date:20170516

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

2017-05-16 Thread peter dalgaard

> On 16 May 2017, at 21:03 , peter dalgaard  wrote:
> 
> I don't think the config flags for R matter in this regard. The behaviour is 
> completely paralleled by wish8.6: 

Hmmm, not sure the wish ::tk::pkgconfig thing proves anything, after I tried 
some of the ActiveState installs and a source build. This stuff is making my 
head spin!

However, I discovered that it is possible to install R-3.4.0.pkg as usual, and 
then a customized install of (say) R-3.3-branch-mavericks.pkg, omitting 
everything except the Tcl/Tk stuff. That gives you R 3.4.0 and Rcmdr with 
antialiased fonts.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-SIG-Mac] R 3.4.0 problem

2017-05-16 Thread David Winsemius


> On Apr 24, 2017, at 11:49 PM, catalin roibu  wrote:
> 
> Dear all,
> 
> I have a problem with the newest R version. I'm trying to install a
> specific package dplR who need the gpm package and I have this error on my
> macbook (OS Sierra):

Generally one reads the error messages. Often, and this is one of those cases, 
the first error message tells what the problem might be. You either do not have 
the system package GMP or it is installed in a location where the R package 
'gmp' cannot find it.

I had difficulties attempting to test the advice I found by (re-)installing the 
GNU GMP package from CRAN/r.research.att.com:

http://r.research.att.com/libs/gmp-6.0.0-darwin.13-x86_64.tar.gz

I got:
~ davidwinsemius$ sudo tar fvxz ~/gmp-6.0.0-darwin.13-x86_64.tar.gz -C /
x usr/: Can't set user=0/group=0 for usrCan't update time for usr
x usr/local/
x usr/local/include/
x usr/local/lib/
x usr/local/share/
x usr/local/share/info/
x usr/local/share/info/dir
x usr/local/share/info/gmp.info
x usr/local/share/info/gmp.info-1
x usr/local/share/info/gmp.info-2
x usr/local/lib/libgmp.a
x usr/local/lib/libgmp.la
x usr/local/include/gmp.h
tar: Error exit delayed from previous errors.

Search on the "Can't update time for usr"-error brought up a bunch of stuff 
about 'XSAN' that I didn't really understand fully but did not seem terribly 
relevant ...

  but the package 'gmp-6.1.2.tar.bz2' at gmplib.org expanded and compiled 
without difficulty usign the switches recommended at the bottom of:

http://r.research.att.com/libs/

davidwinsemius$ sudo tar fvxz /Users/davidwinsemius/Downloads/gmp-6.1.2.tar.bz2 
-C /

(I'm not on Sierra, since Apple has classified my MacPro as "obsolete".)

-- 

David
[R.app GUI 1.70 (7338) x86_64-apple-darwin15.6.0]

> 


>> install.packages("dplR")
> also installing the dependency ‘gmp’
> 
> Packages which are only available in source form, and may
>  need compilation of C/C++/Fortran: ‘gmp’ ‘dplR’
> Do you want to attempt to install these from sources?
> y/n: y
> installing the source packages ‘gmp’, ‘dplR’
> 
> trying URL 'https://cran.rstudio.com/src/contrib/gmp_0.5-13.1.tar.gz'
> Content type 'application/x-gzip' length 131321 bytes (128 KB)
> ==
> downloaded 128 KB
> 
> trying URL 'https://cran.rstudio.com/src/contrib/dplR_1.6.5.tar.gz'
> Content type 'application/x-gzip' length 1672999 bytes (1.6 MB)
> ==
> downloaded 1.6 MB
> 
> * installing *source* package ‘gmp’ ...
> ** package ‘gmp’ successfully unpacked and MD5 sums checked
> creating cache ./config.cache
> checking for __gmpz_ui_sub in -lgmp... no
> configure: error: GNU MP not found, or not 4.1.4 or up, see
> http://gmplib.org
> ERROR: configuration failed for package ‘gmp’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/gmp’
> Warning in install.packages :
>  installation of package ‘gmp’ had non-zero exit status
> ERROR: dependency ‘gmp’ is not available for package ‘dplR’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/dplR’
> Warning in install.packages :
>  installation of package ‘dplR’ had non-zero exit status
> 
> The downloaded source packages are in
> ‘/private/var/folders/c5/6g4vbk5x55586m8ky2v_6pbcgn/T/RtmprYzSE8/
> downloaded_packages’
> 
> 
> All the other packages work in good conditions.
> Please help me to solve this annoying situation.
> 
> Best regards!
> 
> CR
> 
> 
> -- 
> 
> -
> -
> Catalin-Constantin ROIBU
> 
> Lecturer PhD, Forestry engineer
> Forestry Faculty of Suceava
> Str. Universitatii no. 13, Suceava, 720229, Romania
> office phone  +4 0230 52 29 78, ext. 531
> mobile phone+4 0745 53 18 01
> FAX:+4 0230 52 16 64
> silvic.usv.ro 
> 
> 
> 
>   Sent with Mailtrack
> 
> <#>
> 
>   [[alternative HTML version deleted]]
> 
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David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

2017-05-16 Thread Fox, John

Dear Peter and Simon,

I don't fully understand the issues either and, again, haven't observed a 
problem, but I'm grateful that both of you are taking a look at it.

For what it's worth, here's what the Rcmdr package does with fonts. This code 
is from the development version of the Rcmdr, where the code is refactored for 
clarity, but the current CRAN version does the same things.

-- snip 

setupFonts <- function(){
current <- getOption("Rcmdr")
# set up Rcmdr default and text (log) fonts, Tk scaling factor
default.font.family.val <- tclvalue(.Tcl("font actual TkDefaultFont 
-family"))
default.font.family.val <- gsub("\\{", "", gsub("\\}", "", 
default.font.family.val))
default.font.family <- setOption("default.font.family", 
default.font.family.val)
if (!("RcmdrDefaultFont" %in% as.character(.Tcl("font names"{
.Tcl(paste("font create RcmdrDefaultFont", 
tclvalue(tkfont.actual("TkDefaultFont"
.Tcl("option add *font RcmdrDefaultFont")
}

.Tcl(paste("font configure RcmdrDefaultFont -family {", 
default.font.family, "}", sep=""))

if (!("RcmdrTitleFont" %in% as.character(.Tcl("font names"{
.Tcl(paste("font create RcmdrTitleFont", 
tclvalue(tkfont.actual("TkDefaultFont"
}
.Tcl(paste("font configure RcmdrTitleFont -family {", default.font.family, 
"}", sep=""))
if (!("RcmdrOutputMessagesFont" %in% as.character(.Tcl("font names"{
.Tcl(paste("font create RcmdrOutputMessagesFont", 
tclvalue(tkfont.actual("RcmdrTitleFont"
}
.Tcl(paste("font configure RcmdrTitleFont -family {", default.font.family, 
"}", sep=""))
.Tcl(paste("font configure RcmdrOutputMessagesFont -family {", 
default.font.family, "}", sep=""))

.Tcl(paste("font configure TkDefaultFont -family {",  default.font.family, 
"}", sep=""))
log.font.family.val <- tclvalue(.Tcl("font actual TkFixedFont -family"))
log.font.family.val <- gsub("\\{", "", gsub("\\}", "", log.font.family.val))
log.font.family <- setOption("log.font.family", log.font.family.val)
if (!("RcmdrLogFont" %in% as.character(.Tcl("font names"{
.Tcl(paste("font create RcmdrLogFont", 
tclvalue(tkfont.actual("TkFixedFont"
}
.Tcl(paste("font configure RcmdrLogFont -family {", log.font.family, "}", 
sep=""))
.Tcl(paste("font configure TkFixedFont -family {",  log.font.family, "}", 
sep=""))
putRcmdr("logFont", "RcmdrLogFont")
scale.factor <- current$scale.factor

if (!is.null(scale.factor)) .Tcl(paste("tk scaling ", scale.factor, sep=""))
# set various font sizes 
if (WindowsP()){
default.font.size.val <- abs(as.numeric(.Tcl("font actual TkDefaultFont 
-size")))
if (is.na(default.font.size.val)) default.font.size.val <- 10
}
else default.font.size.val <- 10
default.font.size <- setOption("default.font.size", default.font.size.val)
tkfont.configure("RcmdrDefaultFont", size=default.font.size)
tkfont.configure("RcmdrTitleFont", size=default.font.size)
tkfont.configure("RcmdrOutputMessagesFont", size=default.font.size)
tkfont.configure("TkDefaultFont", size=default.font.size)
tkfont.configure("TkTextFont", size=default.font.size)
tkfont.configure("TkCaptionFont", size=default.font.size)
log.font.size <- setOption("log.font.size", 10)
tkfont.configure("RcmdrLogFont", size=log.font.size)
tkfont.configure("TkFixedFont", size=log.font.size)

.Tcl("ttk::style configure TButton -font RcmdrDefaultFont")
.Tcl("ttk::style configure TLabel -font RcmdrDefaultFont")
.Tcl("ttk::style configure TCheckbutton -font RcmdrDefaultFont")
.Tcl("ttk::style configure TRadiobutton -font RcmdrDefaultFont")

standard.title.color <- as.character(.Tcl("ttk::style lookup 
TLabelframe.Label -foreground"))
title.color <- setOption("title.color", standard.title.color) 
if (tolower(title.color) == "black" || title.color == "#00"){
tkfont.configure("RcmdrTitleFont", weight="bold")
}
else tkfont.configure("RcmdrTitleFont", weight="normal")
}

- snip --

In this code, setOption() is a macro that uses user-supplied options if these 
are specified:

setOption <- defmacro(option, default, global=TRUE, expr= {
opt <- if (is.null(current[option][[1]])) default else current[option][[1]]
if (global) putRcmdr(option, opt)
opt
})

Best,
 John

> -Original Message-
> From: Simon Urbanek [mailto:simon.urba...@r-project.org]
> Sent: Tuesday, May 16, 2017 1:31 PM
> To: peter dalgaard 
> Cc: Fox, John ; r-sig-mac@r-project.org
> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
> 
> 
> > On May 16, 2017, at 12:20 PM, peter dalgaard  wrote:
> >
> > Mystery solved after looking into the actual .pkg files. They simply
> > contain a full Tcl/Tk which installs into

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

2017-05-16 Thread Simon Urbanek


> On May 16, 2017, at 12:20 PM, peter dalgaard  wrote:
> 
> Mystery solved after looking into the actual .pkg files. They simply contain 
> a full Tcl/Tk which installs into /usr/local, which obviously affects 
> anything that links it dynamically. I somehow thought that they would install 
> somewhere separate. (Stop grinning, Simon!)
> 

I'm not sure I understand the "they" - is it us? The difference in R 3.4.0 is 
that we are using everything from the system (and XQuartz) whereas before we 
were building dependencies ourselves before.


> Anyways, the way forward must be to get Tcl/Tk compiled exactly as they were 
> in 3.3.x.
> 

R before 3.4.0 we used Tcl/Tk 8.6.0 for OS X Mavericks from 2013, for R 3.4.0 
we are using Tcl/Tk 8.6.6 for El Capitan.

FWIW the config flags were
--disable-corefoundation --disable-framework --disable-aqua --enable-64bit 
--with-tcl=/usr/local/lib --with-x --x-includes=/opt/X11/include 
--x-libraries=/opt/X11/lib CC=clang CXX=clang++

I have no idea what you are talking about here so if anyone has suggestions to 
test, let me know.

Cheers,
Simon



> -pd
> 
> 
> 
> 
>> On 16 May 2017, at 15:18 , peter dalgaard  wrote:
>> 
>> Double-checked: Indeed, installing 3.3-branch-mavericks.pkg enables xft on 
>> my local builds of R-patched and R-devel. H..
>> 
>> -pd 
>> 
>>> On 16 May 2017, at 14:55 , peter dalgaard  wrote:
>>> 
>>> Curiouser and curiouser, now my local build of R-devel stopped using xft 
>>> _without any recompile_ I swear that it worked before I installed 
>>> R-3.4.0.pkg
>>> 
>>> I have both /opt/local/ and /usr/local variants of Tcl/Tk 8.6 and only the 
>>> former has wish8.6 understanding the tk::pkgconfig stuff, so there is 
>>> plenty of room for confusion. The latter seems to be from Simon's site; the 
>>> other one could be a MacPorts relic...
>>> 
>>> -pd
>>> 
 On 16 May 2017, at 13:28 , peter dalgaard  wrote:
 
 It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does 
 something slightly weird[*] with the fonts too, but this seems to be 
 orthogonal to the ugly-font issue).
 
 To see the issue quickly, try 
 
 library(tcltk)
 .Tcl("::tk::pkgconfig get fontsystem")
 
 With CRAN 3.3.3, I get 
 
  xft 
 
 and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says
 
> .Tcl("::tk::pkgconfig get fontsystem")
 Error in .Tcl("::tk::pkgconfig get fontsystem") : 
 could not find function ".Tcl"
 
 as does a local build of R-patched (???!!!). 
 
 This is pretty weird. I'll see if I can dig up some more about where the 
 difference is.
 
 -pd
 
 
 
 [*] Try library(tcltk); demo(tkfaq)  then library(Rcmdr) and watch the 
 font change in the tkfaq window.
 
 
> On 15 May 2017, at 23:17 , Fox, John  wrote:
> 
> Dear Jose,
> 
> It's a bit difficult to respond to your latest messages because you sent 
> so many of them.
> 
> I'm not entirely sure what's producing your font problems -- perhaps 
> Simon will have some additional ideas -- but you should be aware that you 
> can't load the Rcmdr package -- or, more generally, the tcltk package -- 
> without XQuartz (or another X11 system). Normally, XQuartz should start 
> automatically when the Rcmdr (or tcltk) package is loaded. That is, you 
> should not have to start it separately.
> 
> It may help to know that the Rcmdr package selects its default dialog 
> font by querying the default Tk font, via the command
> 
>   tclvalue(.Tcl("font actual TkDefaultFont -family"))
> 
> and sets the font for commands and output by querying the default Tk 
> fixed-width font:
> 
>   tclvalue(.Tcl("font actual TkFixedFont -family"))
> 
> On my Macs, these are respectively the helvetica and courier fonts.
> 
> In any event, I'm glad that you seem to have solved your problem.
> 
> John
> 
>> -Original Message-
>> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
>> Sent: Monday, May 15, 2017 3:18 PM
>> To: Simon Urbanek ; Fox, John
>> ; r-sig-mac@r-project.org
>> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
>> 
>> When I run R without XQuartz, the text from the help screen renders
>> well. I think the problem seems to be related to XQuartz.
>> 
>> José
>> 
>> 
>> José G. Conde, MD, MPH
>> Professor, School of Medicine
>> Director, CentIT2
>> UPR Medical Sciences Campus
>> 
>> Tel  (787) 763-9401 Fax (787) 758-5206
>> 
>> Email: jose.con...@upr.edu
>> 
>> URL: http://rcmi.rcm.upr.edu
>> 
>>> On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
>>  wrote:
>>>

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

2017-05-16 Thread peter dalgaard

Mystery solved after looking into the actual .pkg files. They simply contain a 
full Tcl/Tk which installs into /usr/local, which obviously affects anything 
that links it dynamically. I somehow thought that they would install somewhere 
separate. (Stop grinning, Simon!)

Anyways, the way forward must be to get Tcl/Tk compiled exactly as they were in 
3.3.x.

-pd




> On 16 May 2017, at 15:18 , peter dalgaard  wrote:
> 
> Double-checked: Indeed, installing 3.3-branch-mavericks.pkg enables xft on my 
> local builds of R-patched and R-devel. H..
> 
> -pd 
> 
>> On 16 May 2017, at 14:55 , peter dalgaard  wrote:
>> 
>> Curiouser and curiouser, now my local build of R-devel stopped using xft 
>> _without any recompile_ I swear that it worked before I installed 
>> R-3.4.0.pkg
>> 
>> I have both /opt/local/ and /usr/local variants of Tcl/Tk 8.6 and only the 
>> former has wish8.6 understanding the tk::pkgconfig stuff, so there is plenty 
>> of room for confusion. The latter seems to be from Simon's site; the other 
>> one could be a MacPorts relic...
>> 
>> -pd
>> 
>>> On 16 May 2017, at 13:28 , peter dalgaard  wrote:
>>> 
>>> It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does 
>>> something slightly weird[*] with the fonts too, but this seems to be 
>>> orthogonal to the ugly-font issue).
>>> 
>>> To see the issue quickly, try 
>>> 
>>> library(tcltk)
>>> .Tcl("::tk::pkgconfig get fontsystem")
>>> 
>>> With CRAN 3.3.3, I get 
>>> 
>>>  xft 
>>> 
>>> and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says
>>> 
 .Tcl("::tk::pkgconfig get fontsystem")
>>> Error in .Tcl("::tk::pkgconfig get fontsystem") : 
>>> could not find function ".Tcl"
>>> 
>>> as does a local build of R-patched (???!!!). 
>>> 
>>> This is pretty weird. I'll see if I can dig up some more about where the 
>>> difference is.
>>> 
>>> -pd
>>> 
>>> 
>>> 
>>> [*] Try library(tcltk); demo(tkfaq)  then library(Rcmdr) and watch the font 
>>> change in the tkfaq window.
>>> 
>>> 
 On 15 May 2017, at 23:17 , Fox, John  wrote:
 
 Dear Jose,
 
 It's a bit difficult to respond to your latest messages because you sent 
 so many of them.
 
 I'm not entirely sure what's producing your font problems -- perhaps Simon 
 will have some additional ideas -- but you should be aware that you can't 
 load the Rcmdr package -- or, more generally, the tcltk package -- without 
 XQuartz (or another X11 system). Normally, XQuartz should start 
 automatically when the Rcmdr (or tcltk) package is loaded. That is, you 
 should not have to start it separately.
 
 It may help to know that the Rcmdr package selects its default dialog font 
 by querying the default Tk font, via the command
 
tclvalue(.Tcl("font actual TkDefaultFont -family"))
 
 and sets the font for commands and output by querying the default Tk 
 fixed-width font:
 
tclvalue(.Tcl("font actual TkFixedFont -family"))
 
 On my Macs, these are respectively the helvetica and courier fonts.
 
 In any event, I'm glad that you seem to have solved your problem.
 
 John
 
> -Original Message-
> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
> Sent: Monday, May 15, 2017 3:18 PM
> To: Simon Urbanek ; Fox, John
> ; r-sig-mac@r-project.org
> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
> 
> When I run R without XQuartz, the text from the help screen renders
> well. I think the problem seems to be related to XQuartz.
> 
> José
> 
> 
> José G. Conde, MD, MPH
> Professor, School of Medicine
> Director, CentIT2
> UPR Medical Sciences Campus
> 
> Tel  (787) 763-9401 Fax (787) 758-5206
> 
> Email: jose.con...@upr.edu
> 
> URL: http://rcmi.rcm.upr.edu
> 
>> On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
>  wrote:
>> 
>> … and the same I get the same issue with R “help” screens in my iMac.
> I cannot reproduce this in the macBook.
>> 
>> José
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> José G. Conde, MD, MPH
>> Catedrático, Escuela de Medicina
>> Director, CentIT2
>> Recinto de Ciencias Médicas, UPR
>> 
>> Tel  (787) 763-9401  Fax (787) 758-5206
>> 
>> Correo electrónico: jose.con...@upr.edu
>> 
>> URL: http://rcmi.rcm.upr.edu
>> 
>>> On May 15, 2017, at 2:14 PM, Jose G Conde Santiago
>  wrote:
>>> 
>>> This is the actual resolutions.
>>> 
>>> José
>>> 
>>> 
>>> José G. Conde, MD, MPH
>>> Professor, School of Medicine
>>> Director, CentIT2
>>> UPR Medical Sciences Campus
>>> 
>>> Tel  (787) 763-9401 Fax (787)

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

2017-05-16 Thread Jose G Conde Santiago via R-SIG-Mac

Hello, John.

Thanks for the information and (all) for your patience. Unfortunately I am not 
that familiar with the inner workings of R. I just went back to R 3.3.3 for now.

José

José G. Conde, MD, MPH
Catedrático, Escuela de Medicina
Director, CentIT2
Recinto de Ciencias Médicas, UPR

Tel  (787) 763-9401  Fax (787) 758-5206

Correo electrónico: jose.con...@upr.edu

URL: http://rcmi.rcm.upr.edu

> On May 15, 2017, at 5:17 PM, Fox, John  wrote:
> 
> Dear Jose,
> 
> It's a bit difficult to respond to your latest messages because you sent so 
> many of them.
> 
> I'm not entirely sure what's producing your font problems -- perhaps Simon 
> will have some additional ideas -- but you should be aware that you can't 
> load the Rcmdr package -- or, more generally, the tcltk package -- without 
> XQuartz (or another X11 system). Normally, XQuartz should start automatically 
> when the Rcmdr (or tcltk) package is loaded. That is, you should not have to 
> start it separately.
> 
> It may help to know that the Rcmdr package selects its default dialog font by 
> querying the default Tk font, via the command
> 
>   tclvalue(.Tcl("font actual TkDefaultFont -family"))
> 
> and sets the font for commands and output by querying the default Tk 
> fixed-width font:
> 
>   tclvalue(.Tcl("font actual TkFixedFont -family"))
> 
> On my Macs, these are respectively the helvetica and courier fonts.
> 
> In any event, I'm glad that you seem to have solved your problem.
> 
> John
> 
>> -Original Message-
>> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
>> Sent: Monday, May 15, 2017 3:18 PM
>> To: Simon Urbanek ; Fox, John
>> ; r-sig-mac@r-project.org
>> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
>> 
>> When I run R without XQuartz, the text from the help screen renders
>> well. I think the problem seems to be related to XQuartz.
>> 
>> José
>> 
>> 
>> José G. Conde, MD, MPH
>> Professor, School of Medicine
>> Director, CentIT2
>> UPR Medical Sciences Campus
>> 
>> Tel  (787) 763-9401 Fax (787) 758-5206
>> 
>> Email: jose.con...@upr.edu
>> 
>> URL: http://rcmi.rcm.upr.edu
>> 
>>> On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
>>  wrote:
>>> 
>>> … and the same I get the same issue with R “help” screens in my iMac.
>> I cannot reproduce this in the macBook.
>>> 
>>> José
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> José G. Conde, MD, MPH
>>> Catedrático, Escuela de Medicina
>>> Director, CentIT2
>>> Recinto de Ciencias Médicas, UPR
>>> 
>>> Tel  (787) 763-9401  Fax (787) 758-5206
>>> 
>>> Correo electrónico: jose.con...@upr.edu
>>> 
>>> URL: http://rcmi.rcm.upr.edu
>>> 
 On May 15, 2017, at 2:14 PM, Jose G Conde Santiago
>>  wrote:
 
 This is the actual resolutions.
 
 José
 
 
 José G. Conde, MD, MPH
 Professor, School of Medicine
 Director, CentIT2
 UPR Medical Sciences Campus
 
 Tel  (787) 763-9401 Fax (787) 758-5206
 
 Email: jose.con...@upr.edu
 
 URL: http://rcmi.rcm.upr.edu
 
> On May 15, 2017, at 12:31 PM, Jose G Conde Santiago
>>  wrote:
> 
> 
 
>>> 
> 

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Re: [R-SIG-Mac] R 3.4.0 problem

2017-05-16 Thread Brandon Hurr

The key to understanding your current issue is the following lines in
your output.

checking for __gmpz_ui_sub in -lgmp... no
configure: error: GNU MP not found, or not 4.1.4 or up, see
http://gmplib.org

You need to visit that website and install GMP. The R `gmp` package
requires the GMP library to be installed before it can work so it
fails to install.

HTH,
B


On Mon, Apr 24, 2017 at 11:49 PM, catalin roibu  wrote:
> Dear all,
>
> I have a problem with the newest R version. I'm trying to install a
> specific package dplR who need the gpm package and I have this error on my
> macbook (OS Sierra):
>
>> install.packages("dplR")
> also installing the dependency ‘gmp’
>
> Packages which are only available in source form, and may
>   need compilation of C/C++/Fortran: ‘gmp’ ‘dplR’
> Do you want to attempt to install these from sources?
> y/n: y
> installing the source packages ‘gmp’, ‘dplR’
>
> trying URL 'https://cran.rstudio.com/src/contrib/gmp_0.5-13.1.tar.gz'
> Content type 'application/x-gzip' length 131321 bytes (128 KB)
> ==
> downloaded 128 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/dplR_1.6.5.tar.gz'
> Content type 'application/x-gzip' length 1672999 bytes (1.6 MB)
> ==
> downloaded 1.6 MB
>
> * installing *source* package ‘gmp’ ...
> ** package ‘gmp’ successfully unpacked and MD5 sums checked
> creating cache ./config.cache
> checking for __gmpz_ui_sub in -lgmp... no
> configure: error: GNU MP not found, or not 4.1.4 or up, see
> http://gmplib.org
> ERROR: configuration failed for package ‘gmp’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/gmp’
> Warning in install.packages :
>   installation of package ‘gmp’ had non-zero exit status
> ERROR: dependency ‘gmp’ is not available for package ‘dplR’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/dplR’
> Warning in install.packages :
>   installation of package ‘dplR’ had non-zero exit status
>
> The downloaded source packages are in
> ‘/private/var/folders/c5/6g4vbk5x55586m8ky2v_6pbcgn/T/RtmprYzSE8/
> downloaded_packages’
>
>
> All the other packages work in good conditions.
> Please help me to solve this annoying situation.
>
> Best regards!
>
> CR
>
>
> --
>
> -
> -
> Catalin-Constantin ROIBU
>
> Lecturer PhD, Forestry engineer
> Forestry Faculty of Suceava
> Str. Universitatii no. 13, Suceava, 720229, Romania
> office phone  +4 0230 52 29 78, ext. 531
> mobile phone+4 0745 53 18 01
> FAX:+4 0230 52 16 64
> silvic.usv.ro 
>
>
>
>    Sent with Mailtrack
> 
> <#>
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] missing module when compiling R pkg:rms or external package SYMPHONY (in support of Bioc pkg symphony)

2017-05-16 Thread Frank Harrell

Please remove me from the emails and substitute Cole Beck
Frank


--
Frank E Harrell Jr  Professor and Chairman  School of Medicine

Department of *Biostatistics*  *Vanderbilt University*

On Fri, May 5, 2017 at 2:13 AM, Berend Hasselman  wrote:

>
> > On 5 May 2017, at 03:12, David Winsemius  wrote:
> >
> > Failing to get current rms package to compile (and appears that the CRAN
> build machine fails as well). The penultimate version of rms succeeds.
> >
> > Both from console and cmd-line I get this response in R 3.4.0 (just
> installed today) running El Cap 10.11.6 with Xcode Version 8.2.1 (8C1002):
> >
> > trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rms_5.1-1.tar.gz'
> > Content type 'application/x-gzip' length 521311 bytes (509 KB)
> > ==
> > downloaded 509 KB
> >
> > Loading required package: lattice
> > Loading required package: sos
> > Loading required package: brew
> > Loading required package: rms
> > Loading required package: Hmisc
> > Loading required package: survival
> > Loading required package: Formula
> > Loading required package: stats
> > Loading required package: ggplot2
> >
> > Attaching package: ‘Hmisc’
> >
> > The following objects are masked from ‘package:base’:
> >
> >   format.pval, round.POSIXt, trunc.POSIXt, units
> >
> > Loading required package: SparseM
> >
> > Attaching package: ‘SparseM’
> >
> > The following object is masked from ‘package:base’:
> >
> >   backsolve
> >
> > ##-- 2017-05-04 --##
> > Loading required package: graphics
> >
> > Attaching package: ‘graphics’
> >
> > The following object is masked from ‘package:SparseM’:
> >
> >   image
> >
> > * installing *source* package ‘rms’ ...
> > ** package ‘rms’ successfully unpacked and MD5 sums checked
> > ** libs
> > clang -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
> > gfortran   -fPIC  -g -O2  -c lrmfit.f -o lrmfit.o
> > gfortran   -fPIC  -g -O2  -c mlmats.f -o mlmats.o
> > gfortran   -fPIC  -g -O2  -c ormuv.f -o ormuv.o
> > gfortran   -fPIC  -g -O2  -c robcovf.f -o robcovf.o
> > clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> rms.so init.o lrmfit.o mlmats.o ormuv.o robcovf.o
> -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0
> -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm 
> -F/Library/Frameworks/R.framework/..
> -framework R -Wl,-framework -Wl,CoreFoundation
> > installing to /Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/rms/libs
> > ** R
> > ** demo
> > ** inst
> > ** preparing package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices
> > ** testing if installed package can be loaded
> > Loading required package: lattice
> > Loading required package: sos
> > Loading required package: brew
> > Loading required package: rms
> > Loading required package: Hmisc
> > Loading required package: survival
> > Loading required package: Formula
> > Loading required package: stats
> > Loading required package: ggplot2
> >
> > Attaching package: ‘Hmisc’
> >
> > The following objects are masked from ‘package:base’:
> >
> >   format.pval, round.POSIXt, trunc.POSIXt, units
> >
> > Loading required package: SparseM
> >
> > Attaching package: ‘SparseM’
> >
> > The following object is masked from ‘package:base’:
> >
> >   backsolve
> >
> > Error: package or namespace load failed for ‘rms’ in dyn.load(file,
> DLLpath = DLLpath, ...):
> > unable to load shared object '/Library/Frameworks/R.
> framework/Versions/3.4/Resources/library/rms/libs/rms.so':
> > dlopen(/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/rms/libs/rms.so, 6): Symbol not found: ___addtf3
> > Referenced from: /usr/local/lib/libquadmath.0.dylib
> > Expected in: /usr/local/lib/libgcc_s.1.dylib
> > in /usr/local/lib/libquadmath.0.dylib
> > ##-- 2017-05-04 --##
> > Loading required package: graphics
> >
> > Attaching package: ‘graphics’
> >
> > The following object is masked from ‘package:SparseM’:
> >
> >   image
> >
> > Error: package or namespace load failed for ‘rms’ in dyn.load(file,
> DLLpath = DLLpath, ...):
> > unable to load shared object '/Library/Frameworks/R.
> framework/Versions/3.4/Resources/library/rms/libs/rms.so':
> > dlopen(/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/rms/libs/rms.so, 6): Symbol not found: ___addtf3
> > Referenced from: /usr/local/lib/libquadmath.0.dylib
> > Expected in: /usr/local/lib/libgcc_s.1.dylib
> > in /usr/local/lib/libquadmath.0.dylib
> > Error: loading failed
> > Execution halted
> >
> > The downloaded source packages are in
> >   ‘/private/var/folders/yq/m3j1jqtj6hq6s5mq_
> v0jn3s8gn/T/Rtmpplg8Th/downloaded_packages’
> >
> > (WARNING:

[R-SIG-Mac] Please help! Package Installer doesn't work.

2017-05-16 Thread Luisa Bahnemann

Hello ,
I’ve only installed R (R 3.4.0 GUI 1.70 El Capitan build (7338))
a few days ago . Now every time I try to install a package I can’t even see the 
list of packages and R completely freezes.
Then it shows this :

Warnung: unable to access index for repository 
https://mirrors.cicku.me/CRAN/bin/macosx/el-capitan/contrib/3.4:
  kann URL 
'https://mirrors.cicku.me/CRAN/bin/macosx/el-capitan/contrib/3.4/PACKAGES' 
nicht öffnen

Could you please help me?
I already reinstalled but it didn’t help.

Thankyou !
Luisa Bahnemann
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[R-SIG-Mac] R 3.4.0 problem

2017-05-16 Thread catalin roibu

Dear all,

I have a problem with the newest R version. I'm trying to install a
specific package dplR who need the gpm package and I have this error on my
macbook (OS Sierra):

> install.packages("dplR")
also installing the dependency ‘gmp’

Packages which are only available in source form, and may
  need compilation of C/C++/Fortran: ‘gmp’ ‘dplR’
Do you want to attempt to install these from sources?
y/n: y
installing the source packages ‘gmp’, ‘dplR’

trying URL 'https://cran.rstudio.com/src/contrib/gmp_0.5-13.1.tar.gz'
Content type 'application/x-gzip' length 131321 bytes (128 KB)
==
downloaded 128 KB

trying URL 'https://cran.rstudio.com/src/contrib/dplR_1.6.5.tar.gz'
Content type 'application/x-gzip' length 1672999 bytes (1.6 MB)
==
downloaded 1.6 MB

* installing *source* package ‘gmp’ ...
** package ‘gmp’ successfully unpacked and MD5 sums checked
creating cache ./config.cache
checking for __gmpz_ui_sub in -lgmp... no
configure: error: GNU MP not found, or not 4.1.4 or up, see
http://gmplib.org
ERROR: configuration failed for package ‘gmp’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/
Resources/library/gmp’
Warning in install.packages :
  installation of package ‘gmp’ had non-zero exit status
ERROR: dependency ‘gmp’ is not available for package ‘dplR’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/
Resources/library/dplR’
Warning in install.packages :
  installation of package ‘dplR’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/c5/6g4vbk5x55586m8ky2v_6pbcgn/T/RtmprYzSE8/
downloaded_packages’


All the other packages work in good conditions.
Please help me to solve this annoying situation.

Best regards!

CR


-- 

-
-
Catalin-Constantin ROIBU

Lecturer PhD, Forestry engineer
Forestry Faculty of Suceava
Str. Universitatii no. 13, Suceava, 720229, Romania
office phone  +4 0230 52 29 78, ext. 531
mobile phone+4 0745 53 18 01
FAX:+4 0230 52 16 64
silvic.usv.ro 



   Sent with Mailtrack

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Re: [R-SIG-Mac] Problem with Rcpp on R-3.4 beta (r72492)

2017-05-16 Thread Qiu Xiaojie


Hi R developers, 

We see the same problem and found that re-install all package with the 
argument "type = 'source" solves this problem. I don't know what is the 
reason for this but someone may answer it. 

On Friday, April 7, 2017 at 2:11:26 AM UTC-7, Berend Hasselman wrote:
>
>
> Hi, 
>
> I have downloaded and installed R from R-3.4-r72492-branch-el-capitan.pkg. 
> My OS: OS X El Capitan (10.11.6) 
>
> My packages and all additional tests of these are working correctly. 
>
> I can install Rcpp. 
> Packages requiring Rcpp however don't seem to install or run. 
>
>
> Running otool -L on 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/libs/Rcpp.so
>  
>
> gives 
>
> Rcpp.so: 
> Rcpp.so (compatibility version 0.0.0, current version 0.0.0) 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libR.dylib 
> (compatibility version 3.4.0, current version 3.4.0) 
> 
> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 
> (compatibility version 150.0.0, current version 1259.0.0) 
> /usr/local/clang4/lib/libc++.1.dylib (compatibility version 1.0.0, 
> current version 1.0.0) 
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
> version 1226.10.1) 
>
>
> I don't have  /usr/local/clang4/lib/libc++.1.dylib. 
> I wouldn't know where to get it from. AFAIK The macOS Commandline Tools do 
> not install stuff in /usr/local. 
> If this isn't a mishap: where do we get the necessary libc++.1.dylib from? 
>
> Berend Hasselman 
>
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac 
>
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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

2017-05-16 Thread peter dalgaard

Double-checked: Indeed, installing 3.3-branch-mavericks.pkg enables xft on my 
local builds of R-patched and R-devel. H..

-pd 

> On 16 May 2017, at 14:55 , peter dalgaard  wrote:
> 
> Curiouser and curiouser, now my local build of R-devel stopped using xft 
> _without any recompile_ I swear that it worked before I installed 
> R-3.4.0.pkg
> 
> I have both /opt/local/ and /usr/local variants of Tcl/Tk 8.6 and only the 
> former has wish8.6 understanding the tk::pkgconfig stuff, so there is plenty 
> of room for confusion. The latter seems to be from Simon's site; the other 
> one could be a MacPorts relic...
> 
> -pd
> 
>> On 16 May 2017, at 13:28 , peter dalgaard  wrote:
>> 
>> It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does 
>> something slightly weird[*] with the fonts too, but this seems to be 
>> orthogonal to the ugly-font issue).
>> 
>> To see the issue quickly, try 
>> 
>> library(tcltk)
>> .Tcl("::tk::pkgconfig get fontsystem")
>> 
>> With CRAN 3.3.3, I get 
>> 
>>  xft 
>> 
>> and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says
>> 
>>> .Tcl("::tk::pkgconfig get fontsystem")
>> Error in .Tcl("::tk::pkgconfig get fontsystem") : 
>> could not find function ".Tcl"
>> 
>> as does a local build of R-patched (???!!!). 
>> 
>> This is pretty weird. I'll see if I can dig up some more about where the 
>> difference is.
>> 
>> -pd
>> 
>> 
>> 
>> [*] Try library(tcltk); demo(tkfaq)  then library(Rcmdr) and watch the font 
>> change in the tkfaq window.
>> 
>> 
>>> On 15 May 2017, at 23:17 , Fox, John  wrote:
>>> 
>>> Dear Jose,
>>> 
>>> It's a bit difficult to respond to your latest messages because you sent so 
>>> many of them.
>>> 
>>> I'm not entirely sure what's producing your font problems -- perhaps Simon 
>>> will have some additional ideas -- but you should be aware that you can't 
>>> load the Rcmdr package -- or, more generally, the tcltk package -- without 
>>> XQuartz (or another X11 system). Normally, XQuartz should start 
>>> automatically when the Rcmdr (or tcltk) package is loaded. That is, you 
>>> should not have to start it separately.
>>> 
>>> It may help to know that the Rcmdr package selects its default dialog font 
>>> by querying the default Tk font, via the command
>>> 
>>> tclvalue(.Tcl("font actual TkDefaultFont -family"))
>>> 
>>> and sets the font for commands and output by querying the default Tk 
>>> fixed-width font:
>>> 
>>> tclvalue(.Tcl("font actual TkFixedFont -family"))
>>> 
>>> On my Macs, these are respectively the helvetica and courier fonts.
>>> 
>>> In any event, I'm glad that you seem to have solved your problem.
>>> 
>>> John
>>> 
 -Original Message-
 From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
 Sent: Monday, May 15, 2017 3:18 PM
 To: Simon Urbanek ; Fox, John
 ; r-sig-mac@r-project.org
 Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
 
 When I run R without XQuartz, the text from the help screen renders
 well. I think the problem seems to be related to XQuartz.
 
 José
 
 
 José G. Conde, MD, MPH
 Professor, School of Medicine
 Director, CentIT2
 UPR Medical Sciences Campus
 
 Tel  (787) 763-9401 Fax (787) 758-5206
 
 Email: jose.con...@upr.edu
 
 URL: http://rcmi.rcm.upr.edu
 
> On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
  wrote:
> 
> … and the same I get the same issue with R “help” screens in my iMac.
 I cannot reproduce this in the macBook.
> 
> José
> 
> 
> 
> 
> 
> 
> 
> 
> 
> José G. Conde, MD, MPH
> Catedrático, Escuela de Medicina
> Director, CentIT2
> Recinto de Ciencias Médicas, UPR
> 
> Tel  (787) 763-9401  Fax (787) 758-5206
> 
> Correo electrónico: jose.con...@upr.edu
> 
> URL: http://rcmi.rcm.upr.edu
> 
>> On May 15, 2017, at 2:14 PM, Jose G Conde Santiago
  wrote:
>> 
>> This is the actual resolutions.
>> 
>> José
>> 
>> 
>> José G. Conde, MD, MPH
>> Professor, School of Medicine
>> Director, CentIT2
>> UPR Medical Sciences Campus
>> 
>> Tel  (787) 763-9401 Fax (787) 758-5206
>> 
>> Email: jose.con...@upr.edu
>> 
>> URL: http://rcmi.rcm.upr.edu
>> 
>>> On May 15, 2017, at 12:31 PM, Jose G Conde Santiago
  wrote:
>>> 
>>> 
>> 
> 
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> -- 
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email:

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

2017-05-16 Thread peter dalgaard

Curiouser and curiouser, now my local build of R-devel stopped using xft 
_without any recompile_ I swear that it worked before I installed 
R-3.4.0.pkg

I have both /opt/local/ and /usr/local variants of Tcl/Tk 8.6 and only the 
former has wish8.6 understanding the tk::pkgconfig stuff, so there is plenty of 
room for confusion. The latter seems to be from Simon's site; the other one 
could be a MacPorts relic...

-pd

> On 16 May 2017, at 13:28 , peter dalgaard  wrote:
> 
> It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does 
> something slightly weird[*] with the fonts too, but this seems to be 
> orthogonal to the ugly-font issue).
> 
> To see the issue quickly, try 
> 
> library(tcltk)
> .Tcl("::tk::pkgconfig get fontsystem")
> 
> With CRAN 3.3.3, I get 
> 
>  xft 
> 
> and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says
> 
>> .Tcl("::tk::pkgconfig get fontsystem")
> Error in .Tcl("::tk::pkgconfig get fontsystem") : 
>  could not find function ".Tcl"
> 
> as does a local build of R-patched (???!!!). 
> 
> This is pretty weird. I'll see if I can dig up some more about where the 
> difference is.
> 
> -pd
> 
> 
> 
> [*] Try library(tcltk); demo(tkfaq)  then library(Rcmdr) and watch the font 
> change in the tkfaq window.
> 
> 
>> On 15 May 2017, at 23:17 , Fox, John  wrote:
>> 
>> Dear Jose,
>> 
>> It's a bit difficult to respond to your latest messages because you sent so 
>> many of them.
>> 
>> I'm not entirely sure what's producing your font problems -- perhaps Simon 
>> will have some additional ideas -- but you should be aware that you can't 
>> load the Rcmdr package -- or, more generally, the tcltk package -- without 
>> XQuartz (or another X11 system). Normally, XQuartz should start 
>> automatically when the Rcmdr (or tcltk) package is loaded. That is, you 
>> should not have to start it separately.
>> 
>> It may help to know that the Rcmdr package selects its default dialog font 
>> by querying the default Tk font, via the command
>> 
>>  tclvalue(.Tcl("font actual TkDefaultFont -family"))
>> 
>> and sets the font for commands and output by querying the default Tk 
>> fixed-width font:
>> 
>>  tclvalue(.Tcl("font actual TkFixedFont -family"))
>> 
>> On my Macs, these are respectively the helvetica and courier fonts.
>> 
>> In any event, I'm glad that you seem to have solved your problem.
>> 
>> John
>> 
>>> -Original Message-
>>> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
>>> Sent: Monday, May 15, 2017 3:18 PM
>>> To: Simon Urbanek ; Fox, John
>>> ; r-sig-mac@r-project.org
>>> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
>>> 
>>> When I run R without XQuartz, the text from the help screen renders
>>> well. I think the problem seems to be related to XQuartz.
>>> 
>>> José
>>> 
>>> 
>>> José G. Conde, MD, MPH
>>> Professor, School of Medicine
>>> Director, CentIT2
>>> UPR Medical Sciences Campus
>>> 
>>> Tel  (787) 763-9401 Fax (787) 758-5206
>>> 
>>> Email: jose.con...@upr.edu
>>> 
>>> URL: http://rcmi.rcm.upr.edu
>>> 
 On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
>>>  wrote:
 
 … and the same I get the same issue with R “help” screens in my iMac.
>>> I cannot reproduce this in the macBook.
 
 José
 
 
 
 
 
 
 
 
 
 José G. Conde, MD, MPH
 Catedrático, Escuela de Medicina
 Director, CentIT2
 Recinto de Ciencias Médicas, UPR
 
 Tel  (787) 763-9401  Fax (787) 758-5206
 
 Correo electrónico: jose.con...@upr.edu
 
 URL: http://rcmi.rcm.upr.edu
 
> On May 15, 2017, at 2:14 PM, Jose G Conde Santiago
>>>  wrote:
> 
> This is the actual resolutions.
> 
> José
> 
> 
> José G. Conde, MD, MPH
> Professor, School of Medicine
> Director, CentIT2
> UPR Medical Sciences Campus
> 
> Tel  (787) 763-9401 Fax (787) 758-5206
> 
> Email: jose.con...@upr.edu
> 
> URL: http://rcmi.rcm.upr.edu
> 
>> On May 15, 2017, at 12:31 PM, Jose G Conde Santiago
>>>  wrote:
>> 
>> 
> 
 
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> 
> 
> 
> 
> 
> 
> 
> 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

2017-05-16 Thread peter dalgaard

It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does 
something slightly weird[*] with the fonts too, but this seems to be orthogonal 
to the ugly-font issue).

To see the issue quickly, try 

library(tcltk)
.Tcl("::tk::pkgconfig get fontsystem")

With CRAN 3.3.3, I get 

 xft 

and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says

> .Tcl("::tk::pkgconfig get fontsystem")
Error in .Tcl("::tk::pkgconfig get fontsystem") : 
  could not find function ".Tcl"

as does a local build of R-patched (???!!!). 

This is pretty weird. I'll see if I can dig up some more about where the 
difference is.

-pd



[*] Try library(tcltk); demo(tkfaq)  then library(Rcmdr) and watch the font 
change in the tkfaq window.


> On 15 May 2017, at 23:17 , Fox, John  wrote:
> 
> Dear Jose,
> 
> It's a bit difficult to respond to your latest messages because you sent so 
> many of them.
> 
> I'm not entirely sure what's producing your font problems -- perhaps Simon 
> will have some additional ideas -- but you should be aware that you can't 
> load the Rcmdr package -- or, more generally, the tcltk package -- without 
> XQuartz (or another X11 system). Normally, XQuartz should start automatically 
> when the Rcmdr (or tcltk) package is loaded. That is, you should not have to 
> start it separately.
> 
> It may help to know that the Rcmdr package selects its default dialog font by 
> querying the default Tk font, via the command
> 
>   tclvalue(.Tcl("font actual TkDefaultFont -family"))
> 
> and sets the font for commands and output by querying the default Tk 
> fixed-width font:
> 
>   tclvalue(.Tcl("font actual TkFixedFont -family"))
> 
> On my Macs, these are respectively the helvetica and courier fonts.
> 
> In any event, I'm glad that you seem to have solved your problem.
> 
> John
> 
>> -Original Message-
>> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
>> Sent: Monday, May 15, 2017 3:18 PM
>> To: Simon Urbanek ; Fox, John
>> ; r-sig-mac@r-project.org
>> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
>> 
>> When I run R without XQuartz, the text from the help screen renders
>> well. I think the problem seems to be related to XQuartz.
>> 
>> José
>> 
>> 
>> José G. Conde, MD, MPH
>> Professor, School of Medicine
>> Director, CentIT2
>> UPR Medical Sciences Campus
>> 
>> Tel  (787) 763-9401 Fax (787) 758-5206
>> 
>> Email: jose.con...@upr.edu
>> 
>> URL: http://rcmi.rcm.upr.edu
>> 
>>> On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
>>  wrote:
>>> 
>>> … and the same I get the same issue with R “help” screens in my iMac.
>> I cannot reproduce this in the macBook.
>>> 
>>> José
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> José G. Conde, MD, MPH
>>> Catedrático, Escuela de Medicina
>>> Director, CentIT2
>>> Recinto de Ciencias Médicas, UPR
>>> 
>>> Tel  (787) 763-9401  Fax (787) 758-5206
>>> 
>>> Correo electrónico: jose.con...@upr.edu
>>> 
>>> URL: http://rcmi.rcm.upr.edu
>>> 
 On May 15, 2017, at 2:14 PM, Jose G Conde Santiago
>>  wrote:
 
 This is the actual resolutions.
 
 José
 
 
 José G. Conde, MD, MPH
 Professor, School of Medicine
 Director, CentIT2
 UPR Medical Sciences Campus
 
 Tel  (787) 763-9401 Fax (787) 758-5206
 
 Email: jose.con...@upr.edu
 
 URL: http://rcmi.rcm.upr.edu
 
> On May 15, 2017, at 12:31 PM, Jose G Conde Santiago
>>  wrote:
> 
> 
 
>>> 
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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