Re: [Rd] R 3.2.2 64 bit compilation error on AIX

2015-10-19 Thread Martin Maechler 
> Vinh Nguyen 
> on Fri, 9 Oct 2015 06:35:01 -0700 writes:

> On Oct 8, 2015 11:36 PM, "Martin Maechler"
>  wrote:
>> 
>> > Vinh Nguyen  > on Thu, 8
>> Oct 2015 20:21:32 -0700 writes:
>> 
>> > Ahh, sorry for not googling the error message.  Found >
>> [this](
> 
http://r.789695.n4.nabble.com/Error-compiling-R-2-10-1-on-AIX-td1017862.html
> )
>> > post that suggests modifying
>> /src/extra/tre/tre-internal.h > (
> 
https://r-forge.r-project.org/scm/viewvc.php/patches/aix_R210_tre.patch?view=markup&root=aix
> )
>> > for AIX 64 bit.
>> 
>> > Is it possible to add this information to the AIX
>> section > of the R-admin manual?  Thanks.
>> 
>> Actually, I think we (R Core) should just apply that
>> patch to the R/src/extras/tre/ sources.

> That should be even better!

I've heard no other comments,
tried a version of your patch and checked that it does *not*
break either 32-bit or 64-bit Linux.

At the same time, that (very old) patch looks sensible and
solves your problem and you are one of very few who actively
work on building R on AIX

==> I have committed a corresponding change to src/extra/tre/tre-internal.h
now.  (for R-devel aka "trunk" only).

Martin Maechler, ETH Zurich

>> 
>> But this does not seem to be related to your original
>> problem where compilation stopped during tools package
>> building, or does it ?

> Yes, the patch did fix the error where the tools package
> was building. It also fixed it for [others](
> 
http://r.789695.n4.nabble.com/Error-compiling-R-2-10-1-on-AIX-td1017862.html
> ).

> Thanks.

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Re: [Rd] Linking to documentation from a vignette using markdown?

2015-10-19 Thread Duncan Murdoch 
On 18/10/2015 10:12 PM, Spencer Graves wrote:
> Hi, Duncan:
> 
> 
> On 10/18/2015 8:18 PM, Duncan Murdoch wrote:
>> On 18/10/2015 5:51 PM, Spencer Graves wrote:
>>> Hello:
>>>
>>>
>>> What's the preferred way to link to package documentation from a
>>> vignette using markdown?
>>>
>>>
>>> My current draft includes
>>> "[cumsum](https://stat.ethz.ch/R-manual/R-devel/library/base/html/cumsum.html)"
>>> to link to the help page for cusum{base} and
>>> "[KFAS](https://rweb.crmda.ku.edu/cran/web/packages/KFAS/KFAS.pdf)" to
>>> link to the pdf documentation for the KFAS package.  This works, but it
>>> feels like an ugly hack, and I wonder if there might be some more
>>> elegant way of doing this (documented in a fine manual I have yet to find)?
>> You can include links that work only when R is displaying the help using
>> relative URLs like
>>
>> ../../base/help/cumsum
>>
>> or
>>
>> ../../base/html/cumsum.html
>>
>> (The former is like doing ?cumsum, i.e. it uses the alias; the latter
>> goes directly to a page by its name.)
>>
>> The advantage of this kind of link is it doesn't need an Internet
>> connection, it works with the R help system; the disadvantage is that it
>> only works when the help system is running, so those links won't work in
>> the copy of your vignette on CRAN, for example.
> 
> 
>Thanks.  I think I saw links like these reading html trying to 
> find what I needed for [KFAS];  this helps me understand what I read.  I 
> think I'd prefer having links that work in a pdf that I could pass to 
> someone who may not have R installed.
> 
> 
>What's the easiest way to find links like the absolute web 
> address I gave for [KFAS]?  It took me a couple of hours, because I 
> couldn't find how to get more than "https://rweb.crmda.ku.edu/cran/"; 
> from any of my current web browsers (Safari, Chrome, and SeaMonkey on OS 
> X 10.11, Internet Explorer, Chrome, FireFox and SeaMonkey under Windows 7).
> 

CRAN uses frames, so the displayed address is the outer frame, but
different parts of the display come from different pages, which is why
the address bar doesn't change.  But you can still find the real link.
In Firefox you right click on the link and choose "Copy Link Location".
 I assume other browsers have similar methods.

BTW, I'd recommend using the "Cloud" mirror; it will be fastest for the
majority of users, not just those near ku.edu.

Duncan Murdoch

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Re: [Rd] R 3.2.2 - make check and install package hang

2015-10-19 Thread McCully, Dwayne (NIH/NIAMS) [C] 
Below is the output.   Thanks for the help. 

> Sys.getenv()
BASH_FUNC_module()  () { eval

`/cm/local/apps/environment-modules/3.2.10/Modules/$MODULE_VERSION/bin/modulecmd
bash $*` }
COLUMNS 152
CPATH   /cm/shared/apps/uge/8.2.1/include
CVS_RSH ssh
DISPLAY localhost:10.0
EDITOR  vi
G_BROKEN_FILENAMES  1
HISTCONTROL ignoredups
HISTSIZE1000
HOME/root
HOSTNAMEtest
LANGen_US.UTF-8
LD_LIBRARY_PATH 
/cm/shared/apps/R/3.2.1/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/lib/amd64/server:/cm/shared/apps/uge/8.2.1/lib/lx-amd64
LESSOPEN||/usr/bin/lesspipe.sh %s
LINES   48
_LMFILES_   
/cm/local/modulefiles/shared:/cm/shared/modulefiles/uge/8.2.1:/cm/local/modulefiles/cmsh:/cm/local/modulefiles/cmd:/cm/local/modulefiles/cluster-tools/7.1:/cm/shared/modulefiles/cmgui/7.1:/cm/shared/modulefiles/R/3.2.1
LN_Sln -s
LOADEDMODULES   
shared:uge/8.2.1:cmsh:cmd:cluster-tools/7.1:cmgui/7.1:R/3.2.1
LOGNAME root
LS_COLORS   
rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.tbz=01;31:*.tbz2=01;31:*.bz=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
MAIL/var/spool/mail/root
MAKEmake
MANPATH 
/cm/local/apps/cluster-tools/man:/cm/local/apps/cmd/man:/cm/shared/apps/uge/8.2.1/man:/usr/share/centrifydc/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man/en:/usr/share/man:/cm/local/apps/environment-modules/current/share/man
MINICOM -t ansi-generic
MODULEPATH  /cm/local/modulefiles:/cm/shared/modulefiles
MODULESHOME /cm/local/apps/environment-modules/3.2.10/Modules/3.2.10
MODULE_VERSION  3.2.10
MODULE_VERSION_STACK3.2.10
NXDIR   /usr/NX
PAGER   /usr/bin/less
PATH
/cm/shared/apps/R/3.2.1/bin:/cm/shared/apps/cmgui:/cm/local/apps/cluster-tools/bin:/cm/local/apps/cmd/sbin:/cm/local/apps/cmd/bin:/cm/shared/apps/uge/8.2.1/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/share/centrifydc/sbin:/usr/share/centrifydc/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/cm/local/apps/environment-modules/3.2.10/bin:/usr/NX/bin:/opt/dell/srvadmin/bin:/opt/dell/srvadmin/sbin:/root/bin
PWD /root
QTDIR   /usr/lib64/qt-3.3
QTINC   /usr/lib64/qt-3.3/include
QTLIB   /usr/lib64/qt-3.3/lib
R_ARCH
R_BROWSER   /usr/bin/firefox
R_BZIPCMD   /usr/bin/bzip2
R_DOC_DIR   /cm/shared/apps/R/3.2.1/lib64/R/doc
R_GZIPCMD   /bin/gzip
R_HOME  /cm/shared/apps/R/3.2.1/lib64/R
R_INCLUDE_DIR   /cm/shared/apps/R/3.2.1/lib64/R/include
R_LIBS_SITE
R_LIBS_USER ~/R/x86_64-unknown-linux-gnu-library/3.2
R_PAPERSIZE a4
R_PDFVIEWER /usr/bin/xdg-open
R_PLATFORM  x86_64-unknown-linux-gnu
R_PRINTCMD  lpr
R_RD4PDFtimes,hyper
R_SESSION_TMPDIR/tmp/Rtmphn5m15
R_SHARE_DIR /cm/shared/apps/R/3.2.1/lib64/R/share
R_SYSTEM_ABIlinux,gcc,gxx,gfortran,?
R_TEXI2DVICMD   /usr/bin/texi2dvi
R_UNZIPCMD  /usr/bin/unzip
R_ZIPCMD/usr/bin/zip
SED /bin/sed
SGE_ROOT/cm/shared/apps/uge/8.2.1
SHELL   /bin/bash
SHLVL   1
SSH_ASKPASS /usr/libexec/openssh/gnome-ssh-askpass
TAR /bin/gtar
TERMxterm
USERroot
XAUTHORITY  /root/.xauthtGhzUe

-

Re: [Rd] R 3.2.2 - make check and install package hang

2015-10-19 Thread McCully, Dwayne (NIH/NIAMS) [C] 
When running the "make check"

14736 14735  0 09:03 pts/100:00:00 /bin/sh -c echo 
"tools::testInstalledPackages(scope='base', types='examples', srcdir=\".\", 
commentDonttest=!FALSE)" | LANGUAGE=
14738 14736  0 09:03 pts/100:00:03 /home/test/R-3.2.2/bin/exec/R --slave 
--vanilla
14740 14738  0 09:03 pts/100:00:00 sh /home/test/R-3.2.2/bin/Rcmd BATCH 
--vanilla --no-timing base-Ex.R base-Ex.Rout.fail
14743 14740  0 09:03 pts/100:00:03 /home/test/R-3.2.2/bin/exec/R -f 
base-Ex.R --restore --save --no-readline --vanilla

It just sits at "capabilities()" by viewing the file base-Ex.Rout.fail

[test@test ~]$ tail -f ./R-3.2.2/tests/Examples/base-Ex.Rout.fail
> flush(stderr()); flush(stdout())
>
> ### Name: capabilities
> ### Title: Report Capabilities of this Build of R
> ### Aliases: capabilities
> ### Keywords: utilities
>
> ### ** Examples
>
> capabilities()

-Original Message-
From: McCully, Dwayne (NIH/NIAMS) [C] 
Sent: Monday, October 19, 2015 8:07 AM
To: 'arnaud gaboury' 
Cc: r-devel@r-project.org
Subject: RE: [Rd] R 3.2.2 - make check and install package hang

Below is the output.   Thanks for the help. 

> Sys.getenv()
BASH_FUNC_module()  () { eval

`/cm/local/apps/environment-modules/3.2.10/Modules/$MODULE_VERSION/bin/modulecmd
bash $*` }
COLUMNS 152
CPATH   /cm/shared/apps/uge/8.2.1/include
CVS_RSH ssh
DISPLAY localhost:10.0
EDITOR  vi
G_BROKEN_FILENAMES  1
HISTCONTROL ignoredups
HISTSIZE1000
HOME/root
HOSTNAMEtest
LANGen_US.UTF-8
LD_LIBRARY_PATH 
/cm/shared/apps/R/3.2.1/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/lib/amd64/server:/cm/shared/apps/uge/8.2.1/lib/lx-amd64
LESSOPEN||/usr/bin/lesspipe.sh %s
LINES   48
_LMFILES_   
/cm/local/modulefiles/shared:/cm/shared/modulefiles/uge/8.2.1:/cm/local/modulefiles/cmsh:/cm/local/modulefiles/cmd:/cm/local/modulefiles/cluster-tools/7.1:/cm/shared/modulefiles/cmgui/7.1:/cm/shared/modulefiles/R/3.2.1
LN_Sln -s
LOADEDMODULES   
shared:uge/8.2.1:cmsh:cmd:cluster-tools/7.1:cmgui/7.1:R/3.2.1
LOGNAME root
LS_COLORS   
rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.tbz=01;31:*.tbz2=01;31:*.bz=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
MAIL/var/spool/mail/root
MAKEmake
MANPATH 
/cm/local/apps/cluster-tools/man:/cm/local/apps/cmd/man:/cm/shared/apps/uge/8.2.1/man:/usr/share/centrifydc/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man/en:/usr/share/man:/cm/local/apps/environment-modules/current/share/man
MINICOM -t ansi-generic
MODULEPATH  /cm/local/modulefiles:/cm/shared/modulefiles
MODULESHOME /cm/local/apps/environment-modules/3.2.10/Modules/3.2.10
MODULE_VERSION  3.2.10
MODULE_VERSION_STACK3.2.10
NXDIR   /usr/NX
PAGER   /usr/bin/less
PATH
/cm/shared/apps/R/3.2.1/bin:/cm/shared/apps/cmgui:/cm/local/apps/cluster-tools/bin:/cm/local/apps/cmd/sbin:/cm/local/apps/cmd/bin:/cm/shared/apps/uge/8.2.1/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/share/centrifydc/sbin:/usr/share/centrifydc/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/cm/local/apps/environment-modules/3.2.10/bin:/usr/NX/bin:/opt/dell/srvadmin/bin:/opt/dell/srvadmin/sbin:/root/bin
PWD /root
QTDIR   /usr/lib64/qt-3.3
QTINC   /usr/lib64/qt-3.3/include
QTLIB   /usr/lib64/qt-3.3/lib
R_ARCH
R_BROWSER   /usr/bin/firefox
R_BZIPCMD