[bug#61891] [PATCH] gnu: Add r-biglm, r-cplm, r-som, r-chemometrics, r-metagenomeseq, r-maaslin2, r-mmuphin.

[bug#61891] [PATCH] gnu: Add r-biglm, r-cplm, r-som, r-chemometrics, r-metagenomeseq, r-maaslin2, r-mmuphin.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-biglm, r-cplm, r-som, r-chemometrics): New 
variables.

* gnu/packages/bioconductor.scm (r-metagenomeseq, r-maaslin2, 
r-mmuphin): New variables.

[bug#61891] [PATCH 1/7] gnu: Add r-biglm.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-biglm): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c7a81b96eb..fc8fe1a449 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1145,6 +1145,25 @@ (define-public r-bezier
 degree elevation and curve fitting.")
     (license license:gpl2+)))
 
+(define-public r-biglm
+  (package
+    (name "r-biglm")
+    (version "0.9-2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "biglm" version))
+       (sha256
+        (base32 "0iy9xr2bq42wlizgwlz7w5kh9206yqkw9h2cr6mcsmizgjg3rkvd"))))
+    (properties `((upstream-name . "biglm")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-dbi))
+    (native-inputs (list gfortran))
+    (home-page "https://cran.r-project.org/package=biglm")
+    (synopsis "Bounded memory linear and generalized linear models")
+    (description "Regression for data too large to fit in memory.")
+    (license (list license:gpl2+ license:gpl3+)))) ;;expanded from GPL
+
 (define-public r-bwstest
   (package
     (name "r-bwstest")

base-commit: efa091f9f4e77068353dff24f0ccd2d0613c3f48
-- 
2.39.1

[bug#61891] [PATCH 2/7] gnu: Add r-cplm.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-cplm): New variable.
---
 gnu/packages/cran.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index fc8fe1a449..ddff93aa0d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -325,6 +325,41 @@ (define-public r-collections
 queues, stacks, deques, dicts and ordered dicts.")
     (license license:expat)))
 
+(define-public r-cplm
+  (package
+    (name "r-cplm")
+    (version "0.7-10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "cplm" version))
+       (sha256
+       (base32 "0mqjk10265hq9bc5ihmgbx1l8fzay1gpdlvx3pirqmvr3w1kwlxk"))))
+    (properties `((upstream-name . "cplm")))
+    (build-system r-build-system)
+    (propagated-inputs
+      (list r-biglm
+            r-coda
+            r-ggplot2
+            r-matrix
+            r-minqa
+            r-nlme
+            r-reshape2
+            r-statmod
+            r-tweedie))
+    (home-page "https://github.com/actuaryzhang/cplm")
+    (synopsis "Compound Poisson linear models")
+    (description "The Tweedie compound Poisson distribution is a mixture of a
+degenerate distribution at the origin and a continuous distribution on the positive
+real line.  It has been applied in a wide range of fields in which continuous data
+with exact zeros regularly arise.  The cplm package provides likelihood based and
+Bayesian procedures for fitting common Tweedie compound Poisson linear models.
+In particular, models with hierarchical structures or extra zero inflation can be
+handled.  Further, the package implements the Gini index based on an ordered version
+of the Lorenz curve as a robust model comparison tool involving zero-inflated and
+highly skewed distributions.")
+    (license license:gpl2+)))
+
 (define-public r-curry
   (package
     (name "r-curry")
-- 
2.39.1

[bug#61891]

[Mădălin Ionel Patrașcu]

Date: Thu, 23 Feb 2023 00:56:33 +0100
Subject: [PATCH 3/7] gnu: Add r-som.

* gnu/packages/cran.scm (r-som): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ddff93aa0d..b3aff2ee2c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16017,6 +16017,34 @@ (define-public r-softimpute
 components).")
     (license license:gpl2)))
 
+(define-public r-som
+  (package
+    (name "r-som")
+    (version "0.3-5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "som" version))
+       (sha256
+        (base32 "1fbza1jxvwrkf5x3inkj36vshhkn7mz0ajqlxalbfmk6ngjw1x56"))))
+    (properties `((upstream-name . "som")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/package=som")
+    (synopsis "Self-organizing map")
+    (description
+     "This package implements a self-organizing map which has application in gene
+clustering.  It provides functions like:
+@itemize
+@item filtering data by certain floor, ceiling, max/min ratio, and max - min
+difference;
+@item normalization of the data;
+@item get the average distortion measure;
+@item train a self-organizing map;
+@item summarize a som object;
+@item yeast cell cycle.
+@end itemize")
+    (license license:gpl3+)))
+
 (define-public r-fftwtools
   (package
     (name "r-fftwtools")
-- 
2.39.1

[bug#61891]

[Mădălin Ionel Patrașcu]

Date: Thu, 23 Feb 2023 01:20:10 +0100
Subject: [PATCH 4/7] gnu: Add r-chemometrics.

* gnu/packages/cran.scm (r-chemometrics): New variable.
---
 gnu/packages/cran.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b3aff2ee2c..fc24f3eafc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17025,6 +17025,44 @@ (define-public r-chemometricswithr
 Life Sciences\" by Ron Wehrens, Springer (2011).")
     (license license:gpl2+)))
 
+(define-public r-chemometrics
+  (package
+    (name "r-chemometrics")
+    (version "1.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "chemometrics" version))
+       (sha256
+        (base32 "0shqns0n964pfwnd0q5sadglrlpgs4g5fbv45fsj9p37l4pq61dp"))))
+    (properties `((upstream-name . "chemometrics")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-class
+           r-e1071
+           r-lars
+           r-mass
+           r-mclust
+           r-nnet
+           r-pcapp
+           r-pls
+           r-robustbase
+           r-rpart
+           r-som))
+    (home-page "http://www.statistik.tuwien.ac.at/public/filz/")
+    (synopsis "Multivariate statistical analysis in Chemometrics")
+    (description
+     "Multivariate data analysis is the simultaneous observation of more than one
+characteristic.  In contrast to the analysis of univariate data, in this approach
+not only a single variable or the relation between two variables can be investigated,
+but the relations between many attributes can be considered.  For the statistical
+analysis of chemical data one has to take into account the special structure of
+this type of data.  This package contains about 30 functions, mostly for regression,
+classification and model evaluation and includes some data sets used in the R help
+examples.  It was designed as a R companion to the book \"Introduction to Multivariate
+Statistical Analysis in Chemometrics\" written by K. Varmuza and P. Filzmoser (2009).")
+    (license license:gpl3+)))
+
 (define-public r-als
   (package
     (name "r-als")
-- 
2.39.1

[bug#61891]

[Mădălin Ionel Patrașcu]

Date: Thu, 23 Feb 2023 01:35:43 +0100
Subject: [PATCH 5/7] gnu: Add r-metagenomeseq.

* gnu/packages/bioconductor.scm (r-metagenomeseq): New variable.
---
 gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4b5ec7db28..7de5750e09 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6644,6 +6644,39 @@ (define-public r-maser
 and visualizaton of alternative splicing events generated by rMATS.")
     (license license:expat)))
 
+(define-public r-metagenomeseq
+  (package
+    (name "r-metagenomeseq")
+    (version "1.40.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "metagenomeSeq" version))
+       (sha256
+        (base32 "01wjw4kcm8ysa5sn3cqg4a9i5pyksnwmbdqp5fr6n2l9hllkc9jy"))))
+    (properties `((upstream-name . "metagenomeSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-foreach
+           r-glmnet
+           r-gplots
+           r-limma
+           r-matrix
+           r-matrixstats
+           r-rcolorbrewer
+           r-wrench))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/HCBravoLab/metagenomeSeq")
+    (synopsis "Statistical analysis for sparse high-throughput sequencing")
+    (description
+     "MetagenomeSeq is designed to determine features (be it @acronym{OTU, Operational
+Taxanomic Unit}, species, etc.) that are differentially abundant between two or
+more groups of multiple samples.  This package is designed to address the effects
+of both normalization and under-sampling of microbial communities on disease
+association detection and the testing of feature correlations.")
+    (license license:artistic2.0)))
+
 (define-public r-metaneighbor
   (package
     (name "r-metaneighbor")
-- 
2.39.1

[bug#61891]

[Mădălin Ionel Patrașcu]

Date: Wed, 1 Mar 2023 04:17:48 +0100
Subject: [PATCH 6/7] gnu: Add r-maaslin2.

* gnu/packages/bioconductor.scm (r-maaslin2): New variable.
---
 gnu/packages/bioconductor.scm | 51 +++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7de5750e09..c7f623343e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6533,6 +6533,57 @@ (define-public r-limma
 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
     (license license:gpl2+)))
 
+(define-public r-maaslin2
+  (package
+    (name "r-maaslin2")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Maaslin2" version))
+       (sha256
+        (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89"))))
+    (properties `((upstream-name . "Maaslin2")))
+    (build-system r-build-system)
+    (arguments (list #:tests? #f)) ;test suite is non-deterministic :(
+    (propagated-inputs
+     (list r-biglm
+           r-car
+           r-chemometrics
+           r-cplm
+           r-data-table
+           r-dplyr
+           r-edger
+           r-ggplot2
+           r-glmmtmb
+           r-hash
+           r-lme4
+           r-lmertest
+           r-logging
+           r-lpsymphony
+           r-mass
+           r-mumin
+           r-metagenomeseq
+           r-optparse
+           r-pbapply
+           r-pcapp
+           r-pheatmap
+           r-pscl
+           r-rmarkdown
+           r-robustbase
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "http://huttenhower.sph.harvard.edu/maaslin2")
+    (synopsis
+     "Multivariable association discovery in population-scale meta-omics studies")
+    (description
+     "MaAsLin2 is comprehensive R package for efficiently determining multivariable
+association between clinical metadata and microbial meta'omic features.  This
+package relies on general linear models to accommodate most modern epidemiological
+study designs, including cross-sectional and longitudinal, and offers a variety
+of data exploration, normalization, and transformation methods.")
+    (license license:expat)))
+
 (define-public r-made4
   (package
     (name "r-made4")
-- 
2.39.1

[bug#61891]

[Mădălin Ionel Patrașcu]

Date: Wed, 1 Mar 2023 08:16:27 +0100
Subject: [PATCH 7/7] gnu: Add r-mmuphin.

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c7f623343e..afe969e5de 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6811,6 +6811,46 @@ (define-public r-methylkit
 TAB-Seq.")
     (license license:artistic2.0)))
 
+(define-public r-mmuphin
+  (package
+    (name "r-mmuphin")
+    (version "1.12.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MMUPHin" version))
+       (sha256
+        (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62"))))
+    (properties `((upstream-name . "MMUPHin")))
+    (build-system r-build-system)
+    (arguments
+     (list #:tests? #f)) ;; non deterministic, also it requieres http access
+    (inputs (list glpk))
+    (propagated-inputs
+     (list r-cowplot
+           r-biocstyle
+           r-dplyr
+           r-fpc
+           r-ggplot2
+           r-igraph
+           r-maaslin2
+           r-metafor
+           r-stringr
+           r-tidyr))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/MMUPHin")
+    (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome")
+    (description
+     "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts.  It
+has function interfaces for:
+@itemize
+@item covariate-controlled batch- and cohort effect adjustment;
+@item meta-analysis differential abundance testing;
+@item meta-analysis unsupervised discrete structure (clustering) discovery;
+@item meta-analysis unsupervised continuous structure discovery.
+@end itemize")
+    (license license:expat)))
+
 (define-public r-motifrg
   (package
     (name "r-motifrg")
-- 
2.39.1

[bug#61891]

[Mădălin Ionel Patrașcu]

Date: Wed, 1 Mar 2023 11:50:40 +0100
Subject: [PATCH] gnu: Test builds for r-maaslin and r-mmuphin.scm

This is my try to make the build of these two package reproducible.

I send this only in the case if the reviewer wants to dig more and maybe he can
solve the non deterministic build.
---
 gnu/packages/bioconductor.scm | 138 ++++++++++++++++++++++++++++++++++
 1 file changed, 138 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7de5750e09..15fad711af 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -33,6 +33,7 @@ (define-module (gnu packages bioconductor)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (guix build-system r)
   #:use-module (gnu packages)
@@ -6533,6 +6534,80 @@ (define-public r-limma
 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
     (license license:gpl2+)))
 
+(define-public r-maaslin2
+  (package
+    (name "r-maaslin2")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Maaslin2" version))
+       (sha256
+        (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89"))))
+    (properties `((upstream-name . "Maaslin2")))
+    (build-system r-build-system)
+    (arguments (list ;;#:tests? #f)) ;test suite is non-deterministic :(
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; During the check there is needed for writable cache directory
+          ;; Fontconfig error: No writable cache directories
+          (add-before 'check 'set-cache
+            (lambda _
+              (setenv "XDG_CACHE_HOME" "/tmp/xdg-cache")))
+          ;; The check phase generates some log and pdf files. This cause that
+          ;; the build to be not reproducible
+          (add-after 'check 'make-reproducible
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (string-append (assoc-ref outputs "out") "/site-library/Maaslin2/")))
+                (for-each delete-file-recursively
+                   (list ;;(string-append out "Maaslin2-Ex.Rout")
+                       ;;(string-append #$output "/Maaslin2-Ex.pdf")
+                       ;;(string-append #$output "/Maaslin2-tests/testthat/output")
+                       ;;(string-append #$output "/Maaslin2-tests/testthat/output2")
+                       ;;(string-append #$output "Maaslin2-tests/testthat.Rout")
+                       (string-append out "doc/demo_output/maaslin2.log")
+                       (string-append out "doc/demo_output/figures")
+                       ;;"doc/demo_output"
+                       )))))
+                       )))
+    (propagated-inputs
+     (list r-biglm
+           r-car
+           r-chemometrics
+           r-cplm
+           r-data-table
+           r-dplyr
+           r-edger
+           r-ggplot2
+           r-glmmtmb
+           r-hash
+           r-lme4
+           r-lmertest
+           r-logging
+           r-lpsymphony
+           r-mass
+           r-mumin
+           r-metagenomeseq
+           r-optparse
+           r-pbapply
+           r-pcapp
+           r-pheatmap
+           r-pscl
+           r-rmarkdown
+           r-robustbase
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "http://huttenhower.sph.harvard.edu/maaslin2")
+    (synopsis
+     "Multivariable association discovery in population-scale meta-omics studies")
+    (description
+     "MaAsLin2 is comprehensive R package for efficiently determining multivariable
+association between clinical metadata and microbial meta'omic features.  This
+package relies on general linear models to accommodate most modern epidemiological
+study designs, including cross-sectional and longitudinal, and offers a variety
+of data exploration, normalization, and transformation methods.")
+    (license license:expat)))
+
 (define-public r-made4
   (package
     (name "r-made4")
@@ -6760,6 +6835,69 @@ (define-public r-methylkit
 TAB-Seq.")
     (license license:artistic2.0)))
 
+(define-public r-mmuphin
+  (package
+    (name "r-mmuphin")
+    (version "1.12.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MMUPHin" version))
+       (sha256
+        (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62"))))
+    (properties `((upstream-name . "MMUPHin")))
+    (build-system r-build-system)
+    (arguments
+     (list ;;#:tests? #f)) ;; non deterministic, also it requieres http access
+      #:phases
+      #~(modify-phases %standard-phases
+        (add-after 'unpack 'adjusts-paths
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            (substitute* "inst/doc/MMUPHin.Rmd"
+                       (("../man/figures")
+                        (string-append #$output "/site-library/MMUPHin/help/figures")))
+            ;;(substitute* "inst/doc/MMUPHin.R"
+            ;;           (("library(ggplot2)") "library(ggplot2)\ngetwd()"))
+            ))
+        (add-after 'install 'add-files
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            (install-file "man/figures/structure_types.PNG"
+                          (string-append #$output "/site-library/MMUPHin/help/figures"))
+            (install-file "vignettes/references.bib"
+                          (string-append #$output "/site-library/MMUPHin/doc"))))
+        (add-before 'check 'set-cache
+          (lambda _
+            (setenv "XDG_CACHE_HOME" "/tmp/xdg-cache")))
+        )))
+    (inputs (list glpk
+ ;                 ;;pandoc
+ ;                 ;;r-rmarkdown
+                  ))
+    (propagated-inputs
+     (list r-cowplot
+           r-biocstyle
+           r-dplyr
+           r-fpc
+           r-ggplot2
+           r-igraph
+           r-maaslin2
+           r-metafor
+           r-stringr
+           r-tidyr))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/MMUPHin")
+    (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome")
+    (description
+     "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts.  It
+has function interfaces for:
+@itemize
+@item covariate-controlled batch- and cohort effect adjustment;
+@item meta-analysis differential abundance testing;
+@item meta-analysis unsupervised discrete structure (clustering) discovery;
+@item meta-analysis unsupervised continuous structure discovery.
+@end itemize")
+    (license license:expat)))
+
 (define-public r-motifrg
   (package
     (name "r-motifrg")

base-commit: efa091f9f4e77068353dff24f0ccd2d0613c3f48
prerequisite-patch-id: 9e08f9ff2621a13d751e3d82c0837144b09494e4
prerequisite-patch-id: 4cfeb51eeb402b18b0d23c6782255a3bc1f1ff43
prerequisite-patch-id: cf4c417ccd15ef1f795ada39f3faee9f59bb3c36
prerequisite-patch-id: d79a8e82e46ec03cf54f25ec101a5b54592fdb1b
prerequisite-patch-id: 81871608ddab1ba624de7432ad473e52221efc08
-- 
2.39.1

bug#61891:

[Ricardo Wurmus]

Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

> Date: Wed, 1 Mar 2023 11:50:40 +0100
> Subject: [PATCH] gnu: Test builds for r-maaslin and r-mmuphin.scm
>
> This is my try to make the build of these two package reproducible.
>
> I send this only in the case if the reviewer wants to dig more and maybe he can
> solve the non deterministic build.

I managed to get r-mmuphin to build reproducibly, but for r-maaslin the
problem is that the scatterplots are non-deterministic.  I’ve opened a
new bug report for that and pushed the rest of the patches.

-- 
Ricardo