

-- Build files have been written to: /usr/wip/biology/bamtools/work/.build
===>  Building for bamtools-2.4.0
Scanning dependencies of target APIHeaders
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[ 82%] Linking CXX static library /usr/wip/biology/bamtools/work/bamtools-2.4.0/lib/libjsoncpp.a
[ 82%] Built target jsoncpp
[ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
[ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
[ 85%] Linking CXX static library /usr/wip/biology/bamtools/work/bamtools-2.4.0/lib/libbamtools-utils.a
[ 85%] Built target BamTools-utils
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[ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
[ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
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[ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o
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[ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o
[ 99%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o
[100%] Linking CXX executable /usr/wip/biology/bamtools/work/bamtools-2.4.0/bin/bamtools
[100%] Built target bamtools_cmd
===>  Staging for bamtools-2.4.0
===>   Generating temporary packing list
[  0%] Built target SharedHeaders
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[  0%] Built target AlgorithmsHeaders
[ 38%] Built target BamTools
[ 76%] Built target BamTools-static
[ 80%] Built target jsoncpp
[ 85%] Built target BamTools-utils
[100%] Built target bamtools_cmd
Installing the project stripped...
-- Install configuration: "Release"
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/shared/bamtools_global.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/lib/libbamtools.so.2.4.0
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/lib/libbamtools.so
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/lib/libbamtools.a
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/api_global.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamAlgorithms.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamAlignment.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamAux.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamConstants.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamIndex.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamMultiReader.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamReader.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/BamWriter.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/IBamIODevice.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamConstants.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamHeader.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamProgram.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamProgramChain.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamReadGroup.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamReadGroupDictionary.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamSequence.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/SamSequenceDictionary.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/include/bamtools/api/algorithms/Sort.h
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/bin/bamtools-2.4.0
-- Installing: /usr/wip/biology/bamtools/work/stage/usr/local/bin/bamtools
-- Removed runtime path from "/usr/wip/biology/bamtools/work/stage/usr/local/bin/bamtools-2.4.0"
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
===>  Installing for bamtools-2.4.0
===>   Registering installation for bamtools-2.4.0 as automatic
Installing bamtools-2.4.0...
===>   freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc depends on shared library: libbamtools.so - found (/usr/local/lib/libbamtools.so)
===>   Returning to build of freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc
===>   freebayes-bf31341be12fa616fe1e43c8aef7a04108f7bfdc depends on shared library: libvcflib.so.1 - not found
===>  License MIT accepted by the user
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 for building
===>  Extracting for vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
=> SHA256 Checksum OK for outpaddling-vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73_GH0.tar.gz.
===>  Patching for vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on package: fastahack>=0 - not found
===>   fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155 for building
===>  Extracting for fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155
=> SHA256 Checksum OK for outpaddling-fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155_GH0.tar.gz.
===>  Patching for fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155
===>  Configuring for fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155
===>  Building for fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155
--- Fasta.o ---
--- split.o ---
--- Fasta.o ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing   -D_FILE_OFFSET_BITS=64 -c Fasta.cpp
--- split.o ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing   -D_FILE_OFFSET_BITS=64 -c split.cpp
--- Fasta.o ---
Fasta.cpp:90:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
--- disorder.o ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing   -D_FILE_OFFSET_BITS=64 -c disorder.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
--- FastaHack.o ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing   -D_FILE_OFFSET_BITS=64 -c FastaHack.cpp
--- Fasta.o ---
1 warning generated.
--- fastahack ---
--- libfastahack.a ---
--- fastahack ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing   -D_FILE_OFFSET_BITS=64 Fasta.o split.o disorder.o FastaHack.o -o fastahack
--- libfastahack.a ---
ar -rs libfastahack.a Fasta.o split.o disorder.o
ar: creating libfastahack.a
===>  Staging for fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155
===>   Generating temporary packing list
mkdir -p /usr/wip/biology/fastahack/work/stage/usr/local/bin
mkdir -p /usr/wip/biology/fastahack/work/stage/usr/local/include/fastahack
mkdir -p /usr/wip/biology/fastahack/work/stage/usr/local/lib
install fastahack /usr/wip/biology/fastahack/work/stage/usr/local/bin
install *.h /usr/wip/biology/fastahack/work/stage/usr/local/include/fastahack
install libfastahack.a /usr/wip/biology/fastahack/work/stage/usr/local/lib
strip /usr/wip/biology/fastahack/work/stage/usr/local/bin/fastahack
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
===>  Installing for fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155
===>   Registering installation for fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155 as automatic
Installing fastahack-18ed4b86ef962fa1b40f89b78625b2f271d9b155...
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on package: fastahack>=0 - found
===>   Returning to build of vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on package: filevercmp>=0 - not found
===>  License GPLv3 accepted by the user
===>   filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849 for building
===>  Extracting for filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849
=> SHA256 Checksum OK for outpaddling-filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849_GH0.tar.gz.
===>  Patching for filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849
===>  Configuring for filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849
===>  Building for filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849
--- filevercmp.o ---
--- main.o ---
--- filevercmp.o ---
cc -O2 -pipe  -fstack-protector -fno-strict-aliasing   -c filevercmp.c
--- main.o ---
cc -O2 -pipe  -fstack-protector -fno-strict-aliasing   -c main.c
--- filevercmp ---
--- libfilevercmp.a ---
--- filevercmp ---
cc -O2 -pipe  -fstack-protector -fno-strict-aliasing   -o filevercmp filevercmp.o main.o
--- libfilevercmp.a ---
ar -rs libfilevercmp.a filevercmp.o
ar: creating libfilevercmp.a
===>  Staging for filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849
===>   Generating temporary packing list
mkdir -p /usr/wip/sysutils/filevercmp/work/stage/usr/local/bin
mkdir -p /usr/wip/sysutils/filevercmp/work/stage/usr/local/include
mkdir -p /usr/wip/sysutils/filevercmp/work/stage/usr/local/lib
install filevercmp /usr/wip/sysutils/filevercmp/work/stage/usr/local/bin
install *.h /usr/wip/sysutils/filevercmp/work/stage/usr/local/include
install libfilevercmp.a /usr/wip/sysutils/filevercmp/work/stage/usr/local/lib
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
Warning: 'bin/filevercmp' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
===>  Installing for filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849
===>   Registering installation for filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849 as automatic
Installing filevercmp-261142f1529f6b7464f6ad96d0c77872ff919849...
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on package: filevercmp>=0 - found
===>   Returning to build of vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on package: fsom>=0 - not found
===>  License GPLv3 accepted by the user
===>   fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47 for building
===>  Extracting for fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47
=> SHA256 Checksum OK for outpaddling-fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47_GH0.tar.gz.
===>  Patching for fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47
===>  Configuring for fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47
===>  Building for fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47
--- fsom.o ---
--- split.o ---
--- fsom.o ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fomit-frame-pointer -ffast-math  -c fsom.c
--- split.o ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fomit-frame-pointer -ffast-math  -c split.cpp
--- fsom.o ---
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
--- main.o ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fomit-frame-pointer -ffast-math  -c main.cpp
--- libfsom.a ---
ar -rs libfsom.a fsom.o split.o
ar: creating libfsom.a
--- fsom ---
c++ -o fsom fsom.o split.o main.o -lm
===>  Staging for fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47
===>   Generating temporary packing list
mkdir -p /usr/wip/biology/fsom/work/stage/usr/local/bin
mkdir -p /usr/wip/biology/fsom/work/stage/usr/local/lib
install fsom /usr/wip/biology/fsom/work/stage/usr/local/bin
install libfsom.a /usr/wip/biology/fsom/work/stage/usr/local/lib
strip /usr/wip/biology/fsom/work/stage/usr/local/bin/fsom
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
===>  Installing for fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47
===>   Registering installation for fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47 as automatic
Installing fsom-23c8bb0b0a1de866ef05ed2be283f67bca4d2f47...
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on package: fsom>=0 - found
===>   Returning to build of vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on executable: multichoose - found
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on package: intervaltree>=0 - found
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on executable: gmake - found
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on shared library: libtabix.so.1 - not found
===>   tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7 for building
===>  Extracting for tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7
=> SHA256 Checksum OK for outpaddling-tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7_GH0.tar.xz.
===>  Patching for tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7
===>   tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===>  Configuring for tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7
===>  Building for tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7
--- tabix.o ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include  -fPIC -c tabix.cpp -Ihtslib
--- libtabix.a ---
--- libtabix.so.1 ---
--- libtabix.a ---
ar rs libtabix.a tabix.o
--- libtabix.so.1 ---
c++ -shared -Wl,-soname,libtabix.so.1 -o libtabix.so.1 tabix.o
--- libtabix.a ---
ar: creating libtabix.a
--- tabix++ ---
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include  -fPIC -o tabix++ main.cpp tabix.o -Ihtslib -L/usr/local/lib  -lhts -lpthread -lm -lz
===>  Staging for tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7
===>   Generating temporary packing list
mkdir -p /usr/wip/biology/tabixpp/work/stage/usr/local/bin
mkdir -p /usr/wip/biology/tabixpp/work/stage/usr/local/include
mkdir -p /usr/wip/biology/tabixpp/work/stage/usr/local/lib
install tabix++ /usr/wip/biology/tabixpp/work/stage/usr/local/bin
install *.hpp /usr/wip/biology/tabixpp/work/stage/usr/local/include
install libtabix.a libtabix.so.1 /usr/wip/biology/tabixpp/work/stage/usr/local/lib
strip /usr/wip/biology/tabixpp/work/stage/usr/local/bin/tabix++ /usr/wip/biology/tabixpp/work/stage/usr/local/lib/libtabix.so.1
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
===>  Installing for tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7
===>   Registering installation for tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7 as automatic
Installing tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7...
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on shared library: libtabix.so.1 - found (/usr/local/lib/libtabix.so.1)
===>   Returning to build of vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on shared library: libsw.so.1 - not found
===>   smithwaterman-8e667291798b785d698f0875e58da2710d740567 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by smithwaterman-8e667291798b785d698f0875e58da2710d740567 for building
===>  Extracting for smithwaterman-8e667291798b785d698f0875e58da2710d740567
=> SHA256 Checksum OK for outpaddling-smithwaterman-8e667291798b785d698f0875e58da2710d740567_GH0.tar.gz.
===>  Patching for smithwaterman-8e667291798b785d698f0875e58da2710d740567
===>   smithwaterman-8e667291798b785d698f0875e58da2710d740567 depends on executable: gmake - found
===>  Configuring for smithwaterman-8e667291798b785d698f0875e58da2710d740567
===>  Building for smithwaterman-8e667291798b785d698f0875e58da2710d740567
gmake[6]: Entering directory '/usr/wip/biology/smithwaterman/work/smithwaterman-8e667291798b785d698f0875e58da2710d740567'
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fPIC -c -o disorder.o disorder.cpp -I.
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fPIC -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I.
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fPIC -c -o Repeats.o Repeats.cpp -I.
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fPIC -c -o LeftAlign.o LeftAlign.cpp -I.
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fPIC -c -o IndelAllele.o IndelAllele.cpp -I.
LeftAlign.cpp:679:26: warning: '&&' within '||' [-Wlogical-op-parentheses]
&& (indel.insertion && indel.position == referenceSequence.size()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LeftAlign.cpp:679:26: note: place parentheses around the '&&' expression to silence this warning
&& (indel.insertion && indel.position == referenceSequence.size()
^
(                                                            )
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fPIC -c -o smithwaterman.o smithwaterman.cpp -I.
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -fPIC -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I.
1 warning generated.
c++ -O2 -pipe  -fstack-protector -fno-strict-aliasing smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o disorder.o -I. -o smithwaterman
ar rs libsw.a disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o
ar: creating libsw.a
c++ -shared -Wl,-soname,libsw.so.1 -o libsw.so.1 disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o
ld -r disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -o sw.o -L.
gmake[6]: Leaving directory '/usr/wip/biology/smithwaterman/work/smithwaterman-8e667291798b785d698f0875e58da2710d740567'
===>  Staging for smithwaterman-8e667291798b785d698f0875e58da2710d740567
===>   Generating temporary packing list
gmake[6]: Entering directory '/usr/wip/biology/smithwaterman/work/smithwaterman-8e667291798b785d698f0875e58da2710d740567'
mkdir -p /usr/wip/biology/smithwaterman/work/stage/usr/local/bin
mkdir -p /usr/wip/biology/smithwaterman/work/stage/usr/local/include/smithwaterman
mkdir -p /usr/wip/biology/smithwaterman/work/stage/usr/local/lib
install -c smithwaterman /usr/wip/biology/smithwaterman/work/stage/usr/local/bin
install -c *.h /usr/wip/biology/smithwaterman/work/stage/usr/local/include/smithwaterman
install -c libsw.a libsw.so.1 /usr/wip/biology/smithwaterman/work/stage/usr/local/lib
strip /usr/wip/biology/smithwaterman/work/stage/usr/local/bin/smithwaterman /usr/wip/biology/smithwaterman/work/stage/usr/local/lib/libsw.so.1
gmake[6]: Leaving directory '/usr/wip/biology/smithwaterman/work/smithwaterman-8e667291798b785d698f0875e58da2710d740567'
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
===>  Installing for smithwaterman-8e667291798b785d698f0875e58da2710d740567
===>   Registering installation for smithwaterman-8e667291798b785d698f0875e58da2710d740567 as automatic
Installing smithwaterman-8e667291798b785d698f0875e58da2710d740567...
===>   vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73 depends on shared library: libsw.so.1 - found (/usr/local/lib/libsw.so.1)
===>   Returning to build of vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
===>  Configuring for vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
===>  Building for vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73
gmake[4]: Entering directory '/usr/wip/biology/vcflib/work/vcflib-6451cf639cc7d735137218c4b08f597ba9dd6e73'
c++ -c -o src/Variant.o src/Variant.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC
c++ -c -o src/split.o src/split.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC
cc -O2 -pipe  -fstack-protector -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC   -c -o src/ssw.o src/ssw.c
src/Variant.cpp:214:5: warning: control may reach end of non-void function [-Wreturn-type]
}
^
src/Variant.cpp:336:5: warning: control may reach end of non-void function [-Wreturn-type]
}
^
src/Variant.cpp:370:5: warning: control may reach end of non-void function [-Wreturn-type]
}
^
src/Variant.cpp:408:5: warning: control may reach end of non-void function [-Wreturn-type]
}
^
c++ -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC   -c -o src/ssw_cpp.o src/ssw_cpp.cpp
mkdir -p bin
4 warnings generated.
ar rs libvcflib.a src/Variant.o src/split.o src/ssw.o src/ssw_cpp.o
c++ -shared -Wl,-soname,libvcflib.so.1 -o libvcflib.so.1 src/Variant.o src/split.o src/ssw.o src/ssw_cpp.o
ar: creating libvcflib.a
c++ src/vcfecho.cpp -o bin/vcfecho -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfaltcount.cpp -o bin/vcfaltcount -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfhetcount.cpp -o bin/vcfhetcount -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfhethomratio.cpp -o bin/vcfhethomratio -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
src/vcfhetcount.cpp:13:31: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare]
if (argc == 2 && (argv[1] == "-h" || argv[1] == "--help")) {
^  ~~~~
src/vcfhetcount.cpp:13:50: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare]
if (argc == 2 && (argv[1] == "-h" || argv[1] == "--help")) {
^  ~~~~~~~~
2 warnings generated.
c++ src/vcffilter.cpp -o bin/vcffilter -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcf2tsv.cpp -o bin/vcf2tsv -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfgenotypes.cpp -o bin/vcfgenotypes -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfannotategenotypes.cpp -o bin/vcfannotategenotypes -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
src/vcfgenotypes.cpp:51:32: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare]
if (g->c_str() == ".") {
^  ~~~
1 warning generated.
c++ src/vcfcommonsamples.cpp -o bin/vcfcommonsamples -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfremovesamples.cpp -o bin/vcfremovesamples -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfkeepsamples.cpp -o bin/vcfkeepsamples -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfsamplenames.cpp -o bin/vcfsamplenames -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfgenotypecompare.cpp -o bin/vcfgenotypecompare -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcffixup.cpp -o bin/vcffixup -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfclassify.cpp -o bin/vcfclassify -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfsamplediff.cpp -o bin/vcfsamplediff -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
src/vcfsamplediff.cpp:171:39: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (isHet(gtGermline) && isHomNonRef(gtSomatic) ||
^~~~~~~ ~~
src/vcfsamplediff.cpp:171:39: note: place parentheses around the '&&' expression to silence this warning
if (isHet(gtGermline) && isHomNonRef(gtSomatic) ||
^
(                                          )
src/vcfsamplediff.cpp:172:42: warning: '&&' within '||' [-Wlogical-op-parentheses]
isHomRef(gtGermline) && (isHet(gtSomatic) || isHomNonRef(gtSomatic))) {
~^~~~~~~~~~~~~~~~~~~~~~~~~~~
src/vcfsamplediff.cpp:172:42: note: place parentheses around the '&&' expression to silence this warning
isHomRef(gtGermline) && (isHet(gtSomatic) || isHomNonRef(gtSomatic))) {
^
(                                                                   )
src/vcfsamplediff.cpp:173:43: warning: '&&' within '||' [-Wlogical-op-parentheses]
if (!strict || strict && germlineAltCount == 0) {
~~ ~^~~~~~~~~~~~~~~~~~
src/vcfsamplediff.cpp:173:43: note: place parentheses around the '&&' expression to silence this warning
if (!strict || strict && germlineAltCount == 0) {
^
(                              )
c++ src/vcfremoveaberrantgenotypes.cpp -o bin/vcfremoveaberrantgenotypes -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
3 warnings generated.
c++ src/vcfrandom.cpp -o bin/vcfrandom -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfparsealts.cpp -o bin/vcfparsealts -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfstats.cpp -o bin/vcfstats -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfflatten.cpp -o bin/vcfflatten -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfprimers.cpp -o bin/vcfprimers -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfnumalt.cpp -o bin/vcfnumalt -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfcleancomplex.cpp -o bin/vcfcleancomplex -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfintersect.cpp -o bin/vcfintersect -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfannotate.cpp -o bin/vcfannotate -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfallelicprimitives.cpp -o bin/vcfallelicprimitives -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfoverlay.cpp -o bin/vcfoverlay -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfaddinfo.cpp -o bin/vcfaddinfo -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfkeepinfo.cpp -o bin/vcfkeepinfo -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfkeepgeno.cpp -o bin/vcfkeepgeno -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfafpath.cpp -o bin/vcfafpath -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfcountalleles.cpp -o bin/vcfcountalleles -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcflength.cpp -o bin/vcflength -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector -fno-strict-aliasing  -I/usr/local/include/smithwaterman  -I/usr/local/include/multichoose  -I/usr/local/include/filevercmp  -I/usr/local/include/fastahack  -I/usr/local/include/intervaltree -D_FILE_OFFSET_BITS=64 -fPIC -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm
c++ src/vcfdistance.cpp -o bin/vcfdistance -I/usr/local/includ


The class name of Table title have unexpected ForwardRef prefix.

Describe the bug
The wrappers of title, actions and etc. on the toolbar are having unexpected class names prefix as ForwardRef(MTableToolbarRef).
To Reproduce

Kindly open the sandbox below.
Inspect the table title
Check the table title field HTML on the developer tools.
See "ForwardRef(MTableToolbarRef)-title-9"  class.

Sandbox
Expected behavior
Instead of "ForwardRef(MTableToolbarRef)" it should have "MTableToolbar" prefix on each part's class name
Screenshots

Desktop :

OS: [Window 10]
Browser [chrome]
Version [96.0.4]

Version:
@material-table/core : 4.3.11
@material-ui/core : 4.12.3

Thank you for starting this issue @salmanorak, I'm also facing this issue.

Since these components are using ForwardRef, is this expected behavior? Or should that not show up in the rendered class name when using ForwardRef?
I'm asking because I do not know if this is expected or not when using ForwardRef.

@oze4 This is not expected behaviour, you shouldn't see the ForwardRef in the class name, though technically it doesn't  actually cause any issues as the class has the correct styles.
I had a quick look and changing
export default withStyles(styles)(MTableToolbarRef);

to
export default withStyles(styles, { name: 'MTableToolbar' })(MTableToolbarRef);

Results in the classes having the MTableToolbar prefix:

@ymor thank you so much for figuring this out! I will make the necessary changes and publish a new version.

Published v4.3.14

thanks a lot @oze4  for your quick handling.
Take care and stay healty.

@oze4
I have realized that The same issue is also existing in another field. We have the same issue on MTableHeader.

ForwardRef(MTableHeaderRef)

I have checked all markup but couldn't find any other instance except the ForwardRef(MTableHeaderRef). But please do check the code base for possible other instances.

#441


synchronized with the root

I have merged the master branch and my local repository, i guess we don't have a conflict in merging out repositories now.

I'm closing this PR for now since it seems that there are still a few items we need to work through before this content gets back into the main branch. I think if nothing else, I'll try to cherry-pick some of the 555-timer functions off into something of a new module that I'm working on in the develop branch.
Thank you, again!


[Bug] tests/python/contrib/test_hexagon/topi/test_avg_pool2d_slice.py causes Segmentation fault

It only happens on HDK board due to missing symbols.

This is resolved after upgrading the firmware on HDK boards.


Inconsistent universe annotation silently elaborated and accepted

This code:
val last : (#a:Type u#a) -> l:(list a){Cons? l} -> Tot a
let rec last #a l =
  match l with
  | [hd] -> hd
  | _::tl -> last #a tl

Is checked by F* into:
visible let rec last <uu___244> :
    #a: Type u#uu__univ_bvar_0 ->
    l: Prims.list u#uu__univ_bvar_1 a {Prims.b2t (Cons? u#uu__univ_bvar_2 #a l)}
  -> Prims.Tot u#uu__univ_bvar_2 a = fun #a l ->
  (match l with
    | Prims.Cons #_ hd (Prims.Nil #_) -> hd
    | Prims.Cons #_ _ tl -> Last.last u#0 #a tl)
  <:
  a

Note how the function is universe polymorphic, but is instead applied to u#0 in the recursive call. The uvar actually remains unresolved, and a line in FStar.TypeChecker.Normalize.norm_universe sets it to 0:
https://github.com/FStarLang/FStar/blob/272994209aaef5afd439a684eca389b952364525/src/typechecker/FStar.TypeChecker.Normalize.fs#L187-L191
I noticed this while trying to remove that shady line.

Seems related to #604 since it works correctly without a val.

Tracked this down to lookup_qname which was calling inst_tscheme on recursive definitions, when it should have really been returning the exact same set of names on which the function is being defined. Then, typechecking last was returning something like last<?1> of type #a:Type u#some_univ_name -> l:list a{Cons? l} -> a, with ?1 totally unrelated. This happens since last is pushed into the environment as a Binding_lid which is already instantiated, so calling inst_tscheme on it does nothing on its type, but corrupts the concrete universes.

I fixed this on master already, but leaving it open since 1) I couldn't really add a regression test, since it was silently succeeding anyway; and 2) for better tracking of universe uvars.


npm run eject errors on application run

Hi, I am trying to add scss support on create-react-app. First I run the eject command to change webpack config file:
npm run eject
Then I have added some other npm to support scss.
npm install sass-loader node-sass --save-dev
After that when I run npm run start, the project will stop because of errors.
Error: Cannot find module 'chalk'
After I have install "chalk", I had then another error "Error: Cannot find module 'webpack'". After I have install webpack I had another error webpack-dev-server module cannot find.
How to resolve that ?

I run "npm i" and it worked :)


Clarify use of (SAML) token formats vs grants

continuation of discussion in #110 . Discussion summary inline below:
@joostreuzel : SAML tokens should be send to resource servers in the same way other tokens are send: as opaque bearer tokens.
@joostreuzel : IMHO, the specification should be more clear on the SAML token format. Is this format really necessary? If so, is it also possible to generate SAML tokens from e.g. the code credential flow. As such, I think SAML tokens are independent of SAML grants and should be treated a separate options.
@msmock : The saml option shall not be confused with the saml grant. That‘s right. IUA currently does not support the saml grant, but allows to use saml as client authentication. The saml token option is just for to use the usual XUA assertion as access token. And yes, we need the Saml token option in the Swiss  EPR.
@joostreuzel : The confusion with the SAML token arises from section <IP_ADDRESS>. This section indicates the use of SAML2 grant types. The text mentions that RFC7522 is about "issuing and using SAML 2.0 assertions as access token", which is not true. RFC7522 merely speaks about using SAML Assertions as credentials (grants) to obtain an access token. Nothing is said about the access token structure.
@joostreuzel proposal:

Introduce a separate section for the Get Authorization Token response. The request is different for different grants, but the response is the same in structure
Move the SAML Assertion, as well as JWT token format to the message semantics section of the token response section
Remove the section on token types from the Authorization Client. Tokens are opaque to clients. All tokens to be transmitted as Bearer tokens.
Consequently: remove the use of IHE-SAML as Authorization header, use Bearer only (see #84)
As part of the token handling behavior by the resource server refer to the token formats as described in the token response message and indicate the rules on how to deal with them.

@msmock Question: In the Swiss EPR case (or more general) how do you deal with the token formats? Does the authorization server generate SAML-based access tokens for all resource servers, or does it switch between SAML and JWT formats depending on the intended audience of the token?
Moreover, are the service endpoints that accept the SAML tokens expected to be fully IUA conformant, or are the SAML tokens primarily used to be compatible with existing systems that understand the SAML constructs only?
Reason for asking is that I'm wondering how service and server implementations in your case will deal with the different token formats, especially when configured in a specific environment with "legacy" systems.

I took the liberty to include the suggestions as provided above in the document text. These have been  merged via #112.

@msmock https://github.com/msmock : The saml option shall not be confused with the saml grant. That‘s right. IUA currently does not support the saml grant, but allows to use saml as client authentication. The saml token option is just for to use the usual XUA assertion as access token. And yes, we need the Saml token option in the Swiss EPR.

The text only points to the section of RFC 7522 which defines the way the XUA token shall be encoded. If that’s confusing we must copy all of the text on SAML token encoding from RFC 7522 to our current working version. I thought about this when working on the document but decided not to change the reference to the encoding in RFC 7522, for better readability.

The IUA and MHD in the swiss EPR is currently in a trial implementation state. The service endpoints are IUA compliant and must support the JWT option. The reason to use the IUA SAML option is an advantage for the Authorization Clients (primary systems).
In Switzerland the vendors already implemented the XUA Get Authorization Token transaction to get the XUA token and can incorporate that to RESTful calls. So far no Authorization server supports the SAML token option, but all Resource Server do (or can do with little effort), since by law they must support XUA and policy enforcement using a XUA token.

On 6 Oct 2020, at 12:00, joostreuzel<EMAIL_ADDRESS>wrote:
@msmock https://github.com/msmock Question: In the Swiss EPR case (or more general) how do you deal with the token formats? Does the authorization server generate SAML-based access tokens for all resource servers, or does it switch between SAML and JWT formats depending on the intended audience of the token?
Moreover, are the service endpoints that accept the SAML tokens expected to be fully IUA conformant, or are the SAML tokens primarily used to be compatible with existing systems that understand the SAML constructs only?
Reason for asking is that I'm wondering how service and server implementations in your case will deal with the different token formats, especially when configured in a specific environment with "legacy" systems.
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xt only points to the section of RFC 7522 which defines the way the XUA token shall be encoded. If that’s confusing we must copy all of the text on SAML token encoding from RFC 7522 to our current working version. I thought about this when working on the document but decided not to change the reference to the encoding in RFC 7522, for better reada

Understood. I will see that this logic is kept in my edits.

Copied the serialization requirements from RFC7522 (with reference to the RFC) to the document in 50daa2c2a4077d04ed972c5d5bbf4e4d436cab3a


Plugin 'powerline/fonts' hangs indefinitely on BundleInstall

When executing BundleInstall, it gets to powerline/fonts and just hangs. Adding UnBundle 'powerline/fonts' to .vimrc.bundles.locale breaks spf13 in all sorts of interesting ways.
Any idea why it's hanging? Ubuntu 14.04, have been using spf13 for a while now, just recently pulled from the 3.0 branch and trying to add a new plugin.

Fixed it like this:
UnBundle 'vim-airline/vim-airline'
UnBundle 'vim-airline/vim-airline-themes'
UnBundle 'powerline/fonts

Not a real fix though, because I do want Airline and the powerline fonts (and it was all working fine before this latest pull).


linkage_checker: skip broken linkage in Julia

[x] Have you followed the guidelines in our Contributing document?
[X] Have you checked to ensure there aren't other open Pull Requests for the same change?
[x] Have you added an explanation of what your changes do and why you'd like us to include them?
[ ] Have you written new tests for your changes? Here's an example.

[x] Have you successfully run brew typecheck with your changes locally?
[ ] Have you successfully run brew tests with your changes locally?

Looking into a way to avoid Julia linkage errors since it uses its own dylib lookup logic which brew considers broken linkage.
Seemed to be easier approach rather than trying to inject unneeded RPATHs into the binary that Julia doesn't want.
Example for Julia:
{
  "julia": "share/julia/compiled/**/*"
}

Need to try out a few more things and check on Linux code path.

Can you talk about what's broken about Julia currently? We already have it shipped in homebrew-core with passing linkage.
I feel quite strongly that brew linkage should never return false positives, so if it is that is concerning. I know the RPATH part of it is debated (which is why it has never graduated from a warning) but the broken linkage one is another story.
We did have a DSL allowlist in the past but we removed it because we ended up fixing the issues.
Is there anything except Julia that would use this? If it's only Julia we might as well hardcode in share/julia/compiled as that's an unusual path to be putting binaries anyway.

Can you talk about what's broken about Julia currently? We already have it shipped in homebrew-core with passing linkage.

We shipped it with broken linkage when check was just a warning - https://github.com/Homebrew/homebrew-core/pull/173754/commits/cb36837eca49200b31ff45e96d3ea01788a0b15d
The Linux broken linkage covers the same failure as macOS missing RPATHs. It's just that the missing RPATHs are detected by finding @rpath. We could classify Linux shared libraries with non-resolvable NEEDED libraries and without RPATH/RUNPATH as missing, but it could also just be broken.

Is there anything except Julia that would use this? If it's only Julia we might as well hardcode in share/julia/compiled as that's an unusual path to be installing binaries to anyway.

Not sure about others. We could hardcode in Julia. Right now, the dylibs in that directory are not intended to be used with native dynamic loader which is why they trigger linkage error. I think they are run through Julia's loader instead.

Not sure about Linux - I would have expected that to fail.

Currently it does fail so probably fixed (or at least elevated from warning), e.g.

https://github.com/Homebrew/homebrew-core/pull/182774/files
https://github.com/Homebrew/homebrew-core/pull/183057/files

This linkage check runs even when you are running brew install. audit_exceptions is not available under the API so should not be used to make hard-failing linkage checks pass. Tests that cannot achieve 100% accuracy must be placed under strict mode or relocated to FormulaCellarChecks used by brew audit. So we should not add an allowlist to broken_dylibs as that is checked under non-strict mode.

I guess easiest path for now is the hardcoding of Julia. Moving it to brew audit may be better in long run.

On topic of Julia but unrelated to this PR, it may be nice to detect symlinks to other formulae and use that to avoid some "Dependencies with no linkage". Julia does this for most dependencies thus we get:
Dependencies with no linkage:
  ca-certificates
  gmp
  libnghttp2
  libssh2
  mpfr
  openblas
  openlibm

❯ eza -1 $(brew --prefix julia)/lib/julia/ | rg ' -> \.\.'
libatomic.1.dylib -> ../../../../../opt/gcc/lib/gcc/current/libatomic.1.dylib
libblastrampoline.dylib -> ../../../../../opt/libblastrampoline/lib/libblastrampoline.5.dylib
libcurl.dylib -> ../../../../../opt/curl/lib/libcurl.4.dylib
libgcc_s.1.1.dylib -> ../../../../../opt/gcc/lib/gcc/current/libgcc_s.1.1.dylib
libgfortran.5.dylib -> ../../../../../opt/gcc/lib/gcc/current/libgfortran.5.dylib
libgit2.dylib -> ../../../../../opt/libgit2/lib/libgit2.1.8.dylib
libgmp.dylib -> ../../../../../opt/gmp/lib/libgmp.10.dylib
libgomp.1.dylib -> ../../../../../opt/gcc/lib/gcc/current/libgomp.1.dylib
libmbedcrypto.dylib -><EMAIL_ADDRESS>libmbedtls.dylib -><EMAIL_ADDRESS>libmbedx509.dylib -><EMAIL_ADDRESS>libmpfr.dylib -> ../../../../../opt/mpfr/lib/libmpfr.6.dylib
libnghttp2.dylib -> ../../../../../opt/libnghttp2/lib/libnghttp2.14.dylib
libopenblas.dylib -> ../../../../../opt/openblas/lib/libopenblas.0.dylib
libopenlibm.dylib -> ../../../../../opt/openlibm/lib/libopenlibm.4.dylib
libpcre2-8.dylib -> ../../../../../opt/pcre2/lib/libpcre2-8.0.dylib
libquadmath.0.dylib -> ../../../../../opt/gcc/lib/gcc/current/libquadmath.0.dylib
libssh2.dylib -> ../../../../../opt/libssh2/lib/libssh2.1.dylib
libssp.0.dylib -> ../../../../../opt/gcc/lib/gcc/current/libssp.0.dylib
libstdc++.6.dylib -> ../../../../../opt/gcc/lib/gcc/current/libstdc++.6.dylib

On topic of Julia but unrelated to this PR, it may be nice to detect symlinks to other formulae and use that to avoid some "Dependencies with no linkage".

It's nice, but doesn't seem worth the extra code since no other formula does this.

It's nice, but doesn't seem worth the extra code since no other formula does this.

It would work for things like ca-certificates which we always symlink pem file from.
Maybe also ppsspp though we skip linkage check as molten-vk has an executable.

Also related would be header usage (e.g. boost, eigen, etc) and having a section that details that these deps are in use even though they are not linked libs.

Thanks @cho-m!