It looks like devtools::package_deps is forcing type to be "binary".
if (identical(type, "both")) {
type <- "binary"
}
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
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())
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
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
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