我正在使用pkgdown包为R包生成优雅和静态的手册页(称为RTCGA).当我运行代码以生成静态文档作为网站时,我使用以下命令
> pkgdown::build_site() Initialising site ------------------------------------------------------------------------------------- Copying '/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.3/pkgdown/assets/jquery.sticky-kit.min.js' Copying '/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.3/pkgdown/assets/link.svg' Copying '/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.3/pkgdown/assets/pkgdown.css' Copying '/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.3/pkgdown/assets/pkgdown.js' Building home ----------------------------------------------------------------------------------------- Writing '/home/mkosinski/GitHub/RTCGA/docs/index.html' Building function reference --------------------------------------------------------------------------- Loading RTCGA Welcome to the RTCGA (version: 1.5.1). trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_11_01/data/ACC/20151101/gdac.broadinstitute.org_ACC.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2015110100.0.0.tar.gz' Content type 'unknown' length 309876 bytes (302 KB) ================================================== downloaded 302 KB Warning: Topics missing from index: RTCGA-package,theme_RTCGA Building articles ------------------------------------------------------------------------------------- Building article 'RTCGA_Workflow.html' Building article 'Web_Applications.html'
此代码在RTCGA包项目的根目录中进行评估,并提供已加载RTCGA并创建文档的信息.
Error: package ‘RTCGA’ required by ‘RTCGA.rnaseq’ could not be found
所以没有一个例子可以运行.此外,当我使用build_site后运行库(RTCGA.rnaseq)时,我无法再加载依赖的RTCGA包
> library(RTCGA) > library(RTCGA.rnaseq) Error: package ‘RTCGA’ required by ‘RTCGA.rnaseq’ could not be found
当我在新会话中运行库(RTCGA.rnaseq)而不调用pkgdown :: build_site时,依赖的RTCGA程序包正常加载而没有警告.
我怀疑这是由build_site执行的任何设置引起的,但我不知道如何解决它们以及如何使用pkgdown包构建适当的静态文档.
任何意见？
看起来我发现了一个讨厌的解决方法.
RTCGA软件包在其示例中使用了8个数据包.每个数据包都需要加载RTCGA. pkgdown :: build_site()使用devtools :: load_all(),它奇怪地仅加载来自RTCGA的对象,但不允许在示例运行期间加载此包.
RTCGA软件包在其示例中使用了8个数据包.每个数据包都需要加载RTCGA. pkgdown :: build_site()使用devtools :: load_all(),它奇怪地仅加载来自RTCGA的对象,但不允许在示例运行期间加载此包.
我已经通过更改这些包元信息来删除数据包的Depends中的RTCGA
packages_to_remove_RTCGA_from_Depends <-
c("RTCGA.clinical","RTCGA.mutations","RTCGA.rnaseq","RTCGA.RPPA","RTCGA.mRNA","RTCGA.miRNASeq","RTCGA.methylation","RTCGA.CNV")
sapply(packages_to_remove_RTCGA_from_Depends,function(data_package){
Meta <- readRDS(file.path(.libPaths()[1],data_package,"Meta","package.rds"))
Meta$Depends <- list()
saveRDS(Meta,file.path(.libPaths()[1],"package.rds"))
})
