[PATCH 0/2] Update mash and capnproto.

Done

Details

4 participants

Eric Bavier
Leo Famulari
Ludovic Courtès
Christopher Baines

Owner: unassigned

Submitted by: Christopher Baines

Severity: normal

Debbugs page

Christopher Baines wrote 6 years ago

[PATCH 0/2] Update mosh and capnproto.

Recipients:(address . guix-patches@gnu.org)

Message-ID:87va58hdt1.fsf@cbaines.net

Update the mosh and capnproto packages. I want to update capnproto, and
I updated mosh along with it, as initially it failed to build with the
newer capnproto version.

Christopher Baines (2):
  gnu: mash: Update to 2.1.
  gnu: capnproto: Update to 0.7.0.

 gnu/packages/bioinformatics.scm | 14 +++++++++++---
 gnu/packages/serialization.scm  | 10 ++++++++--
 2 files changed, 19 insertions(+), 5 deletions(-)

Christopher Baines wrote 6 years ago

[PATCH 2/2] gnu: capnproto: Update to 0.7.0.

Recipients:(address . 33308@debbugs.gnu.org)

Message-ID:20181107195654.22832-2-mail@cbaines.net

* gnu/packages/serialization.scm (capnproto)[version]: Change to 0.7.0.
[source]: Update sha256 hash.
[arguments]: Add new 'use-tmp-for-tempory-files phase, to patch some tests to
use /tmp for tempory files, as the default /var/tmp directory doesn't exist.
---
 gnu/packages/serialization.scm | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

Toggle diff (37 lines)diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 40b3d1bae0..77fd070bc7 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -314,7 +314,7 @@ it a convenient format to store user input files.")
 (define-public capnproto
   (package
     (name "capnproto")
-    (version "0.6.1")
+    (version "0.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -322,7 +322,7 @@ it a convenient format to store user input files.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "010s9yhq4531wvdfrdf2477zswhck6cjfby79w73rff3v06090l0"))))
+                "0hfdnhlbskagzgvby8wy6lrxj53zfzpfqimbhga68c0ji2yw1969"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -332,6 +332,12 @@ it a convenient format to store user input files.")
              ;; Workaround for test that tries to resolve port name from
              ;; /etc/services, which is not present in build environment.
              (substitute* "src/kj/async-io-test.c++" ((":http") ":80"))
+             #t))
+         (add-before 'check 'use-tmp-for-tempory-files
+           (lambda _
+             (substitute* "src/kj/filesystem-disk-test.c++"
+               (("VAR\\_TMP \"/var/tmp\"")
+                "VAR_TMP \"/tmp\""))
              #t)))))
     (home-page "https://capnproto.org")
     (synopsis "Capability-based RPC and serialization system")
-- 
2.19.1

Christopher Baines wrote 6 years ago

[PATCH 1/2] gnu: mash: Update to 2.1.

Recipients:(address . 33308@debbugs.gnu.org)

Message-ID:20181107195654.22832-1-mail@cbaines.net

I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore,

update it, and tweak the compilation to allow it to build with 0.7. The

package also builds with the current version of capnproto. I got the idea of

changing the c++ version from here [1].

1: https://github.com/marbl/Mash/issues/98

* gnu/packages/bioinformatics.scm (mash)[version]: Change to 2.1.

[source]: Update sha256 hash.

[arguments]: Add new use-c++14 phase, to patch source to build using c++14.

---

gnu/packages/bioinformatics.scm | 14 +++++++++++---

1 file changed, 11 insertions(+), 3 deletions(-)

Toggle diff (41 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9f0b8025da..93503d82b8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3977,7 +3977,7 @@ sequences).")
 (define-public mash
   (package
     (name "mash")
-    (version "2.0")
+    (version "2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3986,7 +3986,7 @@ sequences).")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
+                "0d5m9wx1bspa5vwikazdbar4i0h6b20lzjjl1icfyl66sy1q9v9q"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -4012,7 +4012,15 @@ sequences).")
                (("^#include \"kseq\\.h\"")
                 "#include \"htslib/kseq.h\""))
              #t))
-         (add-after 'fix-includes 'autoconf
+         (add-after 'fix-includes 'use-c++14
+           (lambda _
+             ;; capnproto 0.7 requires c++14 to build
+             (substitute* "configure.ac"
+               (("c\\+\\+11") "c++14"))
+             (substitute* "Makefile.in"
+               (("c\\+\\+11") "c++14"))
+             #t))
+         (add-after 'use-c++14 'autoconf
            (lambda _ (zero? (system* "autoconf")))))))
     (native-inputs
      `(("autoconf" ,autoconf)
-- 
2.19.1

Leo Famulari wrote 6 years ago

Re: [bug#33308] [PATCH 0/2] Update mosh and capnproto.

Recipients:(name . Christopher Baines)(address . mail@cbaines.net)(address . 33308@debbugs.gnu.org)

Message-ID:20181107201919.GA29144@jasmine.lan

On Wed, Nov 07, 2018 at 07:45:30PM +0000, Christopher Baines wrote:

Toggle quote (4 lines)

> Update the mosh and capnproto packages. I want to update capnproto, and

> I updated mosh along with it, as initially it failed to build with the

> newer capnproto version.

I got excited about a new release of mosh (the mobile shell). You mean

mash, right? :)

Eric Bavier wrote 6 years ago

Re: [bug#33308] [PATCH 1/2] gnu: mash: Update to 2.1.

Recipients:(name . Christopher Baines)(address . mail@cbaines.net)(address . 33308@debbugs.gnu.org)

Message-ID:20181107212327.2b3f7ded@centurylink.net

On Wed, 7 Nov 2018 19:56:53 +0000

Christopher Baines <mail@cbaines.net> wrote:

Toggle quote (3 lines)

> * gnu/packages/bioinformatics.scm (mash)[version]: Change to 2.1.

> [source]: Update sha256 hash.

I think here we typically just say "(mash)[source]: Upgrade to 2.1."

Toggle quote (22 lines)> [arguments]: Add new use-c++14 phase, to patch source to build using c++14.
> ---
>  gnu/packages/bioinformatics.scm | 14 +++++++++++---
>  1 file changed, 11 insertions(+), 3 deletions(-)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 9f0b8025da..93503d82b8 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -4012,7 +4012,15 @@ sequences).")
>                 (("^#include \"kseq\\.h\"")
>                  "#include \"htslib/kseq.h\""))
>               #t))
> -         (add-after 'fix-includes 'autoconf
> +         (add-after 'fix-includes 'use-c++14
> +           (lambda _
> +             ;; capnproto 0.7 requires c++14 to build
> +             (substitute* "configure.ac"
> +               (("c\\+\\+11") "c++14"))
> +             (substitute* "Makefile.in"
> +               (("c\\+\\+11") "c++14"))

I believe the configure.ac patch is sufficient for us here, since the

compile steps will pick up the CPPFLAGS set there. Too bad the

configure.ac is written so poorly... :( one should be able to just

pass "CPPFLAGS=-std=c++14" to `make`.

Toggle quote (4 lines)

> + #t))

> + (add-after 'use-c++14 'autoconf

> (lambda _ (zero? (system* "autoconf")))))))

Maybe you could also update this step to use 'invoke'.

Thanks,

`~Eric

Ludovic Courtès wrote 6 years ago

Re: [bug#33308] [PATCH 2/2] gnu: capnproto: Update to 0.7.0.

Recipients:(name . Christopher Baines)(address . mail@cbaines.net)(address . 33308@debbugs.gnu.org)

Message-ID:875zx4wp2p.fsf@gnu.org

Hello,

Christopher Baines <mail@cbaines.net> skribis:

Toggle quote (5 lines)

> * gnu/packages/serialization.scm (capnproto)[version]: Change to 0.7.0.

> [source]: Update sha256 hash.

> [arguments]: Add new 'use-tmp-for-tempory-files phase, to patch some tests to

> use /tmp for tempory files, as the default /var/tmp directory doesn't exist.

I’d suggest moving the /var/tmp explanation in a comment but otherwise

LGTM, thanks!

Ludo’.

Christopher Baines wrote 6 years ago

[PATCH v2 2/2] gnu: capnproto: Update to 0.7.0.

Recipients:(address . 33308@debbugs.gnu.org)

Message-ID:20181126190433.25295-2-mail@cbaines.net

* gnu/packages/serialization.scm (capnproto): Update to 0.7.0.
[arguments]: Add new 'use-tmp-for-tempory-files phase.
---
 gnu/packages/serialization.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

Toggle diff (39 lines)diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 2df0ce1364..2d61f7451b 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -306,7 +306,7 @@ it a convenient format to store user input files.")
 (define-public capnproto
   (package
     (name "capnproto")
-    (version "0.6.1")
+    (version "0.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -314,7 +314,7 @@ it a convenient format to store user input files.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "010s9yhq4531wvdfrdf2477zswhck6cjfby79w73rff3v06090l0"))))
+                "0hfdnhlbskagzgvby8wy6lrxj53zfzpfqimbhga68c0ji2yw1969"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -324,6 +324,14 @@ it a convenient format to store user input files.")
              ;; Workaround for test that tries to resolve port name from
              ;; /etc/services, which is not present in build environment.
              (substitute* "src/kj/async-io-test.c++" ((":http") ":80"))
+             #t))
+         (add-before 'check 'use-tmp-for-tempory-files
+           (lambda _
+             ;; Use /tmp for tempory files, as the default /var/tmp directory
+             ;; doesn't exist.
+             (substitute* "src/kj/filesystem-disk-test.c++"
+               (("VAR\\_TMP \"/var/tmp\"")
+                "VAR_TMP \"/tmp\""))
              #t)))))
     (home-page "https://capnproto.org")
     (synopsis "Capability-based RPC and serialization system")
-- 
2.19.2

Christopher Baines wrote 6 years ago

[PATCH v2 1/2] gnu: mash: Fix build with capnproto 0.7.

Recipients:(address . 33308@debbugs.gnu.org)

Message-ID:20181126190433.25295-1-mail@cbaines.net

I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore,

tweak the compilation to allow it to build with 0.7. The package also builds

with the current version of capnproto. I got the idea of changing the c++

version from here [1].

1: https://github.com/marbl/Mash/issues/98

* gnu/packages/bioinformatics.scm (mash)[arguments]: Add new use-c++14 phase.

---

gnu/packages/bioinformatics.scm | 8 ++++++++

1 file changed, 8 insertions(+)

Toggle diff (21 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 782af294e0..571d85aed7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4018,6 +4018,14 @@ sequences).")
                             "src/mash/CommandScreen.cpp")
                (("^#include \"kseq\\.h\"")
                 "#include \"htslib/kseq.h\""))
+             #t))
+         (add-after 'fix-includes 'use-c++14
+           (lambda _
+             ;; capnproto 0.7 requires c++14 to build
+             (substitute* "configure.ac"
+               (("c\\+\\+11") "c++14"))
+             (substitute* "Makefile.in"
+               (("c\\+\\+11") "c++14"))
              #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
-- 
2.19.2

Christopher Baines wrote 6 years ago

(no subject)

Recipients:(address . control@debbugs.gnu.org)

Message-ID:87sgznabqt.fsf@cbaines.net

retitle 33308 [PATCH 0/2] Update mash and capnproto.

thanks

Christopher Baines wrote 6 years ago

Re: [bug#33308] [PATCH 0/2] Update mosh and capnproto.

Recipients:(name . Leo Famulari)(address . leo@famulari.name)(address . 33308@debbugs.gnu.org)

Message-ID:87r2f7abej.fsf@cbaines.net

Leo Famulari <leo@famulari.name> writes:

Toggle quote (8 lines)

> On Wed, Nov 07, 2018 at 07:45:30PM +0000, Christopher Baines wrote:

>> Update the mosh and capnproto packages. I want to update capnproto, and

>> I updated mosh along with it, as initially it failed to build with the

>> newer capnproto version.

> I got excited about a new release of mosh (the mobile shell). You mean

> mash, right? :)

Yep, sorry about that, I've fixed the title of the bug now.

Christopher Baines wrote 6 years ago

Re: [bug#33308] [PATCH 2/2] gnu: capnproto: Update to 0.7.0.

Recipients:(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 33308@debbugs.gnu.org)

Message-ID:87pnurabc4.fsf@cbaines.net

Ludovic Courtès <ludo@gnu.org> writes:

Toggle quote (12 lines)> Hello,
>
> Christopher Baines <mail@cbaines.net> skribis:
>
>> * gnu/packages/serialization.scm (capnproto)[version]: Change to 0.7.0.
>> [source]: Update sha256 hash.
>> [arguments]: Add new 'use-tmp-for-tempory-files phase, to patch some tests to
>> use /tmp for tempory files, as the default /var/tmp directory doesn't exist.
>
> I’d suggest moving the /var/tmp explanation in a comment but otherwise
> LGTM, thanks!

Great, I've done this now, and sent some updated patches.

Christopher Baines wrote 6 years ago

Re: [bug#33308] [PATCH 1/2] gnu: mash: Update to 2.1.

Recipients:(name . Eric Bavier)(address . ericbavier@centurylink.net)(address . 33308@debbugs.gnu.org)

Message-ID:87o9abaay9.fsf@cbaines.net

Eric Bavier <ericbavier@centurylink.net> writes:

Toggle quote (9 lines)

> On Wed, 7 Nov 2018 19:56:53 +0000

> Christopher Baines <mail@cbaines.net> wrote:

>> * gnu/packages/bioinformatics.scm (mash)[version]: Change to 2.1.

>> [source]: Update sha256 hash.

> I think here we typically just say "(mash)[source]: Upgrade to 2.1."

Ok, I've sent a new set of patches now, and updated the commit messages.

Toggle quote (27 lines)>> [arguments]: Add new use-c++14 phase, to patch source to build using c++14.
>> ---
>>  gnu/packages/bioinformatics.scm | 14 +++++++++++---
>>  1 file changed, 11 insertions(+), 3 deletions(-)
>>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 9f0b8025da..93503d82b8 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -4012,7 +4012,15 @@ sequences).")
>>                 (("^#include \"kseq\\.h\"")
>>                  "#include \"htslib/kseq.h\""))
>>               #t))
>> -         (add-after 'fix-includes 'autoconf
>> +         (add-after 'fix-includes 'use-c++14
>> +           (lambda _
>> +             ;; capnproto 0.7 requires c++14 to build
>> +             (substitute* "configure.ac"
>> +               (("c\\+\\+11") "c++14"))
>> +             (substitute* "Makefile.in"
>> +               (("c\\+\\+11") "c++14"))
>
> I believe the configure.ac patch is sufficient for us here, since the
> compile steps will pick up the CPPFLAGS set there.  Too bad the
> configure.ac is written so poorly... :(  one should be able to just
> pass "CPPFLAGS=-std=c++14" to `make`.

I tried removing the Makefile.in change, but it didn't work for some

reason.

Toggle quote (6 lines)

>> + #t))

>> + (add-after 'use-c++14 'autoconf

>> (lambda _ (zero? (system* "autoconf")))))))

> Maybe you could also update this step to use 'invoke'.

This patch has now turned in to just fixing the package for the newer
version of capnproto, as Ricardo did the upgrade a few weeks ago. This
particular stage was removed in
e35dce017090685d07aedf10c9899c0cdcc70d9e.

Thanks for your comments Eric :)

Christopher Baines wrote 6 years ago

Re: [bug#33308] [PATCH v2 2/2] gnu: capnproto: Update to 0.7.0.

Recipients:(address . 33308-done@debbugs.gnu.org)

Message-ID:87sgzbogq5.fsf@cbaines.net

I've now gone ahead and pushed these two patches [1]. Thanks for taking

a look :)

1: As 9c5f4b82bb0ed6a0447a68f9cb18c4da5f692acf and

9c5f4b82bb0ed6a0447a68f9cb18c4da5f692acf

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