cmsy_system(): 检查本机的CMSY++运行环境并选择相应设置

英文原页：cmsy_system()

说明

本函数查明电脑的操作系统、R版本和处理器，检查是否已安装JAGS和CMSY++所需的R包，并显示cmsy_run()在该系统上将使用的设置。

English

This function finds the operating system, R version and processor of the computer, checks whether JAGS and the R packages that CMSY++ needs are installed, and shows the settings that cmsy_run() will use on this system.

用法

cmsy_system(
  os = "auto",
  device = c("file", "screen"),
  jags = "recommended",
  silent = fao_setting("silent")
)

参数

os

采用哪个操作系统的设置：“auto”（默认，自动检测）、“windows”、“macos”或”linux”。

English

The operating system whose settings are used: “auto” (default, detect it), “windows”, “macos” or “linux”.

device

CMSY++把图表保存为JPEG文件之前在哪里绘制图表：“file”（默认），即在所有系统上和批处理运行中都能使用的离屏绘图设备；或”screen”，即系统自己的绘图窗口（windows()、quartz()或x11()）。

English

Where CMSY++ draws its charts before saving them as JPEG files: “file” (default), an off-screen device that works on every system and in batch runs, or “screen”, the system’s own window (windows(), quartz() or x11()).

jags

推荐的JAGS版本：“recommended”（默认；针对当前R版本编译的最新JAGS 4版本，可与CRAN上的rjags配合使用）、“latest”（JAGS 5.0.0，需要SourceForge上的rjags 5-x）或版本号，例如”4.3.2”。

English

The JAGS version to recommend: “recommended” (default; the newest JAGS 4 release built for this R version, which works with rjags from CRAN), “latest” (JAGS 5.0.0, which needs rjags 5-x from SourceForge) or a version number such as “4.3.2”.

silent

逻辑值。为TRUE时不输出汇总信息。默认为FALSE，或fao_settings(silent = )设置的值。

English

A logical value. If TRUE, no summary is printed. Default is FALSE, or the value set with fao_settings(silent = ).

返回值

以不可见方式返回一个列表，包括系统信息（os、os_detected、arch、r_version）、已安装的jags和rjags版本、packages表、推荐的jags_installer和rjags_source、图表的device和antialias设置，以及对CMSY++代码所做的修改changes。

English

Invisibly, a list with the system (os, os_detected, arch, r_version), the installed jags and rjags versions, the packages table, the recommended jags_installer and rjags_source, the chart device and antialias settings, and the changes made to the CMSY++ code.

详细说明

CMSY++代码（CMSY++16.R）是在Windows上编写的。其用户手册（第12步）要求Mac用户把所有windows()调用改为quartz()，把antialias = "cleartype"改为antialias = "default"，在其他系统上则把windows()注释掉。代码用grepl("win", sysname)判断是否为Windows，而这一判断在macOS（“Darwin”）上也为真，所以在Mac上代码会调用windows()并报错停止。cmsy_run()会针对本函数检测到的系统，在代码副本中自动完成这些修改；包内的原始代码始终不变。在所有系统上都会进行的其他修改也列在changes元素中。

系统是自动检测的。如需使用其他系统的设置（例如检测有误时），可以设置os，或用options(faofishingreport.cmsy_os = "macos")为本次R会话设置。

English

The CMSY++ code (CMSY++16.R) was written on Windows. Its user guide (step 12) tells Mac users to change every windows() call to quartz() and antialias = "cleartype" to antialias = "default", and to comment out windows() on other systems. The code tests for Windows with grepl("win", sysname), which is also true for macOS (“Darwin”), so on a Mac it calls windows() and stops. cmsy_run() makes these changes automatically for the system found here, in a copy of the code; the bundled original is never changed. The other changes, made on every system, are listed in the changes element.

The system is detected automatically. To use the settings of another system (e.g. when the detection is wrong), set os, or set it for the session with options(faofishingreport.cmsy_os = "macos").

参考文献

Froese, R., Demirel, N., Coro, G. and Winker, H. (2021). User Guide for CMSY++. GEOMAR, Germany, 17 pp. https://oceanrep.geomar.de/id/eprint/52147/

另请参阅

cmsy_setup() to install what is missing, cmsy_sources() for versions and links.

示例

# What this computer has, and the settings cmsy_run() will use on it
sys <- cmsy_system()
sys$changes                      # the changes made to a copy of the CMSY++ code

# The settings that would be used on Windows or macOS, e.g. to check them for a colleague
cmsy_system(os = "windows", silent = TRUE)$changes
cmsy_system(os = "macos", silent = TRUE)$device_call

# The JAGS installer recommended here, and the newest JAGS
cmsy_system(silent = TRUE)$jags_installer[, c("version", "file", "url")]
cmsy_system(jags = "latest", silent = TRUE)$jags_installer[, c("version", "file", "requires")]