[bug#37988] [PATCH 0/6] Add flowWorkspace from BioConductor

[bug#37988] [PATCH 0/6] Add flowWorkspace from BioConductor

[zimoun]

Dear,

The aim of this serie is to add the package flowWorkspace.

It is important to notice that the package RProtobuflib [1] from BioConductor
is not packaged using the correct convention.  RProtobuflib includes its
dependency protobuf-2.6.0 as an archive tgz and compiles it using its
./configure [2].  Therefore, the file ./configure from the unarchived
protobuf-2.6.0 needs to be patched to apply the correct shebang.

It is clearly unconventional and we should distribute our own version of
RProtobuflib using the correct way i.e., packaging protobuf-2.6.0.  However,
do we want to diverge to the official BioConductor and add maintenance burden
when we are not fully able to already package all the BioConductor archive?


All the best,
simon


[1] https://bioconductor.org/packages/release/bioc/html/RProtoBufLib.html
[2] https://github.com/RGLab/RProtoBufLib/blob/trunk/configure#L2860-L2889



zimoun (6):
  gnu: Add r-idpmisc.
  gnu: Add r-flowviz.
  gnu: Add r-rprotobuflib.
  gnu: Add r-cytolib.
  gnu: Add r-ncdfflow.
  gnu: Add r-flowworkspace.

 gnu/packages/bioconductor.scm | 173 ++++++++++++++++++++++++++++++++++
 gnu/packages/cran.scm         |  30 ++++++
 2 files changed, 203 insertions(+)

-- 
2.23.0

[bug#37988] [PATCH 1/6] gnu: Add r-idpmisc.

[zimoun]

* gnu/packages/cran.scm (r-idpmisc): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b16b96dc77..f47eafc3bb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16,6 +16,7 @@
 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
+;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -15653,3 +15654,32 @@ unique identifiers, and whether it is a certain length.  In addition,
 files and to efficiently import multiple tabular data files into one
 data.table.")
     (license license:gpl3)))
+
+(define-public r-idpmisc
+  (package
+    (name "r-idpmisc")
+    (version "1.1.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "IDPmisc" version))
+       (sha256
+        (base32
+         "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd"))))
+    (properties
+     `((upstream-name . "IDPmisc")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)))
+    (home-page "https://cran.r-project.org/web/packages/IDPmisc")
+    (synopsis "Miscellaneous tools of Institute of Data Analyses and Process Design")
+    (description "This package provides different high-level graphics
+functions for displaying large datasets and circular data in a very flexible
+way, finding local maxima, brewing color ramps, drawing nice arrows, zooming
+2D-plots, creating figures with differently colored margin and plot region.
+In addition, the package contains auxiliary functions for data manipulation
+like omitting observations with irregular values or selecting data by logical
+vectors, which include NAs.  Other functions are especially useful in
+spectroscopy and analyses of environmental data: robust baseline fitting,
+finding peaks in spectra, converting humidity measures.")
+    (license license:gpl3+)))
-- 
2.23.0

[bug#37988] [PATCH 2/6] gnu: Add r-flowviz.

[zimoun]

* gnu/packages/bioconductor.scm (r-flowviz): New variable.
---
 gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6467fecb8c..92e5d3ec0b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6137,3 +6137,32 @@ features (e.g.  genes, microRNAs).")
 data.  This modified test allows for testing differential expression in qPCR
 data.")
     (license license:gpl2+)))
+
+(define-public r-flowviz
+  (package
+    (name "r-flowviz")
+    (version "1.48.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "flowViz" version))
+       (sha256
+        (base32
+         "00zwfzpdln62160h1ahcki5b96y06a1na7xjqs63b7571318xj20"))))
+    (properties
+     `((upstream-name . "flowViz")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-flowcore" ,r-flowcore)
+       ("r-hexbin" ,r-hexbin)
+       ("r-idpmisc" ,r-idpmisc)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-lattice" ,r-lattice)
+       ("r-latticeextra" ,r-latticeextra)
+       ("r-mass" ,r-mass)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+    (home-page "https://bioconductor.org/packages/flowViz")
+    (synopsis "Visualization for flow cytometry data")
+    (description "This package provides visualization tools for flow cytometry data.")
+    (license license:artistic2.0)))
-- 
2.23.0

[bug#37988] [PATCH 3/6] gnu: Add r-rprotobuflib.

[zimoun]

* gnu/packages/bioconductor.scm (r-rprotobuflib): New variable.
---
 gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 92e5d3ec0b..7c1761852c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6166,3 +6166,42 @@ data.")
     (synopsis "Visualization for flow cytometry data")
     (description "This package provides visualization tools for flow cytometry data.")
     (license license:artistic2.0)))
+
+(define-public r-rprotobuflib
+  (package
+    (name "r-rprotobuflib")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RProtoBufLib" version))
+       (sha256
+        (base32
+         "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg"))))
+    (properties
+     `((upstream-name . "RProtoBufLib")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Contains unverified binaries:
+         ;; src/win/lib/{i386,x64}/libprotobuf.a
+         (add-after 'unpack 'remove-win-folder
+           (lambda _
+             (delete-file-recursively "src/win")
+             #t))
+         ;; Fix non-conventional packaging.
+         ;; The dependency to protobuf-2.6.0 is included as tgz and build
+         ;; by the R package itself.
+         (add-after 'unpack 'fix-wrong-hard-coded
+           (lambda _
+             (with-directory-excursion "src"
+               (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
+             (substitute* "src/protobuf-2.6.0/configure"
+               (("#! /bin/sh") (string-append "#!" (which "sh"))))
+             #t)))))
+    (home-page "https://bioconductor.org/packages/RProtoBufLib")
+    (synopsis "C++ headers and static libraries of Protocol buffers")
+    (description "This package provides the headers and static library of
+Protocol buffers 2.6.0 for other R packages to compile and link against.")
+    (license license:bsd-3)))
-- 
2.23.0

[bug#37988] [PATCH 3/6] gnu: Add r-rprotobuflib.

[Ricardo Wurmus]

Hi,

thank you for the patches!

> * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable.

> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         ;; Contains unverified binaries:
> +         ;; src/win/lib/{i386,x64}/libprotobuf.a
> +         (add-after 'unpack 'remove-win-folder
> +           (lambda _
> +             (delete-file-recursively "src/win")
> +             #t))

This should be done in a snippet instead.

> +         ;; Fix non-conventional packaging.
> +         ;; The dependency to protobuf-2.6.0 is included as tgz and build
> +         ;; by the R package itself.
> +         (add-after 'unpack 'fix-wrong-hard-coded
> +           (lambda _
> +             (with-directory-excursion "src"
> +               (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
> +             (substitute* "src/protobuf-2.6.0/configure"
> +               (("#! /bin/sh") (string-append "#!" (which "sh"))))
> +             #t)))))

Can we just use our protobuf package instead of using the bundled sources?

> +    (description "This package provides the headers and static library of
> +Protocol buffers 2.6.0 for other R packages to compile and link
> against.")

I would prefer not to mention the specific version here.

-- 
Ricardo

[bug#37988] [PATCH 3/6] gnu: Add r-rprotobuflib.

[zimoun]

Hi Ricardo,

Thank you for reviewing.

On Wed, 30 Oct 2019 at 12:39, Ricardo Wurmus <rekado@elephly.net> wrote:

> > * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable.
>
> > +    (arguments
> > +     `(#:phases
> > +       (modify-phases %standard-phases
> > +         ;; Contains unverified binaries:
> > +         ;; src/win/lib/{i386,x64}/libprotobuf.a
> > +         (add-after 'unpack 'remove-win-folder
> > +           (lambda _
> > +             (delete-file-recursively "src/win")
> > +             #t))
>
> This should be done in a snippet instead.

What does it mean?


> > +         ;; Fix non-conventional packaging.
> > +         ;; The dependency to protobuf-2.6.0 is included as tgz and build
> > +         ;; by the R package itself.
> > +         (add-after 'unpack 'fix-wrong-hard-coded
> > +           (lambda _
> > +             (with-directory-excursion "src"
> > +               (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
> > +             (substitute* "src/protobuf-2.6.0/configure"
> > +               (("#! /bin/sh") (string-append "#!" (which "sh"))))
> > +             #t)))))

> Can we just use our protobuf package instead of using the bundled sources?

I do not know and I have not tried yet.
The package claims the dependency to 2.6.0 and we do not have this one.
As said in the cover letter to these patches, we could patch to
correctly package without the bundle source and this is IMHO the way
to go. However it is more work and it is better to have the package
available than no package at all.

Well, I will give another look to see if a quick improvement can be done. :-0



All the best,
simon

[bug#37988] [PATCH v2 3/6] gnu: Add r-rprotobuflib.

[zimoun]

* gnu/packages/bioconductor.scm (r-rprotobuflib): New variable.
* gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch: New file.
---
 gnu/packages/bioconductor.scm                 | 31 ++++++++++
 .../r-rprotobuflib-unbundle-dependency.patch  | 57 +++++++++++++++++++
 2 files changed, 88 insertions(+)
 create mode 100644 gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 92e5d3ec0b..5a6d629939 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -40,6 +40,7 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web)
+  #:use-module (gnu packages protobuf)
   #:use-module (srfi srfi-1))
 
 \f
@@ -6166,3 +6167,33 @@ data.")
     (synopsis "Visualization for flow cytometry data")
     (description "This package provides visualization tools for flow cytometry data.")
     (license license:artistic2.0)))
+
+(define-public r-rprotobuflib
+  (package
+    (name "r-rprotobuflib")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RProtoBufLib" version))
+       (sha256
+        (base32
+         "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg"))
+       ;; Remove bundled binaries:
+       ;; src/win/lib/{i386,x64}/libprotobuf.a
+       (modules '((guix build utils)))
+       (snippet '(begin
+                   (delete-file-recursively "src/win")
+                   #t))
+       (patches
+        (search-patches "r-rprotobuflib-unbundle-dependency.patch"))))
+    (properties
+     `((upstream-name . "RProtoBufLib")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("protobuf-2" ,protobuf-2)))
+    (home-page "https://bioconductor.org/packages/RProtoBufLib")
+    (synopsis "C++ headers and static libraries of Protocol buffers")
+    (description "This package provides the headers and static library of
+Protocol buffers 2.6.0 for other R packages to compile and link against.")
+    (license license:bsd-3)))
diff --git a/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch
new file mode 100644
index 0000000000..c26b6c7e0f
--- /dev/null
+++ b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch
@@ -0,0 +1,57 @@
+diff --git a/configure b/configure
+index 7edae5f..eff2489 100755
+--- a/configure
++++ b/configure
+@@ -2856,39 +2856,6 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex
+ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+-#untar the lib
+-BASEPBNAME="protobuf-2.6.0"
+-PBTGZNAME=${BASEPBNAME}.tgz
+-cd src
+-if test -d ./${BASEPBNAME}; then
+-	echo 'found ' $BASEPBNAME ' header sources and tar archive;using what is there.'
+-else
+-	echo "untarring protobuf ...";
+-	gunzip -dc ${PBTGZNAME} | tar xf -;
+-fi;
+-
+-#run this bootstrap script to update all the gnu auto build files (e.g.  automake symlinked fils (e.g. ./compile), alocal.m4,etc... )
+-cd ${BASEPBNAME}
+-#./autogen.sh
+-#automake --add-missing #do this because the old Autoconf (e.g. 2.13) may not handle this in autoreconf
+-#mv m4/lt~obsolete.m4 m4/lt-obsolete.m4 # R CMD check gives warning about ~ character in filename
+-cd ..
+-
+-echo "building protobuf...";
+-PBBUILD=$(pwd)/pb_build
+-if test -d ${PBBUILD}; then
+-	echo 'found ' $PBBUILD ' ;using what is there.'
+-else
+-	mkdir ${PBBUILD}
+-fi;
+-
+-cd ${BASEPBNAME};
+-./configure --enable-static=yes --with-pic=yes --enable-shared=no --prefix="${PBBUILD}" --libdir="${PBBUILD}/lib" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}"
+-$MAKE install
+-
+-cd ../../
+-
+-
+
+
+ ac_config_files="$ac_config_files src/Makevars"
+diff --git a/src/Makevars.in b/src/Makevars.in
+index 63803fb..575d507 100644
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -10,9 +10,6 @@ all: copying
+
+ #copy hdf5 library headers to package include
+ copying: $(GS_LIB)
+-	mkdir -p "${USER_INCLUDE}"
+-	cp -r @PBBUILD@/include/google ${USER_INCLUDE}
+ 	mkdir -p "${USER_LIB_DIR}"
+-	cp @PBBUILD@/lib/* ${USER_LIB_DIR}
+ 	cp $(GS_LIB) ${USER_LIB_DIR}/GatingSet.pb.o
-- 
2.23.0

[bug#37988] [PATCH v3 3/6] gnu: Add r-rprotobuflib.

[zimoun]

* gnu/packages/bioconductor.scm (r-rprotobuflib): New variable.
* gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch: New file.
---
 gnu/packages/bioconductor.scm                 | 31 ++++++++++
 .../r-rprotobuflib-unbundle-dependency.patch  | 57 +++++++++++++++++++
 2 files changed, 88 insertions(+)
 create mode 100644 gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 92e5d3ec0b..801e52245b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -38,6 +38,7 @@
   #:use-module (gnu packages netpbm)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web)
   #:use-module (srfi srfi-1))
@@ -6166,3 +6167,33 @@ data.")
     (synopsis "Visualization for flow cytometry data")
     (description "This package provides visualization tools for flow cytometry data.")
     (license license:artistic2.0)))
+
+(define-public r-rprotobuflib
+  (package
+    (name "r-rprotobuflib")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RProtoBufLib" version))
+       (sha256
+        (base32
+         "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg"))
+       ;; Remove bundled binaries:
+       ;; src/win/lib/{i386,x64}/libprotobuf.a
+       (modules '((guix build utils)))
+       (snippet '(begin
+                   (delete-file-recursively "src/win")
+                   #t))
+       (patches
+        (search-patches "r-rprotobuflib-unbundle-dependency.patch"))))
+    (properties
+     `((upstream-name . "RProtoBufLib")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("protobuf-2" ,protobuf-2)))
+    (home-page "https://bioconductor.org/packages/RProtoBufLib")
+    (synopsis "C++ headers and static libraries of Protocol buffers")
+    (description "This package provides the headers and static library of
+Protocol buffers for other R packages to compile and link against.")
+    (license license:bsd-3)))
diff --git a/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch
new file mode 100644
index 0000000000..c26b6c7e0f
--- /dev/null
+++ b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch
@@ -0,0 +1,57 @@
+diff --git a/configure b/configure
+index 7edae5f..eff2489 100755
+--- a/configure
++++ b/configure
+@@ -2856,39 +2856,6 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex
+ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+-#untar the lib
+-BASEPBNAME="protobuf-2.6.0"
+-PBTGZNAME=${BASEPBNAME}.tgz
+-cd src
+-if test -d ./${BASEPBNAME}; then
+-	echo 'found ' $BASEPBNAME ' header sources and tar archive;using what is there.'
+-else
+-	echo "untarring protobuf ...";
+-	gunzip -dc ${PBTGZNAME} | tar xf -;
+-fi;
+-
+-#run this bootstrap script to update all the gnu auto build files (e.g.  automake symlinked fils (e.g. ./compile), alocal.m4,etc... )
+-cd ${BASEPBNAME}
+-#./autogen.sh
+-#automake --add-missing #do this because the old Autoconf (e.g. 2.13) may not handle this in autoreconf
+-#mv m4/lt~obsolete.m4 m4/lt-obsolete.m4 # R CMD check gives warning about ~ character in filename
+-cd ..
+-
+-echo "building protobuf...";
+-PBBUILD=$(pwd)/pb_build
+-if test -d ${PBBUILD}; then
+-	echo 'found ' $PBBUILD ' ;using what is there.'
+-else
+-	mkdir ${PBBUILD}
+-fi;
+-
+-cd ${BASEPBNAME};
+-./configure --enable-static=yes --with-pic=yes --enable-shared=no --prefix="${PBBUILD}" --libdir="${PBBUILD}/lib" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}"
+-$MAKE install
+-
+-cd ../../
+-
+-
+
+
+ ac_config_files="$ac_config_files src/Makevars"
+diff --git a/src/Makevars.in b/src/Makevars.in
+index 63803fb..575d507 100644
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -10,9 +10,6 @@ all: copying
+
+ #copy hdf5 library headers to package include
+ copying: $(GS_LIB)
+-	mkdir -p "${USER_INCLUDE}"
+-	cp -r @PBBUILD@/include/google ${USER_INCLUDE}
+ 	mkdir -p "${USER_LIB_DIR}"
+-	cp @PBBUILD@/lib/* ${USER_LIB_DIR}
+ 	cp $(GS_LIB) ${USER_LIB_DIR}/GatingSet.pb.o
-- 
2.23.0

[bug#37988] [PATCH v4 3/6] gnu: Add r-rprotobuflib.

[zimoun]

* gnu/packages/bioconductor.scm (r-rprotobuflib): New variable.
* gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch: New file.
---
 gnu/local.mk                                  |  2 +
 gnu/packages/bioconductor.scm                 | 31 ++++++++++
 .../r-rprotobuflib-unbundle-dependency.patch  | 57 +++++++++++++++++++
 3 files changed, 90 insertions(+)
 create mode 100644 gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 5b81791542..178c8b903f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -22,6 +22,7 @@
 # Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 # Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 # Copyright © 2019 John Soo <jsoo1@asu.edu>
+# Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
 #
 # This file is part of GNU Guix.
 #
@@ -1295,6 +1296,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/quagga-reproducible-build.patch          \
   %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
   %D%/packages/patches/qtwebkit-pbutils-include.patch		\
+  %D%/packages/patches/r-rprotobuflib-unbundle-dependency.patch \
   %D%/packages/patches/randomjungle-disable-static-build.patch	\
   %D%/packages/patches/rapicorn-isnan.patch			\
   %D%/packages/patches/rapidjson-gcc-compat.patch		\
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 92e5d3ec0b..801e52245b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -38,6 +38,7 @@
   #:use-module (gnu packages netpbm)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web)
   #:use-module (srfi srfi-1))
@@ -6166,3 +6167,33 @@ data.")
     (synopsis "Visualization for flow cytometry data")
     (description "This package provides visualization tools for flow cytometry data.")
     (license license:artistic2.0)))
+
+(define-public r-rprotobuflib
+  (package
+    (name "r-rprotobuflib")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RProtoBufLib" version))
+       (sha256
+        (base32
+         "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg"))
+       ;; Remove bundled binaries:
+       ;; src/win/lib/{i386,x64}/libprotobuf.a
+       (modules '((guix build utils)))
+       (snippet '(begin
+                   (delete-file-recursively "src/win")
+                   #t))
+       (patches
+        (search-patches "r-rprotobuflib-unbundle-dependency.patch"))))
+    (properties
+     `((upstream-name . "RProtoBufLib")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("protobuf-2" ,protobuf-2)))
+    (home-page "https://bioconductor.org/packages/RProtoBufLib")
+    (synopsis "C++ headers and static libraries of Protocol buffers")
+    (description "This package provides the headers and static library of
+Protocol buffers for other R packages to compile and link against.")
+    (license license:bsd-3)))
diff --git a/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch
new file mode 100644
index 0000000000..c26b6c7e0f
--- /dev/null
+++ b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch
@@ -0,0 +1,57 @@
+diff --git a/configure b/configure
+index 7edae5f..eff2489 100755
+--- a/configure
++++ b/configure
+@@ -2856,39 +2856,6 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex
+ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+-#untar the lib
+-BASEPBNAME="protobuf-2.6.0"
+-PBTGZNAME=${BASEPBNAME}.tgz
+-cd src
+-if test -d ./${BASEPBNAME}; then
+-	echo 'found ' $BASEPBNAME ' header sources and tar archive;using what is there.'
+-else
+-	echo "untarring protobuf ...";
+-	gunzip -dc ${PBTGZNAME} | tar xf -;
+-fi;
+-
+-#run this bootstrap script to update all the gnu auto build files (e.g.  automake symlinked fils (e.g. ./compile), alocal.m4,etc... )
+-cd ${BASEPBNAME}
+-#./autogen.sh
+-#automake --add-missing #do this because the old Autoconf (e.g. 2.13) may not handle this in autoreconf
+-#mv m4/lt~obsolete.m4 m4/lt-obsolete.m4 # R CMD check gives warning about ~ character in filename
+-cd ..
+-
+-echo "building protobuf...";
+-PBBUILD=$(pwd)/pb_build
+-if test -d ${PBBUILD}; then
+-	echo 'found ' $PBBUILD ' ;using what is there.'
+-else
+-	mkdir ${PBBUILD}
+-fi;
+-
+-cd ${BASEPBNAME};
+-./configure --enable-static=yes --with-pic=yes --enable-shared=no --prefix="${PBBUILD}" --libdir="${PBBUILD}/lib" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}"
+-$MAKE install
+-
+-cd ../../
+-
+-
+
+
+ ac_config_files="$ac_config_files src/Makevars"
+diff --git a/src/Makevars.in b/src/Makevars.in
+index 63803fb..575d507 100644
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -10,9 +10,6 @@ all: copying
+
+ #copy hdf5 library headers to package include
+ copying: $(GS_LIB)
+-	mkdir -p "${USER_INCLUDE}"
+-	cp -r @PBBUILD@/include/google ${USER_INCLUDE}
+ 	mkdir -p "${USER_LIB_DIR}"
+-	cp @PBBUILD@/lib/* ${USER_LIB_DIR}
+ 	cp $(GS_LIB) ${USER_LIB_DIR}/GatingSet.pb.o
-- 
2.23.0

[bug#37988] [PATCH 4/6] gnu: Add r-cytolib.

[zimoun]

* gnu/packages/bioconductor.scm (r-cytolib): New variable.
---
 gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7c1761852c..a5c6e1ed55 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6205,3 +6205,26 @@ data.")
     (description "This package provides the headers and static library of
 Protocol buffers 2.6.0 for other R packages to compile and link against.")
     (license license:bsd-3)))
+
+(define-public r-cytolib
+  (package
+    (name "r-cytolib")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "cytolib" version))
+       (sha256
+        (base32
+         "10sdkwrmzmp3sh59hl3x0zxwlw77v80jnv8gz1qrv66skjb764cq"))))
+    (properties
+     `((upstream-name . "cytolib")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-rprotobuflib" ,r-rprotobuflib)))
+    (home-page "https://bioconductor.org/packages/cytolib")
+    (synopsis "C++ infrastructure for representing and interacting with the gated cytometry")
+    (description "This package provides the core data structure and API to
+represent and interact with the gated cytometry data.")
+    (license license:artistic2.0)))
-- 
2.23.0

[bug#37988] [PATCH 4/6] gnu: Add r-cytolib.

[Ricardo Wurmus]

zimoun <zimon.toutoune@gmail.com> writes:

> * gnu/packages/bioconductor.scm (r-cytolib): New variable.
[…]
> +    (synopsis "C++ infrastructure for representing and interacting
> with the gated cytometry")

I would remove “the” from “the gated cytometry”.  How about
“Infrastructure for working with gated cytometry data”?

> +    (description "This package provides the core data structure and API to
> +represent and interact with the gated cytometry data.")

Here I’d also remove “the”.

-- 
Ricardo

[bug#37988] [PATCH v2 4/6] gnu: Add r-cytolib.

[zimoun]

* gnu/packages/bioconductor.scm (r-cytolib): New variable.
---
 gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7c1761852c..00b10918ff 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6205,3 +6205,26 @@ data.")
     (description "This package provides the headers and static library of
 Protocol buffers 2.6.0 for other R packages to compile and link against.")
     (license license:bsd-3)))
+
+(define-public r-cytolib
+  (package
+    (name "r-cytolib")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "cytolib" version))
+       (sha256
+        (base32
+         "10sdkwrmzmp3sh59hl3x0zxwlw77v80jnv8gz1qrv66skjb764cq"))))
+    (properties
+     `((upstream-name . "cytolib")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-rprotobuflib" ,r-rprotobuflib)))
+    (home-page "https://bioconductor.org/packages/cytolib")
+    (synopsis "Infrastructure for working with gated cytometry data")
+    (description "This package provides the core data structure and API to
+represent and interact with gated cytometry data.")
+    (license license:artistic2.0)))
-- 
2.23.0

[bug#37988] [PATCH 5/6] gnu: Add r-ncdfflow.

[zimoun]

* gnu/packages/bioconductor.scm (r-ncdfflow): New variable.
---
 gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a5c6e1ed55..2636095e0f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6228,3 +6228,35 @@ Protocol buffers 2.6.0 for other R packages to compile and link against.")
     (description "This package provides the core data structure and API to
 represent and interact with the gated cytometry data.")
     (license license:artistic2.0)))
+
+(define-public r-ncdfflow
+  (package
+    (name "r-ncdfflow")
+    (version "2.30.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ncdfFlow" version))
+       (sha256
+        (base32
+         "02769pr4gipjdlknhk8adica7v37c9fviffv0qscrf9v5j26rxzw"))))
+    (properties
+     `((upstream-name . "ncdfFlow")))
+    (build-system r-build-system)
+    (inputs `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-flowcore" ,r-flowcore)
+       ("r-flowviz" ,r-flowviz)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "https://bioconductor.org/packages/ncdfFlow")
+    (synopsis "Storage based on HDF5 for flow cytometry data")
+    (description
+     "This package provides HDF5 storage based methods and functions for
+manipulation of flow cytometry data.")
+    (license license:artistic2.0)))
-- 
2.23.0

[bug#37988] [PATCH 5/6] gnu: Add r-ncdfflow.

[Ricardo Wurmus]

zimoun <zimon.toutoune@gmail.com> writes:

> * gnu/packages/bioconductor.scm (r-ncdfflow): New variable.

This looks good to me.  Thank you!

-- 
Ricardo

[bug#37988] [PATCH 6/6] gnu: Add r-flowworkspace.

[zimoun]

* gnu/packages/bioconductor.scm (r-flowworkspace): New variable.
---
 gnu/packages/bioconductor.scm | 50 +++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2636095e0f..dabfcb2cb3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6260,3 +6260,53 @@ represent and interact with the gated cytometry data.")
      "This package provides HDF5 storage based methods and functions for
 manipulation of flow cytometry data.")
     (license license:artistic2.0)))
+
+(define-public r-flowworkspace
+  (package
+    (name "r-flowworkspace")
+    (version "3.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "flowWorkspace" version))
+       (sha256
+        (base32
+         "1r1xxqzlp2x2gf79f37ckninnyjkxcb7xz7rffg2nadmapl5shvw"))))
+    (properties
+     `((upstream-name . "flowWorkspace")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-cytolib" ,r-cytolib)
+       ("r-data-table" ,r-data-table)
+       ("r-digest" ,r-digest)
+       ("r-dplyr" ,r-dplyr)
+       ("r-flowcore" ,r-flowcore)
+       ("r-flowviz" ,r-flowviz)
+       ("r-graph" ,r-graph)
+       ("r-gridextra" ,r-gridextra)
+       ("r-lattice" ,r-lattice)
+       ("r-latticeextra" ,r-latticeextra)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-ncdfflow" ,r-ncdfflow)
+       ("r-rbgl" ,r-rbgl)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppparallel" ,r-rcppparallel)
+       ("r-rgraphviz" ,r-rgraphviz)
+       ("r-rprotobuflib" ,r-rprotobuflib)
+       ("r-scales" ,r-scales)
+       ("r-stringr" ,r-stringr)))
+    (home-page
+     "https://bioconductor.org/packages/flowWorkspace")
+    (synopsis "Infrastructure for representing and interacting with cytometry data sets")
+    (description
+     "This package provides importer for basic workspaces from the proprietary
+software FlowJo into the BioConductor package flowCore.  It is designed to
+facilitate comparison of automated gating methods against manual gating.
+Gating hierarchies, groups of samples, compensation, and transformation are
+performed so that the output matches the analysis from the proprietary
+software FlowJo.")
+    (license license:artistic2.0)))
-- 
2.23.0

[bug#37988] why?

[zimoun]

Hi Ricardo,

Why did you pushed your commits instead of mines?
Especially when they had not fallen in the crack.

I sent them the October 30, 2019.
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988

And you commented them the same day:
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#26

I modified one the November 5th, 2019:
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#47


And you committed and pushed the same packages on the December, 15th.


Cheers,
simon

[bug#37988] why?

[Ricardo Wurmus]

Hi,

> Why did you pushed your commits instead of mines?
> Especially when they had not fallen in the crack.
>
> I sent them the October 30, 2019.
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988
>
> And you commented them the same day:
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#26
>
> I modified one the November 5th, 2019:
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#47

Uh, that’s odd.  I remember working with your r-flow* patches.  I did
not have my own versions of these patches.  I know this because I had
not previously encountered flow cytometry.  (I don’t specifically
remember r-rprotobuflib from this series.)

My guess is that I wasn’t able to apply them cleanly, so I copy & pasted
the diff, adjusted as needed, and then forgot to override the commit
author before pushing :-(

December is a blur.  It’s quite possible that I didn’t work on the
patches all in one go, got interrupted, and then pushed them together
with some other work (I see that there are R update commits after these
pushes).

I’m very sorry to have messed up the authorship here.  This was
definitely not intended :(

--
Ricardo

[bug#37988] why?

[zimoun]

Hi Ricardo,

On Fri, 21 Feb 2020 at 19:39, Ricardo Wurmus <rekado@elephly.net> wrote:

> > Why did you pushed your commits instead of mines?
> > Especially when they had not fallen in the crack.
> >
> > I sent them the October 30, 2019.
> > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988
> >
> > And you commented them the same day:
> > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#26
> >
> > I modified one the November 5th, 2019:
> > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#47
>
> Uh, that’s odd.  I remember working with your r-flow* patches.  I did
> not have my own versions of these patches.  I know this because I had
> not previously encountered flow cytometry.  (I don’t specifically
> remember r-rprotobuflib from this series.)

That's why I found weird the twist. :-)
I thought I did something unexpected and/or there was a special
motivation. And so my "why?". :-)


> My guess is that I wasn’t able to apply them cleanly, so I copy & pasted
> the diff, adjusted as needed, and then forgot to override the commit
> author before pushing :-(

> I’m very sorry to have messed up the authorship here.  This was
> definitely not intended :(

I am ok about the authorship; my salary does not depend on the number
of commits accepted. ;-)
The most important is that the packages end in Guix; who committed
them is less important.


Thanks,
simon