[bug#36789] [PATCH 00/11] Add r packages to process flow cytometry data

[bug#36789] [PATCH 00/11] Add r packages to process flow cytometry data

[zimoun]

Dear,

This serie adds packages used in flow cytometry data analysis; and their dependencies. They are the result of the command `guix import cran --archive=bioconductor --recursive`.


Please let me know if it is correct.

All the best,
simon


zimoun (11):
  gnu: Add r-umap.
  gnu: Add r-kableextra.
  gnu: Add r-all.
  gnu: Add r-flowcore.
  gnu: Add r-flowutils.
  gnu: Add r-consensusclusterplus.
  gnu: Add r-flowmeans.
  gnu: Add r-flowpeaks.
  gnu: Add r-flowsom.
  gnu: Add r-mixomics.
  gnu: Add r-depecher.

 gnu/packages/bioconductor.scm | 288 ++++++++++++++++++++++++++++++++++
 gnu/packages/cran.scm         |  67 ++++++++
 2 files changed, 355 insertions(+)

-- 
2.21.0

[bug#36790] [PATCH 01/11] gnu: Add r-umap.

[zimoun]

* gnu/packages/cran.scm (r-umap): New variable.
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3f0d819df7..768a7d09c5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14530,3 +14530,30 @@ including regression, classification and ranking.  The package is made to be
 extensible, so that users are also allowed to define their own objectives
 easily.")
     (license license:asl2.0)))
+
+(define-public r-umap
+  (package
+    (name "r-umap")
+    (version "0.2.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "umap" version))
+        (sha256
+          (base32
+            "1s82w9gy1387h7cprjfbhp49l89zbmn3gc9s0wzqb1s73nza9n31"))))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-rcpp" ,r-rcpp)
+        ("r-reticulate" ,r-reticulate)
+        ("r-rspectra" ,r-rspectra)))
+    (home-page "https://github.com/tkonopka/umap")
+    (synopsis
+      "Uniform Manifold Approximation and Projection")
+    (description
+      "Uniform manifold approximation and projection is a technique for
+dimension reduction.  The algorithm was described by McInnes and Healy (2018)
+in <arXiv:1802.03426>.  This package provides an interface to the UMAP
+algorithm in R, including a translation of the original algorithm into R with
+minimal dependencies.")
+    (license license:expat)))
-- 
2.21.0

[bug#36791] [PATCH 02/11] gnu: Add r-kableextra.

[zimoun]

* gnu/packages/cran.scm (r-kableextra): New variable.
---
 gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 768a7d09c5..7349a9513e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14557,3 +14557,43 @@ in <arXiv:1802.03426>.  This package provides an interface to the UMAP
 algorithm in R, including a translation of the original algorithm into R with
 minimal dependencies.")
     (license license:expat)))
+
+(define-public r-kableextra
+  (package
+    (name "r-kableextra")
+    (version "1.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "kableExtra" version))
+        (sha256
+          (base32
+            "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
+    (properties `((upstream-name . "kableExtra")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-digest" ,r-digest)
+        ("r-glue" ,r-glue)
+        ("r-htmltools" ,r-htmltools)
+        ("r-knitr" ,r-knitr)
+        ("r-magrittr" ,r-magrittr)
+        ("r-readr" ,r-readr)
+        ("r-rmarkdown" ,r-rmarkdown)
+        ("r-rstudioapi" ,r-rstudioapi)
+        ("r-rvest" ,r-rvest)
+        ("r-scales" ,r-scales)
+        ("r-stringr" ,r-stringr)
+        ("r-viridislite" ,r-viridislite)
+        ("r-webshot" ,r-webshot)
+        ("r-xml2" ,r-xml2)))
+    (home-page
+      "http://haozhu233.github.io/kableExtra/")
+    (synopsis
+      "Construct Complex Table with 'kable' and Pipe Syntax")
+    (description
+      "Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and
+the piping syntax from 'magrittr'.  Function 'kable()' is a light weight table
+generator coming from 'knitr'.  This package simplifies the way to manipulate
+the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct
+complex tables and customize styles using a readable syntax.")
+    (license license:expat)))
-- 
2.21.0

[bug#36792] [PATCH 03/11] gnu: Add r-all.

[zimoun]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e5a2d66b2d..18b5711496 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -865,6 +865,36 @@ which were then sequenced to a depth of ~4 million reads per library,
 resulting in a complete gene expression profile for each cell.")
     (license license:artistic2.0)))
 
+(define-public r-all
+  (package
+    (name "r-all")
+    (version "1.26.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/experiment/" instead of "bioc/".
+              (uri (string-append "https://www.bioconductor.org/packages/"
+                                  "release/data/experiment/src/contrib/"
+                                  "ALL_" version ".tar.gz"))
+              (sha256
+               (base32
+                "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
+    (properties
+      `((upstream-name . "ConsensusClusterPlus")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-biobase" ,r-biobase)))
+    (home-page
+      "https://bioconductor.org/packages/ALL")
+    (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
+    (description
+      "The data consist of microarrays from 128 different individuals with
+acute lymphoblastic leukemia (ALL). A number of additional covariates are
+available. The data have been normalized (using rma) and it is the jointly
+normalized data that are available here. The data are presented in the form of
+an exprSet object.")
+    (license license:artistic2.0)))
+
 \f
 ;;; Packages
 
-- 
2.21.0

[bug#36793] [PATCH 04/11] gnu: Add r-flowcore.

[zimoun]

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 18b5711496..3a38042537 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4799,3 +4799,33 @@ read mapping, read counting, SNP calling, structural variant detection and
 gene fusion discovery.  It can be applied to all major sequencing techologies
 and to both short and long sequence reads.")
     (license license:gpl3)))
+
+(define-public r-flowcore
+  (package
+    (name "r-flowcore")
+    (version "1.50.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "flowCore" version))
+        (sha256
+          (base32
+            "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
+    (properties `((upstream-name . "flowCore")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-bh" ,r-bh)
+        ("r-biobase" ,r-biobase)
+        ("r-biocgenerics" ,r-biocgenerics)
+        ("r-corpcor" ,r-corpcor)
+        ("r-graph" ,r-graph)
+        ("r-mass" ,r-mass)
+        ("r-matrixstats" ,r-matrixstats)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rrcov" ,r-rrcov)))
+    (home-page
+      "https://bioconductor.org/packages/flowCore")
+    (synopsis "Basic structures for flow cytometry data")
+    (description
+      "Provides S4 data structures and basic functions to deal with flow cytometry data.")
+    (license license:artistic2.0)))
-- 
2.21.0

[bug#36794] [PATCH 05/11] gnu: Add r-flowutils.

[zimoun]

* gnu/packages/bioconductor.scm (r-flowutils): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3a38042537..d79ff729fc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4800,6 +4800,33 @@ gene fusion discovery.  It can be applied to all major sequencing techologies
 and to both short and long sequence reads.")
     (license license:gpl3)))
 
+(define-public r-flowutils
+  (package
+    (name "r-flowutils")
+    (version "1.48.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "flowUtils" version))
+        (sha256
+          (base32
+            "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
+    (properties `((upstream-name . "flowUtils")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-biobase" ,r-biobase)
+        ("r-corpcor" ,r-corpcor)
+        ("r-flowcore" ,r-flowcore)
+        ("r-graph" ,r-graph)
+        ("r-runit" ,r-runit)
+        ("r-xml" ,r-xml)))
+    (home-page
+      "https://github.com/jspidlen/flowUtils")
+    (synopsis "Utilities for flow cytometry")
+    (description
+      "Provides utilities for flow cytometry data.")
+    (license license:artistic2.0)))
+
 (define-public r-flowcore
   (package
     (name "r-flowcore")
-- 
2.21.0

[bug#36795] [PATCH 06/11] gnu: Add r-consensusclusterplus.

[zimoun]

* gnu/packages/bioconductor.scm (r-consensusclusterplus): New variable.
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d79ff729fc..d5bd512972 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4827,6 +4827,31 @@ and to both short and long sequence reads.")
       "Provides utilities for flow cytometry data.")
     (license license:artistic2.0)))
 
+(define-public r-consensusclusterplus
+  (package
+    (name "r-consensusclusterplus")
+    (version "1.48.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "ConsensusClusterPlus" version))
+        (sha256
+          (base32
+            "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
+    (properties
+      `((upstream-name . "ConsensusClusterPlus")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-all" ,r-all)
+        ("r-biobase" ,r-biobase)
+        ("r-cluster" ,r-cluster)))
+    (home-page
+      "https://bioconductor.org/packages/ConsensusClusterPlus")
+    (synopsis "Clustering algorithm")
+    (description
+      "Algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.")
+    (license license:gpl2)))
+
 (define-public r-flowcore
   (package
     (name "r-flowcore")
-- 
2.21.0

[bug#36796] [PATCH 07/11] gnu: Add r-flowmeans.

[zimoun]

* gnu/packages/bioconductor.scm (r-flowmeans): New variable.
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d5bd512972..0f023665c2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4881,3 +4881,29 @@ and to both short and long sequence reads.")
     (description
       "Provides S4 data structures and basic functions to deal with flow cytometry data.")
     (license license:artistic2.0)))
+
+(define-public r-flowmeans
+  (package
+    (name "r-flowmeans")
+    (version "1.44.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "flowMeans" version))
+        (sha256
+          (base32
+            "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
+    (properties `((upstream-name . "flowMeans")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-biobase" ,r-biobase)
+        ("r-feature" ,r-feature)
+        ("r-flowcore" ,r-flowcore)
+        ("r-rrcov" ,r-rrcov)))
+    (home-page
+      "https://bioconductor.org/packages/flowMeans")
+    (synopsis
+      "Non-parametric Flow Cytometry Data Gating")
+    (description
+      "Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.  Note: R 2.11.0 or newer is required.")
+    (license license:artistic2.0)))
-- 
2.21.0

[bug#36797] [PATCH 08/11] gnu: Add r-flowpeaks.

[zimoun]

* gnu/packages/bioconductor.scm (r-flowpeaks): 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 0f023665c2..ab4d9f4075 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4907,3 +4907,26 @@ and to both short and long sequence reads.")
     (description
       "Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.  Note: R 2.11.0 or newer is required.")
     (license license:artistic2.0)))
+
+(define-public r-flowpeaks
+  (package
+    (name "r-flowpeaks")
+    (version "1.30.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "flowPeaks" version))
+        (sha256
+          (base32
+            "1ncz7n6n39svi444yy29ip53398392s3m6z0h2a77rhcnzg456wy"))))
+    (properties `((upstream-name . "flowPeaks")))
+    (build-system r-build-system)
+    (inputs `(("gsl" ,gsl)))
+    (home-page
+      "https://bioconductor.org/packages/flowPeaks")
+    (synopsis
+      "An R package for flow data clustering")
+    (description
+      "This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.")
+    (license license:artistic2.0)))     ;TODO: artistic1.0 does not exist
+
-- 
2.21.0

[bug#36798] [PATCH 09/11] gnu: Add r-flowsom.

[zimoun]

* gnu/packages/bioconductor.scm (r-flowsom): 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 ab4d9f4075..dd6570ed17 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4930,3 +4930,32 @@ and to both short and long sequence reads.")
       "This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.")
     (license license:artistic2.0)))     ;TODO: artistic1.0 does not exist
 
+(define-public r-flowsom
+  (package
+    (name "r-flowsom")
+    (version "1.16.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "FlowSOM" version))
+        (sha256
+          (base32
+            "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
+    (properties `((upstream-name . "FlowSOM")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-biocgenerics" ,r-biocgenerics)
+        ("r-consensusclusterplus"
+         ,r-consensusclusterplus)
+        ("r-flowcore" ,r-flowcore)
+        ("r-flowutils" ,r-flowutils)
+        ("r-igraph" ,r-igraph)
+        ("r-tsne" ,r-tsne)
+        ("r-xml" ,r-xml)))
+    (home-page "http://www.r-project.org")
+    (synopsis
+      "Using self-organizing maps for visualization and interpretation of cytometry data")
+    (description
+      "FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.")
+    (license license:gpl2+)))
+
-- 
2.21.0

[bug#36799] [PATCH 10/11] gnu: Add r-mixomics.

[zimoun]

* gnu/packages/bioconductor.scm (r-mixomics): New variable.
---
 gnu/packages/bioconductor.scm | 54 +++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dd6570ed17..64625aedd4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4959,3 +4959,57 @@ and to both short and long sequence reads.")
       "FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.")
     (license license:gpl2+)))
 
+(define-public r-mixomics
+  (package
+    (name "r-mixomics")
+    (version "6.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "mixOmics" version))
+        (sha256
+          (base32
+            "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk"))))
+    (properties `((upstream-name . "mixOmics")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-corpcor" ,r-corpcor)
+        ("r-dplyr" ,r-dplyr)
+        ("r-ellipse" ,r-ellipse)
+        ("r-ggplot2" ,r-ggplot2)
+        ("r-gridextra" ,r-gridextra)
+        ("r-igraph" ,r-igraph)
+        ("r-lattice" ,r-lattice)
+        ("r-mass" ,r-mass)
+        ("r-matrixstats" ,r-matrixstats)
+        ("r-rarpack" ,r-rarpack)
+        ("r-rcolorbrewer" ,r-rcolorbrewer)
+        ("r-reshape2" ,r-reshape2)
+        ("r-tidyr" ,r-tidyr)))
+    (home-page "http://www.mixOmics.org")
+    (synopsis "Omics Data Integration Project")
+    (description
+      "Multivariate methods are well suited to large omics data sets where the
+number of variables (e.g.  genes, proteins, metabolites) is much larger than
+the number of samples (patients, cells, mice).  They have the appealing
+properties of reducing the dimension of the data by using instrumental
+variables (components), which are defined as combinations of all variables.
+Those components are then used to produce useful graphical outputs that enable
+better understanding of the relationships and correlation structures between
+the different data sets that are integrated.  mixOmics offers a wide range of
+multivariate methods for the exploration and integration of biological
+datasets with a particular focus on variable selection.  The package proposes
+several sparse multivariate models we have developed to identify the key
+variables that are highly correlated, and/or explain the biological outcome of
+interest.  The data that can be analysed with mixOmics may come from high
+throughput sequencing technologies, such as omics data (transcriptomics,
+metabolomics, proteomics, metagenomics etc) but also beyond the realm of
+omics (e.g.  spectral imaging).  The methods implemented in mixOmics can also
+handle missing values without having to delete entire rows with missing data.
+A non exhaustive list of methods include variants of generalised Canonical
+Correlation Analysis, sparse Partial Least Squares and sparse Discriminant
+Analysis.  Recently we implemented integrative methods to combine multiple
+data sets: N-integration with variants of Generalised Canonical Correlation
+Analysis and P-integration with variants of multi-group Partial Least
+Squares.")
+    (license license:gpl2+)))
-- 
2.21.0

[bug#36800] [PATCH 11/11] gnu: Add r-depecher.

[zimoun]

* gnu/packages/bioconductor.scm (r-depecher): New variable.
---
 gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 64625aedd4..7c9a3b7417 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5013,3 +5013,47 @@ data sets: N-integration with variants of Generalised Canonical Correlation
 Analysis and P-integration with variants of multi-group Partial Least
 Squares.")
     (license license:gpl2+)))
+
+(define-public r-depecher
+  (package
+    (name "r-depecher")
+    (version "1.0.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "DepecheR" version))
+        (sha256
+          (base32
+            "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
+    (properties `((upstream-name . "DepecheR")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-beanplot" ,r-beanplot)
+        ("r-biocparallel" ,r-biocparallel)
+        ("r-dosnow" ,r-dosnow)
+        ("r-dplyr" ,r-dplyr)
+        ("r-foreach" ,r-foreach)
+        ("r-ggplot2" ,r-ggplot2)
+        ("r-gplots" ,r-gplots)
+        ("r-mass" ,r-mass)
+        ("r-matrixstats" ,r-matrixstats)
+        ("r-mixomics" ,r-mixomics)
+        ("r-moments" ,r-moments)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rcppeigen" ,r-rcppeigen)
+        ("r-reshape2" ,r-reshape2)
+        ("r-viridis" ,r-viridis)))
+    (home-page
+      "https://bioconductor.org/packages/DepecheR")
+    (synopsis
+      "Determination of essential phenotypic elements of clusters in high-dimensional entities")
+    (description
+     "The purpose of this package is to identify traits in a dataset that can
+separate groups.  This is done on two levels.  First, clustering is performed,
+using an implementation of sparse K-means.  Secondly, the generated clusters
+are used to predict outcomes of groups of individuals based on their
+distribution of observations in the different clusters.  As certain clusters
+with separating information will be identified, and these clusters are defined
+by a sparse number of variables, this method can reduce the complexity of
+data, to only emphasize the data that actually matters.")
+    (license license:expat)))
-- 
2.21.0

[bug#36790] Merge 36789 36790

[zimoun]

merge 36789 36790
thanks

[bug#36800] [PATCH 11/11] gnu: Add r-depecher.

[Ricardo Wurmus]

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

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

This package cannot actually be built:

--8<---------------cut here---------------start------------->8---
…
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug DepecheR.so; fi
/gnu/store/q19l04vd2za80mk1845pz7r8cz29qk43-bash-minimal-4.4.23/bin/bash: /usr/bin/strip: No such file or directory
make: *** [Makevars:6: strippedLib] Error 127
ERROR: compilation failed for package ‘DepecheR’
* removing ‘/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depecher-1.0.3/site-library/DepecheR’
Backtrace:
           4 (primitive-load "/gnu/store/f1ky8a22c7s5p053nci05a536j7…")
In ice-9/eval.scm:
   191:35  3 (_ #f)
In srfi/srfi-1.scm:
   863:16  2 (every1 #<procedure 725d80 at /gnu/store/4p2vk30zhkwxq…> …)
In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/gnu-build-system.scm:
   799:28  1 (_ _)
In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/utils.scm:
    616:6  0 (invoke _ . _)

/gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/utils.scm:616:6: In procedure invoke:
Throw to key `srfi-34' with args `(#<condition &invoke-error [program: "R" arguments: ("CMD" "INSTALL" "--install-tests" "--library=/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depecher-1.0.3/site-library/" "--built-timestamp=1970-01-01" ".") exit-status: 1 term-signal: #f stop-signal: #f] 7c4ec0>)'.
builder for `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv' failed with exit code 1
build of /gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv failed
View build log at '/var/log/guix/drvs/mw/cdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv.bz2'.
guix build: error: build of `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv' failed
--8<---------------cut here---------------end--------------->8---

I’ll modify the build phases to patch out this call to /usr/bin/strip.

-- 
Ricardo

[bug#36797] [PATCH 08/11] gnu: Add r-flowpeaks.

[Ricardo Wurmus]

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

> * gnu/packages/bioconductor.scm (r-flowpeaks): New variable.
[…]
> +    (license license:artistic2.0)))     ;TODO: artistic1.0 does not exist

Unfortunately, version 1.0 of the Artistic License is too unclear to be
considered a free license.  I have excluded this package from the
set of patches that I’ll apply to the master branch.

-- 
Ricardo

[bug#36800] [PATCH 11/11] gnu: Add r-depecher.

[zimoun]

Hi Ricardo,

Thank you for your quick feedback.

On Wed, 24 Jul 2019 at 22:50, Ricardo Wurmus <rekado@elephly.net> wrote:
>
> zimoun <zimon.toutoune@gmail.com> writes:
>
> > * gnu/packages/bioconductor.scm (r-depecher): New variable.
>
> This package cannot actually be built:

Sorry for the annoyance.
I missed `--pure` when I built the package.


> --8<---------------cut here---------------start------------->8---
> …
> if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug DepecheR.so; fi
> /gnu/store/q19l04vd2za80mk1845pz7r8cz29qk43-bash-minimal-4.4.23/bin/bash: /usr/bin/strip: No such file or directory
> make: *** [Makevars:6: strippedLib] Error 127
> ERROR: compilation failed for package ‘DepecheR’
> * removing ‘/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depecher-1.0.3/site-library/DepecheR’
> Backtrace:
>            4 (primitive-load "/gnu/store/f1ky8a22c7s5p053nci05a536j7…")
> In ice-9/eval.scm:
>    191:35  3 (_ #f)
> In srfi/srfi-1.scm:
>    863:16  2 (every1 #<procedure 725d80 at /gnu/store/4p2vk30zhkwxq…> …)
> In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/gnu-build-system.scm:
>    799:28  1 (_ _)
> In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/utils.scm:
>     616:6  0 (invoke _ . _)
>
> /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/utils.scm:616:6: In procedure invoke:
> Throw to key `srfi-34' with args `(#<condition &invoke-error [program: "R" arguments: ("CMD" "INSTALL" "--install-tests" "--library=/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depecher-1.0.3/site-library/" "--built-timestamp=1970-01-01" ".") exit-status: 1 term-signal: #f stop-signal: #f] 7c4ec0>)'.
> builder for `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv' failed with exit code 1
> build of /gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv failed
> View build log at '/var/log/guix/drvs/mw/cdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv.bz2'.
> guix build: error: build of `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv' failed
> --8<---------------cut here---------------end--------------->8---
>
> I’ll modify the build phases to patch out this call to /usr/bin/strip.

Just to understand, you mean patch the file `DepecheR/src/Makevars` to
remove the absolute path `/usr/bin/strip` to simply `strip`. Right?


All the best,
simon

[bug#36800] [PATCH 11/11] gnu: Add r-depecher.

[Ricardo Wurmus]

Hi,

> On Wed, 24 Jul 2019 at 22:50, Ricardo Wurmus <rekado@elephly.net> wrote:
>>
>> zimoun <zimon.toutoune@gmail.com> writes:
>>
>> > * gnu/packages/bioconductor.scm (r-depecher): New variable.
>>
>> This package cannot actually be built:
>
> Sorry for the annoyance.
> I missed `--pure` when I built the package.

You don’t need “--pure” because /usr won’t be available in the build
environment either way.

>> --8<---------------cut here---------------start------------->8---
>> …
>> if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug DepecheR.so; fi
>> /gnu/store/q19l04vd2za80mk1845pz7r8cz29qk43-bash-minimal-4.4.23/bin/bash: /usr/bin/strip: No such file or directory
>> make: *** [Makevars:6: strippedLib] Error 127
>> ERROR: compilation failed for package ‘DepecheR’
>> * removing ‘/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depecher-1.0.3/site-library/DepecheR’
>> Backtrace:
>>            4 (primitive-load "/gnu/store/f1ky8a22c7s5p053nci05a536j7…")
>> In ice-9/eval.scm:
>>    191:35  3 (_ #f)
>> In srfi/srfi-1.scm:
>>    863:16  2 (every1 #<procedure 725d80 at /gnu/store/4p2vk30zhkwxq…> …)
>> In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/gnu-build-system.scm:
>>    799:28  1 (_ _)
>> In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/utils.scm:
>>     616:6  0 (invoke _ . _)
>>
>> /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/utils.scm:616:6: In procedure invoke:
>> Throw to key `srfi-34' with args `(#<condition &invoke-error [program: "R" arguments: ("CMD" "INSTALL" "--install-tests" "--library=/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depecher-1.0.3/site-library/" "--built-timestamp=1970-01-01" ".") exit-status: 1 term-signal: #f stop-signal: #f] 7c4ec0>)'.
>> builder for `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv' failed with exit code 1
>> build of /gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv failed
>> View build log at '/var/log/guix/drvs/mw/cdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv.bz2'.
>> guix build: error: build of `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv' failed
>> --8<---------------cut here---------------end--------------->8---
>>
>> I’ll modify the build phases to patch out this call to /usr/bin/strip.
>
> Just to understand, you mean patch the file `DepecheR/src/Makevars` to
> remove the absolute path `/usr/bin/strip` to simply `strip`. Right?

The Makevars file contains a syntax error.  Instead of joining the
checks with “&&” they used “&” which is for background execution.  So
instead of checking things and proceeding only if the checks passed they
would attempt to execute /usr/bin/strip unconditionally.

I only replaced the & with the intended &&, so now the check for
/usr/bin/strip fails and it’s not executed, which is just fine.

-- 
Ricardo

bug#36797: patches merged

[zimoun]

Dear,

All the patches are merged now; except r-flowpeaks. Because this
package use Artistic1.0 which is not enough clear to be considered
"free" [1,2] (GNU's point of view [3]) and upstream are not
responsive, let clean the bug tracker. :-)

[1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16
[2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html
[3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense

All the best,
simon