version 1.0

DESCRIPTION

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+Package: bioC.logs
+Type: Package
+Title: BioConductor Package Downloads Stats
+Version: 1.0
+Date: 2020-01-30
+Author: Marcelo Ponce [aut, cre]
+Maintainer: Marcelo Ponce <mponce@scinet.utoronto.ca>
+Description: Download stats reports from the BioConductor.org stats website.
+Imports:
+Suggests: knitr, devtools, roxygen2, testthat
+License: GPL (>= 2)
+URL: https://github.com/mponce0/bioC.logs
+BugReports: https://github.com/mponce0/bioC.logs/issues
+RoxygenNote: 6.1.99.9001
+VignetteBuilder: knitr
+NeedsCompilation: no
+Packaged: 2020-01-29 17:35:25 UTC; marcelo
+Repository: CRAN
+Date/Publication: 2020-02-09 16:50:09 UTC

MD5

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+db052d72f4bcfc140af23549ba03869a *DESCRIPTION
+04745393c053f4bdc0ee97deb4e3c010 *NAMESPACE
+88120b57df9509f28d27ed96b6537da3 *R/bioC_logs.R
+5bddfb0fc14039966bc23db9a3e1b016 *README.md
+c24c7ae9e7bbb60722f5c5fdd6d7841c *build/vignette.rds
+3c9e2d06e8560272e30c98b0c827478b *inst/doc/bioC.logs.R
+5110dbd41904072d7d9d356009f9f177 *inst/doc/bioC.logs.Rmd
+d3eef214a95bea5353ed7eda390e1b9c *inst/doc/bioC.logs.html
+706eb66f1ed2a9b8ea80254cd78e985c *man/bioC_downloads.Rd
+5110dbd41904072d7d9d356009f9f177 *vignettes/bioC.logs.Rmd

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(bioC_downloads)
+importFrom(utils,read.table)

R/bioC_logs.R

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+bioC_downloads <- function(pckg=NULL, format="bioC", verbose=TRUE) {
+#' function to download logs from bioConductor stats
+#' @param  pckg  list of packages names
+#' @param  format  two options: "bioC" (default) will report the downloads as reported by bioconductor, ie. "Year Month Nb_of_distinct_IPs Nb_of_downloads"; or, "CRAN" will report as CRAN logs does, ie. "Date  Nb_of_downloads package_Name"
+#' @param  verbose  boolean flag indicating whether to print information about the processes...
+#'
+#' @return a list containing a dataframe per package entered with columns as indicated by the format argument
+#'
+#' @importFrom utils  read.table
+#' @export
+#'
+#' @examples
+#' bioC_downloads(c("ABarray","a4Classif"))
+#' bioC_downloads("edgeR",verbose=FALSE)
+#' edgeR.logs <- bioC_downloads("edgeR",format="CRAN")
+#' 
+
+	## function for error handling
+	errorHandling.Msg <- function(condition,pck) {
+		message("A problem was detected when trying to retrieve the data for the package: ",pck)
+		if (grepl("404 Not Found",condition)) {
+			message("It is possible that you misspeled the name of this package! Please check!")
+		} else {
+			message("It is possible that your internet connection is down! Please check!")
+		}
+		message(condition,'\n')
+
+		# update problems counter
+		pkg.env$problems <- pkg.env$problems + 1
+	}
+
+
+	# Define bioConductor URL and file ending
+	bioC.url <- "http://bioconductor.org/packages/stats/bioc/"
+	ending <- "_stats.tab"
+
+	# initialize container for results
+	pckgs.stats <-c() 
+
+	# check valid argument
+	if (is.null(pckg) || !is.character(pckg)) {
+		warning("Must specify a valid package name!")
+		return(NULL)
+	}
+
+	# Counter for detection or problems, defined within the pckg environ to avoid global variables, ie. <<- 
+	pkg.env <- new.env()
+	pkg.env$problems <- 0
+
+	# process package list
+	for (i in seq_along(pckg)) {
+		pck <- pckg[i]
+
+		pckgFile <- paste0(pck,'/',pck,ending)
+		pckg.URL <- paste0(bioC.url,pckgFile)
+
+		# Attempt to protect against bad internet conenction or misspelled package name
+		tryCatch(
+			{
+			pckg.data <- read.table(pckg.URL, header=TRUE)
+
+			if (format=="CRAN") {
+				if (i==1 && verbose) message("Data will be returned as 'date  downloads  packageName'")
+
+				# clean the entrie 'all' totals per year...
+				clean.data <- pckg.data[!as.character(pckg.data$Month)=="all",]
+				new.df <- data.frame(date=as.Date(paste0("28",clean.data$Month,clean.data$Year), "%d%b%Y"),
+					downloads=as.numeric(clean.data$Nb_of_downloads), package=pck)
+				pckg.data <- new.df
+			}
+
+			pckgs.stats[[i]] <- pckg.data 
+			},
+
+			# warning
+			warning = function(cond) {
+					errorHandling.Msg(cond,pck)
+				},
+			# error
+			error = function(e){
+					errorHandling.Msg(e,pck)
+				}
+			)
+	}
+
+	# final report
+	if (verbose) {
+		message(paste(i-pkg.env$problems)," packages processed from a total of ",i," requests!")
+		if ((i-pkg.env$problems) != 0) message("Data was retrieved from ",bioC.url," using the *",format,"* format.")
+
+		# problems report
+		if (pkg.env$problems != 0)
+			message(pkg.env$problems," problems detected, the associated entry will be set to NULL")
+	}
+
+	# return results
+	return(pckgs.stats)
+}

README.md

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+# bioC.logs
+
+## Introduction
+This package allows you to download the statistics of BioConductor packages'
+downloads as reported by http://bioconductor.org/packages/stats/.
+
+
+## Usage
+The main function of this package is called ```bioC_downloads```.
+The function accepts several arguments: `packages names`, `format` and `verbose`.
+
+argument	 | Description
+-----------|---------------
+`packages names` | is the name(s) of the package(s) you want to download the stats, for multiple package it should be a list of the packages names
+`format`     | accepts two options: `"bioC"` (default) will report the downloads as reported by bioconductor, ie. *"Year Month Nb_of_distinct_IPs Nb_of_downloads"*; or, `"CRAN"` will report as CRAN logs does, ie. *"Date  Nb_of_downloads package_Name"*
+`verbose`    | is a boolean flag indicating whether to print information about the processes
+---------------------------
+
+* The function will return a list containing a dataframe per package entered with columns as indicated by the `format` argument
+Notice that when the `format` is set to "CRAN", the date will be formatted to days-month-year. Because BioConductor reports only totals per month the "day" in this case will be set to **28** for every month.
+
+* The function will also attempt to report when a package names has been misspelled or just the server is not reachable.
+If you are receiving warning messages please check either of these situations.
+
+
+
+## Installation
+
+For using the "bioC.logs" package, first you will need to install it.
+
+Thes table version can be downloaded from the CRAN repository:
+```
+install.packages("bioC.logs")
+```
+
+To obtain the development version you can get it from the github repository, i.e.
+```
+# need devtools for installing from the github repo
+install.packages("devtools")
+
+# install bioC.logs
+devtools::install_github("mponce0/bioC.logs")
+
+# load bioC.logs
+library(bioC.logs)
+```
+
+
+## Examples
+You will need an active internet connection, as bioC.logs will download the
+reports from the BioConductor website on demand.
+
+```
+bioC_downloads(c("ABarray","a4Classif"))
+
+bioC_downloads("edgeR",verbose=FALSE)
+
+edgeR.logs <- bioC_downloads("edgeR",format="CRAN")
+```

inst/doc/bioC.logs.R

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+## ---- include = FALSE---------------------------------------------------------
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+

inst/doc/bioC.logs.Rmd

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+---
+title: "bioC.logs: Stats logs from BioConductor packages downloads"
+author: "Marcelo Ponce"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{bioC.logs Package}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+  %\usepackage[UTF-8]{inputenc}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r child = "../README.md"}
+```
+