Hi All,
I am on a fully updated MacBook Pro, running 10.8.2. I get:
uname -m
x86_64
from the terminal, as would be expected.
I have been using the CRAN OSX binaries for some time now, rather than building
from source, which I had been doing previously.
Somewhere along the way in the past few weeks, apparently since I installed R
2.15.2, the default architecture under which R is running is now 32 bit, not 64
bit, which was the case previously. I just noted this today due to some funny
encoding issues that I had not seen before and have spent the past few hours
trying to figure out what changed.
I initially thought something was amiss with the latest 2.15.2 release .pkg
file. I completely removed R (Framework and symlinks to the startup scripts,
etc.) and re-installed. Same thing. 32 bit R was the default link from 'R'.
So I removed R again and re-installed 2.15.1 (getting the older binary from
CRAN), since that was the last version of R that I had installed which
defaulted to 64 bit.
Funny, same thing, it defaulted to 32 bit R.
Then I wondered if there was something related to some anti-virus software
(Avast) that I had recently installed due to some events that had occurred
recently. I completely removed the AV software, rebooted, removed R and then
re-installed R. Same thing, 32 bit R as the default.
What am I missing here? What is the installation program and/or the R startup
script itself looking for that determines whether 64 or 32 bit R should the
default when one simply uses 'R' to start it up? A read of the R startup script
suggests that the output (as above) of 'uname -m' being 'x86_64' may be all
that is needed, but perhaps I am missing something else.
I am also attaching the full installation log file here (for 2.15.2). I did not
see anything there obvious to my eyes.
I can't recall the timeline well enough right now to consider whether some OSX
update changed something, or if there is something strictly unique to my MBP
that is causing this problem.
Thanks for any insights.
Regards,
Marc
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: @(#)PROGRAM:Install
PROJECT:Install-735
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: @(#)PROGRAM:Installer
PROJECT:Installer-614
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Hardware:
MacBookPro5,2 @ 2.93 GHz (x 2), 8192 MB RAM
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Running OS Build: Mac
OS X 10.8.2 (12C60)
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
PATH=/usr/bin:/bin:/usr/sbin:/sbin
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
TMPDIR=/var/folders/gs/c40xg0qx2gx1xsxjtkhvj9_m0000gn/T/
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env: SHELL=/bin/bash
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
HOME=/Users/marcschwartz
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env: USER=marcschwartz
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
LOGNAME=marcschwartz
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
SSH_AUTH_SOCK=/tmp/launch-hGcfqP/Listeners
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
Apple_Ubiquity_Message=/tmp/launch-q7Pvlb/Apple_Ubiquity_Message
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
Apple_PubSub_Socket_Render=/tmp/launch-a5t0gM/Render
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
DISPLAY=/tmp/launch-pAOUPH/org.macosforge.xquartz:0
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
COMMAND_MODE=unix2003
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Env:
__CF_USER_TEXT_ENCODING=0x1F5:0:0
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: R 2.15.2 for Mac OS X
10.5 or higher (Leopard build) Installation Log
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Opened from:
/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg
Nov 13 12:12:28 ws195.mednetregistry.com Installer[1078]: Product archive
/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg
trustLevel=202
Nov 13 12:13:51 ws195.mednetregistry.com Installer[1078]:
InstallerStatusNotifications plugin loaded
Nov 13 12:14:04 ws195.mednetregistry.com runner[1088]: Administrator
authorization granted.
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]:
================================================================================
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]: User picked Standard
Install
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]: Choices selected for
installation:
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]: Upgrade: "R
2.15.2 for Mac OS X 10.5 or higher (Leopard build)"
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]: Upgrade: "R
2.15.2 Framework"
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]:
R-2.15.2.pkg#r.pkg : org.r-project.R.Leopard.fw.pkg : 201561015
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]: Upgrade: "R GUI
1.53 (32-bit)"
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]:
R-2.15.2.pkg#r-1.pkg : org.r-project.R.Leopard.GUI.pkg : 1.53
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]: Upgrade: "R GUI
1.53 (64-bit)"
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]:
R-2.15.2.pkg#r64.pkg : org.r-project.R.Leopard.GUI64.pkg : 1.53
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]:
================================================================================
Nov 13 12:14:04 ws195.mednetregistry.com Installer[1078]: It took 0.00 seconds
to summarize the package selections.
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]:
-[IFDInstallController(Private) _buildInstallPlan]: location = file://localhost
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]:
-[IFDInstallController(Private) _buildInstallPlan]:
file://localhost/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg#r.pkg
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]:
-[IFDInstallController(Private) _buildInstallPlan]:
file://localhost/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg#r-1.pkg
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]:
-[IFDInstallController(Private) _buildInstallPlan]:
file://localhost/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg#r64.pkg
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]: Set authorization
level to root for session
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]: Will use PK session
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]: Starting installation:
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]: Configuring volume
"Macintosh HD"
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]: Preparing disk for
local booted install.
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]: Free space on
"Macintosh HD": 36.51 GB (36507176960 bytes).
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]: Create temporary
directory "/var/folders/gs/c40xg0qx2gx1xsxjtkhvj9_m0000gn/T//Install.1078dwr5SI"
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]: IFPKInstallElement (3
packages)
Nov 13 12:14:05 ws195.mednetregistry.com Installer[1078]: Using authorization
level of root for IFPKInstallElement
Nov 13 12:14:05 ws195.mednetregistry.com installd[1091]: installd: Starting
Nov 13 12:14:05 ws195.mednetregistry.com installd[1091]: installd: uid=0, euid=0
Nov 13 12:14:05 ws195.mednetregistry.com installd[1091]: PackageKit: -----
Begin install -----
Nov 13 12:14:05 ws195.mednetregistry.com installd[1091]: PackageKit:
request=PKInstallRequest <3 packages, destination=/>
Nov 13 12:14:05 ws195.mednetregistry.com installd[1091]: PackageKit: packages=(
"PKLeopardPackage
<file://localhost/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg#r.pkg>",
"PKLeopardPackage
<file://localhost/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg#r-1.pkg>",
"PKLeopardPackage
<file://localhost/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg#r64.pkg>"
)
Nov 13 12:14:05 ws195.mednetregistry.com installd[1091]: PackageKit: Will do
receipt-based obsoleting for package identifier org.r-project.R.Leopard.fw.pkg
(prefix path=Library/Frameworks)
Nov 13 12:14:05 ws195.mednetregistry.com installd[1091]: PackageKit: Will do
receipt-based obsoleting for package identifier org.r-project.R.Leopard.GUI.pkg
(prefix path=Applications)
Nov 13 12:14:05 ws195.mednetregistry.com installd[1091]: PackageKit: Will do
receipt-based obsoleting for package identifier
org.r-project.R.Leopard.GUI64.pkg (prefix path=Applications)
Nov 13 12:14:06 ws195.mednetregistry.com installd[1091]: PackageKit: Extracting
file://localhost/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg#r.pkg
(destination=/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/Cleanup At
Startup/PKInstallSandboxManager/1.sandbox/Root/Library/Frameworks, uid=0)
Nov 13 12:14:12 ws195.mednetregistry.com installd[1091]: PackageKit: Extracting
file://localhost/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg#r-1.pkg
(destination=/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/Cleanup At
Startup/PKInstallSandboxManager/1.sandbox/Root/Applications, uid=0)
Nov 13 12:14:12 ws195.mednetregistry.com installd[1091]: PackageKit: Extracting
file://localhost/Users/marcschwartz/R.Files/SourceAndBinaries/OSX-Binary/Release/R-2.15.2.pkg#r64.pkg
(destination=/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/Cleanup At
Startup/PKInstallSandboxManager/1.sandbox/Root/Applications, uid=0)
Nov 13 12:14:13 ws195.mednetregistry.com installd[1091]: PackageKit: prevent
user idle system sleep
Nov 13 12:14:13 ws195.mednetregistry.com installd[1091]: PackageKit: suspending
backupd
Nov 13 12:14:13 ws195.mednetregistry.com installd[1091]: PackageKit: Shoving
/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/Cleanup At
Startup/PKInstallSandboxManager/1.sandbox/Root (2 items) to /
Nov 13 12:14:13 ws195.mednetregistry.com install_monitor[1097]: Temporarily
excluding: /Applications, /Library, /System, /bin, /private, /sbin, /usr
Nov 13 12:14:14 ws195.mednetregistry.com installd[1091]: PackageKit: Executing
script "./postinstall" in
/private/tmp/PKInstallSandbox.5h6j8r/Scripts/org.r-project.R.Leopard.fw.pkg.3CzwEp
Nov 13 12:15:10 ws195.mednetregistry.com installd[1091]: PackageKit: Writing
receipt for org.r-project.R.Leopard.fw.pkg to /private/var/db/receipts
Nov 13 12:15:10 ws195.mednetregistry.com installd[1091]: PackageKit: Writing
receipt for org.r-project.R.Leopard.GUI.pkg to /private/var/db/receipts
Nov 13 12:15:10 ws195.mednetregistry.com installd[1091]: PackageKit: Writing
receipt for org.r-project.R.Leopard.GUI64.pkg to /private/var/db/receipts
Nov 13 12:15:10 ws195.mednetregistry.com installd[1091]: PackageKit: Touched
bundle Applications/R.app
Nov 13 12:15:10 ws195.mednetregistry.com installd[1091]: PackageKit: Touched
bundle Applications/R64.app
Nov 13 12:15:10 ws195.mednetregistry.com installd[1091]: Installed "R 2.15.2
for Mac OS X 10.5 or higher (Leopard build)" ()
Nov 13 12:15:10 ws195.mednetregistry.com install_monitor[1097]: Re-included:
/Applications, /Library, /System, /bin, /private, /sbin, /usr
Nov 13 12:15:10 ws195.mednetregistry.com installd[1091]: PackageKit: releasing
backupd
Nov 13 12:15:10 ws195.mednetregistry.com installd[1091]: PackageKit: allow user
idle system sleep
Nov 13 12:15:10 ws195.mednetregistry.com installd[1091]: PackageKit: ----- End
install -----
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: PackageKit:
Registered bundle file://localhost/Applications/R.app/ for uid 501
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: PackageKit:
Registered bundle file://localhost/Applications/R64.app/ for uid 501
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: Running install
actions
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: Removing temporary
directory "/var/folders/gs/c40xg0qx2gx1xsxjtkhvj9_m0000gn/T//Install.1078dwr5SI"
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: Finalize disk
"Macintosh HD"
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: Notifying system of
updated components
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]:
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: **** Summary
Information ****
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: Operation
Elapsed time
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]:
-----------------------------
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: disk 0.01
seconds
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: script 0.00
seconds
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: zero 0.05
seconds
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: install
66.31 seconds
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: -total-
66.37 seconds
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]:
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: IFDInstallController
D98881B0 state = 5
Nov 13 12:15:11 ws195.mednetregistry.com Installer[1078]: Displaying 'Install
Succeeded' UI.
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