From astokes at esica.com  Sun May 31 06:45:09 2009
From: astokes at esica.com (astokes at esica.com)
Date: Sun, 31 May 2009 06:45:09 +0200 (CEST)
Subject: [Rd] install.packages hangs RGui with frozen rpwd process at bottom
	of process tree (PR#13734)
Message-ID: <20090531044509.BA68C2830319@mail.pubhealth.ku.dk>

Full_Name: Allan Stokes
Version: 2.8.1
OS: XP
Submission from: (NULL) (24.108.0.245)


I've just spent a hellish six hours trying to create my own R package with a
bare bones "hello world" R function inside.  I was able to create a
package.tar.gz file eventually with much perseverance.  

My remaining problem is that when I try to install my simple package under RGui,
it hangs.  

install.packages("c:/testR/scupper_1.0.tar.gz", repos=NULL, type="source",
lib="c:/allanR")

The hung process tree as shown by SysInternals Process Explorer.  

1. Rgui.exe
cmd="C:\Program Files\R\R-2.8.1\bin\Rgui.exe" 
cd=Z:\ 
2. R.exe
cmd=C:\PROGRA~1\R\R-28~1.1\bin\R.exe CMD INSTALL -l "c:/allanR" 
"c:/allanR/scupper_1.0.tar.gz"
cd=Z:\
3. cmd.exe
cmd=C:\WINDOWS\system32\cmd.exe /c perl C:\PROGRA~1\R\R-28~1.1/bin/INSTALL -l
c:/allanR c:/allanR/scupper_1.0.tar.gz
cd=Z:\
4. perl.exe
cmd=perl C:\PROGRA~1\R\R-28~1.1/bin/INSTALL -l c:/allanR
c:/allanR/scupper_1.0.tar.gz
Z:\
5. make.exe
cmd=make --no-print-directory -C C:/PROGRA~1/R/R-28~1.1/src/gnuwin32
PKGDIR=Z:/R.INSTALL.5532 PKGNAME=scupper RLIB=c:/allanR DPKG=c:/allanR/scupper
scupper-LAZY=true HELP=YES WINHELP=CHM pkg-scupper
dir=C:\Program Files\R\R-2.8.1\src\gnuwin32\
6. make.exe
cmd=c:\Rtools\bin\make.exe
dir=C:\WINDOWS\system32\
7. Rpwd.exe 
cmd=c:\PROGRA~1\R\R-28~1.1\src\gnuwin32\Rpwd.exe ../..
dir=C:\Program Files\R\R-2.8.1\src\gnuwin32\

First, one stupid thing is that one time I ran the make cmd under the CMD prompt
and it successfully generated a CHM file, as shown by this fragment of the
output I captured: 

 >>> Building/Updating help pages for package 'scupper'
     Formats: text html latex example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling z:\R.INSTALL.6416\scupper\chm\scupper.chm

Compile time: 0 minutes, 0 seconds
1       Topic
0       Local links
0       Internet links
1       Graphic

Created z:\R.INSTALL.6416\scupper\chm\scupper.chm, 14,448 bytes
Compression increased file by 9,624 bytes.

That didn't work when I tried it again, but the R temp directories sometimes
vanish in the meantime.  

Using System Internals File Monitor, I can see the last access to the file
system by rpwd.exe 

9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION
C:\PROGRA~1\R\R-28~1.1\src\gnuwin32\Rpwd.exe	SUCCESS	FileNameInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\Prefetch\RPWD.EXE-1615C3C8.pf	SUCCESS
Options: Open  Access: Read	
9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION
C:\WINDOWS\Prefetch\RPWD.EXE-1615C3C8.pf	SUCCESS	Length: 3882	
9:25:26 PM	Rpwd.exe:6328	READ 	C:\WINDOWS\Prefetch\RPWD.EXE-1615C3C8.pf	SUCCESS
Offset: 0 Length: 3882	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:	SUCCESS	Options: Open  Access: 00100180	
9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION	C:	SUCCESS	FileFsVolumeInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\	SUCCESS	Options: Open Directory  Access:
00100001	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\	SUCCESS	FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\	NO MORE FILES	FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\PROGRA~1\	SUCCESS	Options: Open Directory 
Access: 00100001	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\	SUCCESS	FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\	NO MORE FILES
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\PROGRA~1\R\	SUCCESS	Options: Open Directory 
Access: 00100001	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\R\	SUCCESS	FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\R\	NO MORE FILES
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\PROGRA~1\R\R-28~1.1\	SUCCESS	Options: Open
Directory  Access: 00100001	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\R\R-28~1.1\	SUCCESS
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\R\R-28~1.1\	NO MORE FILES
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\PROGRA~1\R\R-28~1.1\SRC\	SUCCESS	Options: Open
Directory  Access: 00100001	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\R\R-28~1.1\SRC\	SUCCESS
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\R\R-28~1.1\SRC\	NO MORE FILES
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\PROGRA~1\R\R-28~1.1\SRC\GNUWIN32\	SUCCESS
Options: Open Directory  Access: 00100001	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\R\R-28~1.1\SRC\GNUWIN32\	SUCCESS
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\PROGRA~1\R\R-28~1.1\SRC\GNUWIN32\	NO MORE
FILES	FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\	SUCCESS	Options: Open Directory 
Access: 00100001	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\	SUCCESS	FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\	SUCCESS	FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\	NO MORE FILES
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\	SUCCESS	Options: Open
Directory  Access: 00100001	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\SYSTEM32\	SUCCESS
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\SYSTEM32\	SUCCESS
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\SYSTEM32\	SUCCESS
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\SYSTEM32\	SUCCESS
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\SYSTEM32\	SUCCESS
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\SYSTEM32\	SUCCESS
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	DIRECTORY	C:\WINDOWS\SYSTEM32\	NO MORE FILES
FileNamesInformation	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\NTDLL.DLL	SUCCESS	Options:
Open  Access: 00000081	
9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION	C:\WINDOWS\SYSTEM32\NTDLL.DLL	SUCCESS
Length: 714752	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\KERNEL32.DLL	SUCCESS	Options:
Open  Access: 00000081	
9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION	C:\WINDOWS\SYSTEM32\KERNEL32.DLL
SUCCESS	Length: 989696	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\UNICODE.NLS	SUCCESS	Options:
Open  Access: 00000081	
9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION	C:\WINDOWS\SYSTEM32\UNICODE.NLS
SUCCESS	Length: 89588	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\LOCALE.NLS	SUCCESS	Options:
Open  Access: 00000081	
9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION	C:\WINDOWS\SYSTEM32\LOCALE.NLS
SUCCESS	Length: 265948	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\SORTTBLS.NLS	SUCCESS	Options:
Open  Access: 00000081	
9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION	C:\WINDOWS\SYSTEM32\SORTTBLS.NLS
SUCCESS	Length: 23044	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\PROGRA~1\R\R-28~1.1\SRC\GNUWIN32\RPWD.EXE
SUCCESS	Options: Open  Access: 00000081	
9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION
C:\PROGRA~1\R\R-28~1.1\SRC\GNUWIN32\RPWD.EXE	SUCCESS	Length: 9216	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\MSVCRT.DLL	SUCCESS	Options:
Open  Access: 00000081	
9:25:26 PM	Rpwd.exe:6328	QUERY INFORMATION	C:\WINDOWS\SYSTEM32\MSVCRT.DLL
SUCCESS	Length: 343040	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\NTDLL.DLL	SUCCESS	Options:
Open  Access: Execute	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\KERNEL32.DLL	SUCCESS	Options:
Open  Access: Execute	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\PROGRA~1\R\R-28~1.1\SRC\GNUWIN32\RPWD.EXE
SUCCESS	Options: Open  Access: Execute	
9:25:26 PM	Rpwd.exe:6328	OPEN	C:\WINDOWS\SYSTEM32\MSVCRT.DLL	SUCCESS	Options:
Open  Access: Execute	

I've tried this under Rtools 2.9 and then 2.8.  I also updated my Cygwin config
(which was pretty current).  

No dice.  

My little package contains an R function as such: 

`ahoy` <-
function () { cat ("Shiver me timbers!\n")}

And a DESCRIPTION file like this: 

Package: scupper
Type: Package
Title: Ship ahoy
Version: 1.0
Date: 2009-05-30
Author: Allan Stokes
Maintainer: <astokes at esica.com>
Description: Responds to ahoy() greeting.  
License: internal use only
LazyLoad: yes

There are empty data, man, and test directories.  

I would reboot my system and try again, but I'd have to shut down 30 programs on
nine desktops, and I haven't got that many lives.  I have been sure to restart
RGui with the correct PATH env. for each test run.



[Rd] install.packages hangs RGui with frozen rpwd process at bottom of process tree (PR#13734)
astokes at esica.com