[Bioc-devel] Challenges with package installation on fresh R
It looks like devtools::package_deps is forcing type to be "binary".
if (identical(type, "both")) {
type <- "binary"
}
devtools::package_deps
function (pkg, dependencies = NA, repos = getOption("repos"),
type = getOption("pkgType"))
{
if (identical(type, "both")) {
type <- "binary"
}
if (length(repos) == 0)
repos <- character()
repos[repos == "@CRAN@"] <- "http://cran.rstudio.com"
cran <- available_packages(repos, type)
if (missing(pkg)) {
pkg <- as.package(".")$package
}
deps <- sort(find_deps(pkg, cran, top_dep = dependencies))
inst <- installed.packages()
base <- unname(inst[inst[, "Priority"] %in% c("base", "recommended"),
"Package"])
deps <- setdiff(deps, base)
inst_ver <- unname(inst[, "Version"][match(deps, rownames(inst))])
cran_ver <- unname(cran[, "Version"][match(deps, rownames(cran))])
diff <- compare_versions(inst_ver, cran_ver)
structure(data.frame(package = deps, installed = inst_ver,
available = cran_ver, diff = diff, stringsAsFactors = FALSE),
class = c("package_deps", "data.frame"), repos = repos,
type = type)
}
<environment: namespace:devtools>
On Fri, Jun 26, 2015 at 2:12 PM, Vladislav Petyuk <petyuk at gmail.com> wrote:
Dan, Herve, thanks for taking a look. This gives some leads. On Thu, Jun 25, 2015 at 7:26 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
----- Original Message -----
From: "Herv? Pag?s" <hpages at fredhutch.org> To: "Vladislav Petyuk" <petyuk at gmail.com>, "Dan Tenenbaum" <
dtenenba at fredhutch.org>
Cc: Bioc-devel at r-project.org Sent: Thursday, June 25, 2015 6:56:56 PM Subject: Re: [Bioc-devel] Challenges with package installation on fresh
R
Hi Vladislav, On 06/25/2015 01:13 PM, Vladislav Petyuk wrote:
Yes, the issue is the same if I use
devtools::install_github("vladpetyuk/toypack",
build_vignettes=TRUE,
dependencies=TRUE)
I posted on Bioc-devel list because all the problematic packages
are
suspiciously similar - all related to Bioconductor and deal with
some sort
of databases (GO/KEGG/Reactome).
What all these packages have in common is that we don't provide binaries for them anymore. That's because install.packages() (and thus biocLite(), which uses install.packages() internally) knows how to deal with this (via type="both", which is now the default on Windows and Mac). However, some core utilities like utils::download.packages() have not been properly adapted to handle the situation where a binary is missing. For example with R-3.2.1 on Windows:
> library(BiocInstaller)
> download.packages("GO.db", destdir=".",
> repos=biocinstallRepos())
trying URL '
Error in download.file(url, destfile, method, mode = "wb", ...) :
cannot open URL
'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
cannot open: HTTP status was '404 Not Found'
Warning in download.packages("GO.db", destdir = ".", repos =
biocinstallRepos()):
download of package 'GO.db' failed
[,1] [,2]
This could be what breaks install_github() (which doesn't seem to
use install.packages() internally but to instead handle the
downloading
of the packages itself).
install_github() calls install() whose documentation says that its ... arguments are passed to install.packages() in order to install dependencies. But I agree that something else seems to be going on here and that devtools decides the packages can't be installed without running install.packages(). Dan
Cheers, H.
On Thu, Jun 25, 2015 at 1:08 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
----- Original Message -----
From: "Vladislav Petyuk" <petyuk at gmail.com> To: "Dan Tenenbaum" <dtenenba at fredhutch.org> Cc: Bioc-devel at r-project.org Sent: Thursday, June 25, 2015 12:55:56 PM Subject: Re: [Bioc-devel] Challenges with package installation on fresh R Just added the full output to the README.md file https://github.com/vladpetyuk/toypack/blob/master/README.md
Do you get the same results if you do:
devtools::install_github("vladpetyuk/toypack",
build_vignettes=TRUE,
dependencies=TRUE)
?
When you pass biocLite() a username/repos argument as you've done,
it just
delegates all the work to devtools::install_github().
If you get the same issue with install_github(), then the issue
has
nothing to do with Bioconductor and you need to discuss it with
the
maintainer of devtools.
If not, then maybe there is an issue with the way we delegate to
that
command.
Dan
On Thu, Jun 25, 2015 at 12:28 PM, Dan Tenenbaum < dtenenba at fredhutch.org > wrote: ----- Original Message -----
From: "Vladislav Petyuk" < petyuk at gmail.com > To: Bioc-devel at r-project.org Sent: Thursday, June 25, 2015 12:16:50 PM Subject: [Bioc-devel] Challenges with package installation on fresh R Hi all, I ran into a problem with dependencies during package installation. Here is an example that intends to reproduce the problem https://github.com/vladpetyuk/toypack Majority of the packages (in Imports/Depends/Suggests and their Imports/Depends/Suggests) install just fine. However there is a handful of packages ("DO.db", "GO.db", "org.Ce.eg.db", "org.Hs.eg.db" and "reactome.db") that are being skipped for not an obvious to me reason. In this toy example there is no use of those skipped packages. So it won't results in any kind of error. But in the real package their lack results in errors.
You need to provide the complete output of R when you try and install the package. The error is in that output somewhere. Dan
Thank you, Vlad [[alternative HTML version deleted]]
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-- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319