I am using pkgdown
package to generate the elegant and static manual page for R package (called RTCGA). When I run the code to produce the static documentation as website I use following commands
> 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'
This code is evaluated in the root of RTCGA
package project and gives information that RTCGA was loaded and the documentation was created.
But I have found a bug in the documentation in most pages - there is an error telling
Error: package ‘RTCGA’ required by ‘RTCGA.rnaseq’ could not be found
So none of examples can be run. Moreover when I run library(RTCGA.rnaseq)
after I used build_site
I can not load dependent RTCGA
package anymore
> library(RTCGA)
> library(RTCGA.rnaseq)
Error: package ‘RTCGA’ required by ‘RTCGA.rnaseq’ could not be found
When I run library(RTCGA.rnaseq)
in the new session without calling the pkgdown::build_site
the dependent RTCGA
package loads normally with no warnings.
I suspect that this is caused by any settings that build_site
performs but I have no idea on how to resolve them and how to build proper static documentation with the usage of pkgdown
package.
Any comments?
It looks like I have found a nasty work-around.
RTCGA
software package uses 8 data packages in its examples. Each data package required RTCGA to be loaded. pkgdown::build_site()
uses devtools::load_all()
which weirdly loads only objects from RTCGA but does not allow to load this package during examples run.
I have removed RTCGA
from Depends
of the data packages by changing those packages meta-informations like
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], data_package, "Meta", "package.rds"))
})
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