[med-svn] [r-bioc-biocinstaller] 01/04: New upstream version 1.26.1

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-biocinstaller.

commit 880a67431c208a0171b6f01abc07c4b29f0651bd
Author: Andreas Tille <tille at debian.org>
Date:   Sun Sep 24 00:41:14 2017 +0200

    New upstream version 1.26.1
---
 DESCRIPTION          |  4 ++--
 R/biocLite.R         |  2 +-
 R/biocinstallRepos.R | 16 ++++++++++++++--
 3 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7ea8d2b..b09ab18 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: BiocInstaller
 Title: Install/Update Bioconductor, CRAN, and github Packages
 Description: This package is used to install and update Bioconductor,
     CRAN, and (some) github packages.
-Version: 1.26.0
+Version: 1.26.1
 Author: Dan Tenenbaum and Biocore Team
 Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
 biocViews: Infrastructure
@@ -10,4 +10,4 @@ Depends: R (>= 3.4.0)
 Suggests: devtools, RUnit, BiocGenerics
 License: Artistic-2.0
 NeedsCompilation: no
-Packaged: 2017-04-24 23:03:38 UTC; biocbuild
+Packaged: 2017-08-31 23:08:27 UTC; biocbuild
diff --git a/R/biocLite.R b/R/biocLite.R
index a571d67..df871d4 100644
--- a/R/biocLite.R
+++ b/R/biocLite.R
@@ -94,7 +94,7 @@
     if (is.logical(suppressUpdates) && suppressUpdates)
         return(invisible(pkgs))
 
-    oldPkgs <- old.packages(lib.loc)
+    oldPkgs <- old.packages(lib.loc, checkBuilt=TRUE)
     if (is.null(oldPkgs))
         return(invisible(pkgs))
 
diff --git a/R/biocinstallRepos.R b/R/biocinstallRepos.R
index 4c21fc1..859fd36 100644
--- a/R/biocinstallRepos.R
+++ b/R/biocinstallRepos.R
@@ -78,8 +78,20 @@ biocinstallRepos <-
 
     repos <- subset(repos, !is.na(repos))
 
-    if ("@CRAN@" %in% repos)
-        repos["CRAN"] <- sprintf("%s//cran.rstudio.com", .protocol())
+    CRAN_repo <- repos[["CRAN"]]
+    ## Microsoft R Open is shipped with getOption("repos")[["CRAN"]]
+    ## pointing to a *snapshot* of CRAN (e.g.
+    ## https://mran.microsoft.com/snapshot/2017-05-01), and not
+    ## to a CRAN mirror that is current. For the current release and devel
+    ## BioC versions, biocinstallRepos() needs to point to a CRAN mirror
+    ## that is current so biocLite() and biocValid() behave the same for
+    ## all BioC users, whether they use mainstream R or Microsoft R Open.
+    ## However, since old versions of BioC are frozen, it would probably
+    ## make sense to point to a *snapshot* of CRAN instead of a CRAN mirror
+    ## that is current.
+    snapshot_pattern <- "/snapshot/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]"
+    if (CRAN_repo == "@CRAN@" || grepl(snapshot_pattern, CRAN_repo))
+        repos[["CRAN"]] <- sprintf("%s//cran.rstudio.com", .protocol())
     if (includeMBNI &&
         (getOption("pkgType") %in% c("source", "win.binary")))
         repos[["MBNI"]] <- mbniUrl

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