Disable ENCODE and Zebrafish support.

The requireNamespace() calls cause a WARNING if the packages are not
in the Suggests line of DESCRIPTION.  The warnign causes GitHub CI
to stop in error.  Adding the packages in Suggests causes the CI
to crash at package install time because they are only available
from http://promshift.genereg.net/CAGEr/PackageSource.  I attempted
to solve this using the following in DESCRIPTION

Remotes:
    - url::http://promshift.genereg.net/CAGEr/PackageSource/ENCODEprojectCAGE_1.0.1.tar.gz,
    - url::http://promshift.genereg.net/CAGEr/PackageSource/ZebrafishDevelopmentalCAGE_0.99.0.tar.gz

However, this causes crashes because ENCODEprojectCAGE needs
pdflatex to build.  I do not know how to support that in Win
and Mac, therefore I am giving up for the momment.

The best solution would be to get these packages in Bioconductor too.

Author: Charles Plessy

R/ImportMethods.R

@@ -822,44 +822,45 @@ setGeneric("importPublicData",
 }
 
 .importPublicData_ENCODE <- function (dataset, group = NULL, sample = NULL) {
-  if (length(unique(dataset))>1) stop ("Merging datasets not supported yet.")
-  if (! requireNamespace("ENCODEprojectCAGE"))
-    stop ("This function requires the ", dQuote("ENCODEprojectCAGE"), " package.",
-          " package; please install it from http://promshift.genereg.net/CAGEr/PackageSource/.")
-  if (dataset == "ENCODEtissueCAGEfly") {
-    if (group != "embryo") stop("Only 'embryo' is allowed as group for dataset 'ENCODEtissueCAGEfly'.")
-    if (sample != "mixed_embryos_0-24hr") stop("Only 'mixed_embryos_0-24hr' is allowed as sample for dataset 'ENCODEtissueCAGEfly'.")
-    if (! requireNamespace("BSgenome.Dmelanogaster.UCSC.dm3"))
-      stop ("This function requires the ", dQuote("BSgenome.Dmelanogaster.UCSC.dm3"), " package.")
-    genome.name <- "BSgenome.Dmelanogaster.UCSC.dm3"
-    ENCODEtissueCAGEfly <- NULL
-    data("ENCODEtissueCAGEfly", package = "ENCODEprojectCAGE", envir = environment())
-    df <- ENCODEtissueCAGEfly$embryo
-  } else {
-    if (! requireNamespace("BSgenome.Hsapiens.UCSC.hg19"))
-      stop ("This function requires the ", dQuote("BSgenome.Hsapiens.UCSC.hg19"), " package.")
-    genome.name <- "BSgenome.Hsapiens.UCSC.hg19"
-    ENCODEhumanCellLinesSamples <- NULL
-    data("ENCODEhumanCellLinesSamples", package = "ENCODEprojectCAGE", envir = environment())
-    info.df <- ENCODEhumanCellLinesSamples
-    if(!(all(dataset %in% info.df$dataset)))
-      stop("Specified dataset(s) not found! Call data(ENCODEhumanCellLinesSamples) and check 'dataset' column for available ENCODE datasets!")
-    if(!(all(group %in% info.df[info.df$dataset == dataset,"group"])))
-      stop("Some of the provided groups cannot be found in the specified dataset!")
-    if(!(all(sample %in% info.df[,"sample"])))
-      stop("Some of the provided samples cannot be found!")
-    data(list= dataset, package = "ENCODEprojectCAGE", envir = environment())
-    df <- get(dataset)[[group]]
-  }
-  se <- .df2SE(df, sample, genome.name)
-  ce <- CAGEexp(genomeName = genome.name,
-                colData = DataFrame( sampleLabels = make.names(sample),
-                                     inputFiles = NA,
-                                     inputFilesType = 'ctss',
-                                     librarySizes = sapply(assay(se), sum),
-                                     row.names = make.names(sample)))
-  CTSStagCountSE(ce) <- se
-  ce
+  stop("ENCODE data support disabled until I find a way to suggest ENCODEprojectCAGE without causing CI crash in GitHub because of WARNING.")
+  # if (length(unique(dataset))>1) stop ("Merging datasets not supported yet.")
+  # if (! requireNamespace("ENCODEprojectCAGE"))
+  #   stop ("This function requires the ", dQuote("ENCODEprojectCAGE"), " package.",
+  #         " package; please install it from http://promshift.genereg.net/CAGEr/PackageSource/.")
+  # if (dataset == "ENCODEtissueCAGEfly") {
+  #   if (group != "embryo") stop("Only 'embryo' is allowed as group for dataset 'ENCODEtissueCAGEfly'.")
+  #   if (sample != "mixed_embryos_0-24hr") stop("Only 'mixed_embryos_0-24hr' is allowed as sample for dataset 'ENCODEtissueCAGEfly'.")
+  #   if (! requireNamespace("BSgenome.Dmelanogaster.UCSC.dm3"))
+  #     stop ("This function requires the ", dQuote("BSgenome.Dmelanogaster.UCSC.dm3"), " package.")
+  #   genome.name <- "BSgenome.Dmelanogaster.UCSC.dm3"
+  #   ENCODEtissueCAGEfly <- NULL
+  #   data("ENCODEtissueCAGEfly", package = "ENCODEprojectCAGE", envir = environment())
+  #   df <- ENCODEtissueCAGEfly$embryo
+  # } else {
+  #   if (! requireNamespace("BSgenome.Hsapiens.UCSC.hg19"))
+  #     stop ("This function requires the ", dQuote("BSgenome.Hsapiens.UCSC.hg19"), " package.")
+  #   genome.name <- "BSgenome.Hsapiens.UCSC.hg19"
+  #   ENCODEhumanCellLinesSamples <- NULL
+  #   data("ENCODEhumanCellLinesSamples", package = "ENCODEprojectCAGE", envir = environment())
+  #   info.df <- ENCODEhumanCellLinesSamples
+  #   if(!(all(dataset %in% info.df$dataset)))
+  #     stop("Specified dataset(s) not found! Call data(ENCODEhumanCellLinesSamples) and check 'dataset' column for available ENCODE datasets!")
+  #   if(!(all(group %in% info.df[info.df$dataset == dataset,"group"])))
+  #     stop("Some of the provided groups cannot be found in the specified dataset!")
+  #   if(!(all(sample %in% info.df[,"sample"])))
+  #     stop("Some of the provided samples cannot be found!")
+  #   data(list= dataset, package = "ENCODEprojectCAGE", envir = environment())
+  #   df <- get(dataset)[[group]]
+  # }
+  # se <- .df2SE(df, sample, genome.name)
+  # ce <- CAGEexp(genomeName = genome.name,
+  #               colData = DataFrame( sampleLabels = make.names(sample),
+  #                                    inputFiles = NA,
+  #                                    inputFilesType = 'ctss',
+  #                                    librarySizes = sapply(assay(se), sum),
+  #                                    row.names = make.names(sample)))
+  # CTSStagCountSE(ce) <- se
+  # ce
 } 
 
 .importPublicData_F34 <- function (dataset, group = NULL, sample = NULL) {
@@ -945,35 +946,36 @@ setGeneric("importPublicData",
 }
 
 .importPublicData_ZF <- function(group = "development", sample = NULL) {
-  if (group != "development")
-    stop("Invalid group name! There is only one group in this dataset named 'development'.")
-  if (! requireNamespace("ZebrafishDevelopmentalCAGE"))
-    stop ("This function requires the ", dQuote("ZebrafishDevelopmentalCAGE"),
-          " package; please install it from http://promshift.genereg.net/CAGEr/PackageSource/.")
-  if (! requireNamespace("BSgenome.Drerio.UCSC.danRer7"))
-    stop ("This function requires the ", dQuote("BSgenome.Drerio.UCSC.danRer7"), " package.")
-
-  ZebrafishSamples <- NULL
-  data("ZebrafishSamples", package = "ZebrafishDevelopmentalCAGE", envir = environment())
-  
-  validSampleNames <- levels(ZebrafishSamples$sample)
-  if (is.null(sample )) sample <- validSampleNames
-  if ( ! all(sample %in% validSampleNames))
-    stop("At least one sample name is not valid. ",
-         "Valid sample names are: ", paste(validSampleNames, collapse = ", "), ".")
-  
-  ZebrafishCAGE <- NULL
-  data("ZebrafishCAGE", package = "ZebrafishDevelopmentalCAGE", envir = environment())
-  # The vignette of ZebrafishDevelopmentalCAGE states that the provided coordinates are 1-based.
-  ctssSE <- .df2SE(ZebrafishCAGE$development, sample, "BSgenome.Drerio.UCSC.danRer7")
-  ce <- CAGEexp(genomeName = "BSgenome.Drerio.UCSC.danRer7",
-                colData = DataFrame( sampleLabels = sample,
-                                     inputFiles = NA,
-                                     inputFilesType = 'ctss',
-                                     librarySizes = sapply(assay(ctssSE), sum),
-                                     row.names = sample))
-  CTSStagCountSE(ce) <- ctssSE
-  ce
+  stop("Zebrafish data support disabled until I find a way to suggest ZebrafishDevelopmentalCAGE without causing CI crash in GitHub because of WARNING.")
+  # if (group != "development")
+  #   stop("Invalid group name! There is only one group in this dataset named 'development'.")
+  # if (! requireNamespace("ZebrafishDevelopmentalCAGE"))
+  #   stop ("This function requires the ", dQuote("ZebrafishDevelopmentalCAGE"),
+  #         " package; please install it from http://promshift.genereg.net/CAGEr/PackageSource/.")
+  # if (! requireNamespace("BSgenome.Drerio.UCSC.danRer7"))
+  #   stop ("This function requires the ", dQuote("BSgenome.Drerio.UCSC.danRer7"), " package.")
+  # 
+  # ZebrafishSamples <- NULL
+  # data("ZebrafishSamples", package = "ZebrafishDevelopmentalCAGE", envir = environment())
+  # 
+  # validSampleNames <- levels(ZebrafishSamples$sample)
+  # if (is.null(sample )) sample <- validSampleNames
+  # if ( ! all(sample %in% validSampleNames))
+  #   stop("At least one sample name is not valid. ",
+  #        "Valid sample names are: ", paste(validSampleNames, collapse = ", "), ".")
+  # 
+  # ZebrafishCAGE <- NULL
+  # data("ZebrafishCAGE", package = "ZebrafishDevelopmentalCAGE", envir = environment())
+  # # The vignette of ZebrafishDevelopmentalCAGE states that the provided coordinates are 1-based.
+  # ctssSE <- .df2SE(ZebrafishCAGE$development, sample, "BSgenome.Drerio.UCSC.danRer7")
+  # ce <- CAGEexp(genomeName = "BSgenome.Drerio.UCSC.danRer7",
+  #               colData = DataFrame( sampleLabels = sample,
+  #                                    inputFiles = NA,
+  #                                    inputFilesType = 'ctss',
+  #                                    librarySizes = sapply(assay(ctssSE), sum),
+  #                                    row.names = sample))
+  # CTSStagCountSE(ce) <- ctssSE
+  # ce
 }
 
 #' @rdname importPublicData