[Rd] formatR 1.0 caused error
Recently in our R 3.1.0 installation the package formatR was upgraded to
version 1.0, doing my usual thing, I got the following error, and the
destination html file was not generated.
What can I do if I want to stay at the current formatR version?
Jun
Error: unrecognized fields specified in html_dependency: attachment
In addition: Warning messages:
1: 'function (...)
{
.Deprecated(tidy_source, package = formatR)
tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help(Deprecated) and help(formatR-deprecated).
2: In tidy_source(...) :
The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
3: 'function (...)
{
.Deprecated(tidy_source, package = formatR)
tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help(Deprecated) and help(formatR-deprecated).
4: In tidy_source(...) :
The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
5: 'function (...)
{
.Deprecated(tidy_source, package = formatR)
tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help(Deprecated) and help(formatR-deprecated).
6: In tidy_source(...) :
The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
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Re: [Rd] formatR 1.0 caused error
Problem solved. User library location had an older rmarkdown, removed that, so
that the current rmarkdown 0.3.3 at the system library location is being used.
-Original Message-
From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On
Behalf Of Zhang,Jun
Sent: Thursday, September 18, 2014 1:08 PM
To: r-devel@r-project.org
Subject: [Rd] formatR 1.0 caused error
Recently in our R 3.1.0 installation the package formatR was upgraded to
version 1.0, doing my usual thing, I got the following error, and the
destination html file was not generated.
What can I do if I want to stay at the current formatR version?
Jun
Error: unrecognized fields specified in html_dependency: attachment In
addition: Warning messages:
1: 'function (...)
{
.Deprecated(tidy_source, package = formatR)
tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help(Deprecated) and help(formatR-deprecated).
2: In tidy_source(...) :
The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
3: 'function (...)
{
.Deprecated(tidy_source, package = formatR)
tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help(Deprecated) and help(formatR-deprecated).
4: In tidy_source(...) :
The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
5: 'function (...)
{
.Deprecated(tidy_source, package = formatR)
tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help(Deprecated) and help(formatR-deprecated).
6: In tidy_source(...) :
The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
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Re: [Rd] formatR 1.0 caused error
Yihui,
I installed knitr_1.6.18, and user reported no warning any more. In my other
related posting I thought rmarkdown was the problem, actually there are two
part of the problems. Using older version of rmarkdown caused no html file
generated, which is more serious, and the warning was cleared by your
development knitr.
Thanks!
Jun
-Original Message-
From: xieyi...@gmail.com [mailto:xieyi...@gmail.com] On Behalf Of Yihui Xie
Sent: Thursday, September 18, 2014 1:39 PM
To: Zhang,Jun
Cc: r-devel@r-project.org
Subject: Re: [Rd] formatR 1.0 caused error
Sorry, but this is a wrong list to write to. I'll reply anyway this time...
The formatR package should be irrelevant in this case -- you were seeing
warnings of deprecation. The error came from elsewhere. It is hard to say what
the problem was without a reproducible example.
Anyway, to fix the warnings, you can install the development version of knitr
(which I plan to release to CRAN relatively soon):
install.packages('knitr', repos = c('http://rforge.net',
'http://cran.rstudio.com'), type = 'source')
You posted your sessionInfo() but it seems you deleted an important
part: the versions of packages, which makes it even more difficult for others
to tell what the problem could possibly be.
Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Web: http://yihui.name
On Thu, Sep 18, 2014 at 1:07 PM, Zhang,Jun jhzh...@mdanderson.org wrote:
Recently in our R 3.1.0 installation the package formatR was upgraded to
version 1.0, doing my usual thing, I got the following error, and the
destination html file was not generated.
What can I do if I want to stay at the current formatR version?
Jun
Error: unrecognized fields specified in html_dependency: attachment In
addition: Warning messages:
1: 'function (...)
{
.Deprecated(tidy_source, package = formatR)
tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help(Deprecated) and help(formatR-deprecated).
2: In tidy_source(...) :
The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
3: 'function (...)
{
.Deprecated(tidy_source, package = formatR)
tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help(Deprecated) and help(formatR-deprecated).
4: In tidy_source(...) :
The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
5: 'function (...)
{
.Deprecated(tidy_source, package = formatR)
tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help(Deprecated) and help(formatR-deprecated).
6: In tidy_source(...) :
The option 'keep.blank.line' is deprecated; please use 'formatR.blank'
sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
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[Rd] Can the output of Sys.getenv() be improved?
Within an R session, type Sys.getenv() will list all the environment variables, but each one of them occupies about a page, so scrolling to find one is difficult. Is this because I don't know how to use it or something could be improved? Usually I'm not sure the exact name of a variable but want to look it up. Recently I installed rjags, with the JAGS-3.4.0's lib, include, modules information provided during compilation. When I load rjags, I was told that it linked to JAGS 3.3.0 (a package also available in my environment). This made me think there must be a variable to make that to happen. What can I do to make rjags to link to JAGS 3.4.0? Jun [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Can the output of Sys.getenv() be improved?
That is a great command to have. Once the better formatted envvars with value is listed, I noticed that JAGS-3.3.0/bin is in the PATH, so that problem is also solved for my user. Thanks, Jun -Original Message- From: xieyi...@gmail.com [mailto:xieyi...@gmail.com] On Behalf Of Yihui Xie Sent: Friday, April 18, 2014 11:52 AM To: Zhang,Jun Cc: r-devel@r-project.org Subject: Re: [Rd] Can the output of Sys.getenv() be improved? For your first question, try str(as.list(Sys.getenv())). I do not know the answer for the JAGS question, and I'll leave it to someone else to tell you which mailing list to use for such questions... Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Fri, Apr 18, 2014 at 11:38 AM, Zhang,Jun jhzh...@mdanderson.org wrote: Within an R session, type Sys.getenv() will list all the environment variables, but each one of them occupies about a page, so scrolling to find one is difficult. Is this because I don't know how to use it or something could be improved? Usually I'm not sure the exact name of a variable but want to look it up. Recently I installed rjags, with the JAGS-3.4.0's lib, include, modules information provided during compilation. When I load rjags, I was told that it linked to JAGS 3.3.0 (a package also available in my environment). This made me think there must be a variable to make that to happen. What can I do to make rjags to link to JAGS 3.4.0? Jun __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Can the output of Sys.getenv() be improved?
I take the latter part back. I could not possibly load rjags with JAGS-3.4.0 linked. -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Zhang,Jun Sent: Friday, April 18, 2014 12:03 PM To: 'Yihui Xie' Cc: r-devel@r-project.org Subject: Re: [Rd] Can the output of Sys.getenv() be improved? That is a great command to have. Once the better formatted envvars with value is listed, I noticed that JAGS-3.3.0/bin is in the PATH, so that problem is also solved for my user. Thanks, Jun -Original Message- From: xieyi...@gmail.com [mailto:xieyi...@gmail.com] On Behalf Of Yihui Xie Sent: Friday, April 18, 2014 11:52 AM To: Zhang,Jun Cc: r-devel@r-project.org Subject: Re: [Rd] Can the output of Sys.getenv() be improved? For your first question, try str(as.list(Sys.getenv())). I do not know the answer for the JAGS question, and I'll leave it to someone else to tell you which mailing list to use for such questions... Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Fri, Apr 18, 2014 at 11:38 AM, Zhang,Jun jhzh...@mdanderson.org wrote: Within an R session, type Sys.getenv() will list all the environment variables, but each one of them occupies about a page, so scrolling to find one is difficult. Is this because I don't know how to use it or something could be improved? Usually I'm not sure the exact name of a variable but want to look it up. Recently I installed rjags, with the JAGS-3.4.0's lib, include, modules information provided during compilation. When I load rjags, I was told that it linked to JAGS 3.3.0 (a package also available in my environment). This made me think there must be a variable to make that to happen. What can I do to make rjags to link to JAGS 3.4.0? Jun __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Can the output of Sys.getenv() be improved?
Thank you very much for your reply. This seems better used for Windows. Best regards, Jun -Original Message- From: William Dunlap [mailto:wdun...@tibco.com] Sent: Friday, April 18, 2014 11:50 AM To: Zhang,Jun; r-devel@r-project.org Subject: RE: Can the output of Sys.getenv() be improved? Within an R session, type Sys.getenv() will list all the environment variables, but each one of them occupies about a page, so scrolling to find one is difficult. Is this because I don't know how to use it or something could be improved? Attaching the class simple.list to the output of Sys.getenv() gives it a nicer print method: structure(Sys.getenv(), class=simple.list) _ ! ! ALCKPathC:\\Program Files\\Lenovo\\AutoLock
Re: [Rd] Can the output of Sys.getenv() be improved?
Thanks Gabor, really appreciate your help. -Jun -Original Message- From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com] Sent: Friday, April 18, 2014 3:54 PM To: Zhang,Jun Cc: r-devel@r-project.org Subject: Re: [Rd] Can the output of Sys.getenv() be improved? On Fri, Apr 18, 2014 at 12:38 PM, Zhang,Jun jhzh...@mdanderson.org wrote: Within an R session, type Sys.getenv() will list all the environment variables, but each one of them occupies about a page, so scrolling to find one is difficult. Is this because I don't know how to use it or something could be improved? Usually I'm not sure the exact name of a variable but want to look it up. Recently I installed rjags, with the JAGS-3.4.0's lib, include, modules information provided during compilation. When I load rjags, I was told that it linked to JAGS 3.3.0 (a package also available in my environment). This made me think there must be a variable to make that to happen. What can I do to make rjags to link to JAGS 3.4.0? Try this: str(as.list(Sys.getenv())) or this: View(as.matrix(Sys.getenv())) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Problem installing MCMCpack on SPARC Solaris 10
Hi list, I tried to install MCMCpack to R-2.12.0, got the following error, R CMD INSTALL MCMCpack_1.0-9.tar.gz .. CC -m64 -library=stlport4 -I/apps/sparcv9/R-2.12.0/lib/R/include -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DHAVE_TRUNC -DHAVE_IEEEFP_H -I/opt/csw/include-KPIC -g -c MCMCSVDreg.cchttp://MCMCSVDreg.cc -o MCMCSVDreg.o error.h, line 598: Error: The function abort must have a prototype. distributions.h, line 550: Error: The function trunc must have a prototype. distributions.h, line 550: Error: log1p is not a member of file level. distributions.h, line 566: Error: The function trunc must have a prototype. distributions.h, line 566: Error: log1p is not a member of file level. distributions.h, line 2177: Error: sqrt is not a member of file level. 6 Error(s) detected. make: *** [MCMCSVDreg.o] Error 2 ERROR: compilation failed for package 'MCMCpack' * removing '/apps/sparcv9/R-2.12.0/lib/R/library/MCMCpack' root@dqssun4 local# which cc /opt/solstudio12.2/bin/cc root@dqssun4 local# which R /apps/sparcv9/R-2.12.0/bin/R The configure script for the successful R installation is the following, CC=cc -xc99 -m64 -xarch=sparcvis2 CPPFLAGS=-I/opt/csw/include CFLAGS=-xcode=abs64 -xlibmieee -xtarget=ultra3 -xarch=sparcvis2 F77=f95 CXX=CC -m64 -library=stlport4 FC=$F77 FFLAGS=-m64 -xarch=sparcvis2 FCFLAGS=$FFLAGS LDFLAGS=-L/opt/csw/lib/sparcv9 -L/opt/solstudio12.2/prod/lib/v9 export CC CPPFLAGS CFLAGS F77 FFLAGS CXX CXXFLAGS FC FCFLAGS LDFLAGS ./configure --prefix=/apps/sparcv9/R-2.12.0 --with-tcl-config=/opt/csw/lib/tclCo nfig.shhttp://nfig.sh --with-tk-config=/opt/csw/lib/tkConfig.sh --disable-nls Jun Zhang [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error in generating sweave-tex - pdf file
The sub-package texinfo-tex is freely available on the internet. Install it,
and /usr/bin/texi2dvi should be one of its components. You may need admin
privilege to do that.
Jun
-Original Message-
From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On
Behalf Of carol white
Sent: Thursday, December 23, 2010 12:02 PM
To: Kasper Daniel Hansen
Cc: r-devel@r-project.org
Subject: Re: [Rd] Error in generating sweave-tex - pdf file
Thanks for all replies.
I found Sweave.sty in the system files of my local machine. It was sitting in
/usr/share/R/texmf/. The content is the same as the file sent previously. So
the
file has always been in the system but R has been unable to find it.
I put the sty file in the home directory, in the folder where the Rnw file is,
used \usepackage{/usr/share/R/texmf/Sweave.sty},
set SWEAVE_STYLEPATH_DEFAUL = TRUE,
still with R CMD check, texi2dvi can't be found.
Recall that before I started to create the package vignette, I could generated
the pdf file of the tex file by invoking texi2dvi in an R session after loading
library(tools).
Best,
Carol
- Original Message
From: Kasper Daniel Hansen kasperdanielhan...@gmail.com
To: carol white wht_...@yahoo.com
Cc: Duncan Murdoch murdoch.dun...@gmail.com; r-devel@r-project.org
Sent: Thu, December 23, 2010 5:13:58 PM
Subject: Re: [Rd] Error in generating sweave-tex - pdf file
Hi Carol
As you now know, this is because per default R/Sweave puts the line
\usepackage{Sweave}
in the generated tex file. This means the tex file is portable, but
it also implies that Sweave.sty needs to be installed in your tex
installation. Or you can put the Sweave.sty in the directory of the
Rnw file since tex usually is set up to search the same directory.
An alternative is to get R to generate a line like
\usepackage{FULL_PATH_TO_SWEAVE.STY}
in the tex document. This implies that the tex file can only be
tex'ed on a setup where the Sweave.sty is at the same place - hence it
kind of break portability. Now portability of the tex file does not
matter to many users - most of us think of the tex file as an
intermediate file and only care about the Rnw file and the final PDF.
You get this behaviour by setting the environment variable
SWEAVE_STYLEPATH_DEFAULT
to
TRUE
An easy way to do this is to include the following line in your .Rprofile
Sys.setenv(SWEAVE_STYLEPATH_DEFAULT = TRUE)
This trick also fixes running Sweave on a system where you do not have
admin rights.
Kasper
On Thu, Dec 23, 2010 at 5:14 AM, carol white wht_...@yahoo.com wrote:
Another question that I have is the following:
If I want to create the package vignette on a server for which I don't have
admin rights to install Sweave.sty, where is the best place to save this file
if
I want to run from anywhere in my home directoy or do I have to put this file
in
a directory where I should always run from there?
I also attach Sweave.sty to check if it the right file.
- Original Message
From: Duncan Murdoch murdoch.dun...@gmail.com
To: carol white wht_...@yahoo.com
Cc: r-devel@r-project.org
Sent: Thu, December 23, 2010 2:01:26 PM
Subject: Re: [Rd] Error in generating sweave-tex - pdf file
On 23/12/2010 7:46 AM, carol white wrote:
R installation and admin manual doesn't tell where to save Sweave.sty.
You shouldn't need to move it.
I use R 2.10.0, fedora 10 and, tex Version 3.141592-1.40.3 (Web2C 7.5.6)
That R is pretty old. I wouldn't be surprised if the current release
handled things better. But the thing that appears to be missing on your
system is texinfo, and that's not part of R.
Duncan Murdoch
Cheers,
- Original Message
From: Duncan Murdochmurdoch.dun...@gmail.com
To: carol whitewht_...@yahoo.com
Cc: r-devel@r-project.org
Sent: Thu, December 23, 2010 1:21:14 PM
Subject: Re: [Rd] Error in generating sweave-tex - pdf file
On 23/12/2010 5:26 AM, carol white wrote:
When I copied Sweave.sty in the directory where I ran R, I didn't have any
error. But this is not the good solution as R can be run in any folder.
I copied Sweave.sty in /usr/share/texmf/. I put my Rnw file in inst/doc
folder
in my R package to create the vignette. I ran R CMD check and it doesn find
texi2dvi.
texi2dvi is both a function name in R (in the tools package) and a GNU
utility that comes with texinfo and some TeX distributions, but
apparently not with yours. See the R Installation and Administration
manual for suggestions on where to get it. If that doesn't help, you
might get help on this list by stating the versions of everything you're
using: R, your OS, and TeX.
Duncan Murdoch
- Original Message
From: Duncan Murdochmurdoch.dun...@gmail.com
To: carol whitewht_...@yahoo.com
Cc: r-devel@r-project.org
Sent: Wed, December 22, 2010 10:33:01 PM
Subject: Re: [Rd] Error in generating sweave-tex - pdf file
On 22/12/2010 1:30 PM, carol white wrote:
Should the
Re: [Rd] Error in generating sweave-tex - pdf file
Define the envvar LC_ALL with value C will reduce the texi2dvi error.
Sweave.sty need to be at the right location depend on the kind of tex
installation.
Jun
- Original Message -
From: carol white [mailto:wht_...@yahoo.com]
Sent: Wednesday, December 22, 2010 12:30 PM
To: Duncan Murdoch murdoch.dun...@gmail.com
Cc: r-devel@r-project.org r-devel@r-project.org
Subject: Re: [Rd] Error in generating sweave-tex - pdf file
Should the Sweave package be in /usr/share/texmf/tex/latex/? How about
Sweave.sty?
Thanks
- Original Message
From: Duncan Murdoch murdoch.dun...@gmail.com
To: carol white wht_...@yahoo.com
Cc: r-devel@r-project.org
Sent: Wed, December 22, 2010 6:42:07 PM
Subject: Re: [Rd] Error in generating sweave-tex - pdf file
On 22/12/2010 12:27 PM, carol white wrote:
Hi,
I created a Sweave file (see below). when I want to convert tex
file generated from it into pdf, I get error message as follows:
texi2dvi(test.tex, pdf=TRUE)
Error in texi2dvi(test.tex, pdf = TRUE) :
Running 'texi2dvi' on 'test.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.8 \begin
{Schunk}
The Schunk, Sinput, and Soutput environments are defined in Sweave package.
Something went wrong and latex didn't find them, either because it didn't find
Sweave.sty, or because it did, but that file has been messed up.
?
! Interruption.
! Interruption.
to be read again
{
l.8 \begin{
Schunk}
! Undefined control sequence.
l.9 \begin
{Sinput}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
test.Rnw
\usepackage{Sweave}
\ documentclass [ a4paper ]{ article }
\ title { Sweave Example 1}
\ begin { document }
\ maketitle
Are there really spaces between the backslashes and the macros? I think that
doesn't work. You should also have the \usepackage{Sweave} line after the
opening \documentclass line.
Duncan Murdoch
In this example we embed parts of the examples from the
help page into a \ LaTeX {} document :
a=
y=2
y = y +1
@
which shows that the location parameter of the Ozone
distribution varies significantly from month to month . Finally we
include a boxplot of the data :
\end{ document }
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Re: [Rd] Problem installing RCurl
Thank you both for your reply. After reading your responses, I removed the existing CSWcurl, and compiled curl-7.21.2 from source using solstudio (the same compiler I got R-2.12.0 in place) to /opt/csw. Tried to install RCurl, I got the same error, the only difference is the include file's line number, /opt/csw/include/curl/curlrules.h, line 143: zero or negative subscript The line 143 is the third line of the following, the variable must have been defined outside the file. typedef char __curl_rule_01__ [CurlchkszEQ(long, CURL_SIZEOF_LONG)]; I don't know what value the compiler expect, but can I define it here if I know? As to the bit, this machine's got 64G memory, I simply has no choice but to compile 64-bit R. Jun -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Prof Brian Ripley Sent: Saturday, December 04, 2010 1:03 AM To: Duncan Temple Lang Cc: r-devel@r-project.org Subject: Re: [Rd] Problem installing RCurl On Fri, 3 Dec 2010, Duncan Temple Lang wrote: Hi Jun On 12/3/10 2:15 PM, Zhang,Jun wrote: I have 64-bit R 2 12 0 installed on Solaris 10 of Sun Sparc. When I tried to install RCurl, it failed with the following lines, ... Version has CURLOPT_SSL_SESSIONID_CACHE libcurl version: libcurl 7.19.6 configure: creating ./config.status config.status: creating src/Makevars ** libs cc -xc99 -m64 -xarch=sparcvis2 -I/apps/sparcv9/R-2.12.0/lib/R/include -I/opt/csw/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 .(omitted here is very long, all upper case) -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/opt/csw/include-KPIC -xcode=abs64 -xlibmieee -xtarget=ultra3 -xarch=sparcvis2 -c base64.c -o base64.o /opt/csw/include/curl/curlrules.h, line 144: zero or negative subscript This error indicates that the compiler (cc with flags -xc99 -m64, etc.) sees the size of the 'long' data type in C is different from what was seen when libcurl was configured, built and installed. So basically the compiler and/or the compiler flags were different. How was libcurl installed - from source or from a pre-built binary ? What compiler and flags were used? The header is from a prebuilt binary (from OpenCSW). That is built with gcc and not the Sun compiler. And curlbuild.h says /* Allow 32 and 64 bit headers to coexist */ #if defined __amd64 || defined __x86_64 || defined __sparcv9 #include curlbuild-64.h #else #include curlbuild-32.h #endif which AFAIK are gcc and not Sun defines. You could try adding -D__sparcv9 to the CPPFLAGS, or compile RCurl with OpenCSW's gcc build (but 64-bit gcc is another can of worms). I've pointed out to Jun Zhang several times that 64-bit Sparc Solaris is really pushing it, and 32-bit R on Sparc Solaris has been much more successful. Given that x86_64 boxes (Solaris or Linux) are so much faster at computation than Sparc ones, I don't see the point of building 64-bit Sparc Solaris R -- if 32-bit R is not enough you need a faster machine. D. base64.c, line 25: warning: assignment type mismatch: pointer to const char = pointer to unsigned char base64.c, line 39: warning: argument #1 is incompatible with prototype: prototype: pointer to const char : /apps/sparcv9/R-2.12.0/lib/R/include/Rinternals.h, line 1042 argument : pointer to unsigned char base64.c, line 60: warning: assignment type mismatch: pointer to const char = pointer to unsigned char cc: acomp failed for base64.c make: *** [base64.o] Error 2 ERROR: compilation failed for package 'RCurl' * removing '/apps/sparcv9/R-2.12.0/lib/R/library/RCurl' The downloaded packages are in '/tmp/Rtmpo67mNX/downloaded_packages' Updating HTML index of packages in '.Library' Warning message: In install.packages(RCurl) : installation of package 'RCurl' had non-zero exit status What is the problem? Jun [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Problem installing RCurl
I tried to give CPPFLAGS the value -D__sparcv9, the compiler complaint about cross compiling. And then I tried CPPFLAGS=-D__sparcv9 -U__sparcv8, export it, installation of curl-7.21.2 is fine, but give me just the 32-bit result. Any hint will be appreciated to buil the 64-bit curl (only then I have hope to install RCurl). Jun -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Zhang,Jun Sent: Monday, December 06, 2010 1:27 PM To: 'Prof Brian Ripley'; 'Duncan Temple Lang' Cc: 'r-devel@r-project.org' Subject: Re: [Rd] Problem installing RCurl Thank you both for your reply. After reading your responses, I removed the existing CSWcurl, and compiled curl-7.21.2 from source using solstudio (the same compiler I got R-2.12.0 in place) to /opt/csw. Tried to install RCurl, I got the same error, the only difference is the include file's line number, /opt/csw/include/curl/curlrules.h, line 143: zero or negative subscript The line 143 is the third line of the following, the variable must have been defined outside the file. typedef char __curl_rule_01__ [CurlchkszEQ(long, CURL_SIZEOF_LONG)]; I don't know what value the compiler expect, but can I define it here if I know? As to the bit, this machine's got 64G memory, I simply has no choice but to compile 64-bit R. Jun -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Prof Brian Ripley Sent: Saturday, December 04, 2010 1:03 AM To: Duncan Temple Lang Cc: r-devel@r-project.org Subject: Re: [Rd] Problem installing RCurl On Fri, 3 Dec 2010, Duncan Temple Lang wrote: Hi Jun On 12/3/10 2:15 PM, Zhang,Jun wrote: I have 64-bit R 2 12 0 installed on Solaris 10 of Sun Sparc. When I tried to install RCurl, it failed with the following lines, ... Version has CURLOPT_SSL_SESSIONID_CACHE libcurl version: libcurl 7.19.6 configure: creating ./config.status config.status: creating src/Makevars ** libs cc -xc99 -m64 -xarch=sparcvis2 -I/apps/sparcv9/R-2.12.0/lib/R/include -I/opt/csw/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 .(omitted here is very long, all upper case) -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/opt/csw/include-KPIC -xcode=abs64 -xlibmieee -xtarget=ultra3 -xarch=sparcvis2 -c base64.c -o base64.o /opt/csw/include/curl/curlrules.h, line 144: zero or negative subscript This error indicates that the compiler (cc with flags -xc99 -m64, etc.) sees the size of the 'long' data type in C is different from what was seen when libcurl was configured, built and installed. So basically the compiler and/or the compiler flags were different. How was libcurl installed - from source or from a pre-built binary ? What compiler and flags were used? The header is from a prebuilt binary (from OpenCSW). That is built with gcc and not the Sun compiler. And curlbuild.h says /* Allow 32 and 64 bit headers to coexist */ #if defined __amd64 || defined __x86_64 || defined __sparcv9 #include curlbuild-64.h #else #include curlbuild-32.h #endif which AFAIK are gcc and not Sun defines. You could try adding -D__sparcv9 to the CPPFLAGS, or compile RCurl with OpenCSW's gcc build (but 64-bit gcc is another can of worms). I've pointed out to Jun Zhang several times that 64-bit Sparc Solaris is really pushing it, and 32-bit R on Sparc Solaris has been much more successful. Given that x86_64 boxes (Solaris or Linux) are so much faster at computation than Sparc ones, I don't see the point of building 64-bit Sparc Solaris R -- if 32-bit R is not enough you need a faster machine. D. base64.c, line 25: warning: assignment type mismatch: pointer to const char = pointer to unsigned char base64.c, line 39: warning: argument #1 is incompatible with prototype: prototype: pointer to const char : /apps/sparcv9/R-2.12.0/lib/R/include/Rinternals.h, line 1042 argument : pointer to unsigned char base64.c, line 60: warning: assignment type mismatch: pointer to const char = pointer to unsigned char cc: acomp failed for base64.c make: *** [base64.o] Error 2 ERROR: compilation failed for package 'RCurl' * removing '/apps/sparcv9/R-2.12.0/lib/R/library/RCurl' The downloaded packages are in '/tmp/Rtmpo67mNX/downloaded_packages' Updating HTML index of packages in '.Library' Warning message: In install.packages(RCurl) : installation of package 'RCurl' had non-zero exit status What is the problem? Jun [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics
[Rd] Problem installing RCurl
I have 64-bit R 2 12 0 installed on Solaris 10 of Sun Sparc. When I tried to install RCurl, it failed with the following lines, ... Version has CURLOPT_SSL_SESSIONID_CACHE libcurl version: libcurl 7.19.6 configure: creating ./config.status config.status: creating src/Makevars ** libs cc -xc99 -m64 -xarch=sparcvis2 -I/apps/sparcv9/R-2.12.0/lib/R/include -I/opt/csw/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 .(omitted here is very long, all upper case) -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/opt/csw/include-KPIC -xcode=abs64 -xlibmieee -xtarget=ultra3 -xarch=sparcvis2 -c base64.c -o base64.o /opt/csw/include/curl/curlrules.h, line 144: zero or negative subscript base64.c, line 25: warning: assignment type mismatch: pointer to const char = pointer to unsigned char base64.c, line 39: warning: argument #1 is incompatible with prototype: prototype: pointer to const char : /apps/sparcv9/R-2.12.0/lib/R/include/Rinternals.h, line 1042 argument : pointer to unsigned char base64.c, line 60: warning: assignment type mismatch: pointer to const char = pointer to unsigned char cc: acomp failed for base64.c make: *** [base64.o] Error 2 ERROR: compilation failed for package 'RCurl' * removing '/apps/sparcv9/R-2.12.0/lib/R/library/RCurl' The downloaded packages are in '/tmp/Rtmpo67mNX/downloaded_packages' Updating HTML index of packages in '.Library' Warning message: In install.packages(RCurl) : installation of package 'RCurl' had non-zero exit status What is the problem? Jun [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Install package 'Matrix' problem
Prof. Ripley, I've just done the installation of the R package 'Matrix' to my 64-bit R 2.12.0, and it is loaded fine. Seems adding -m64 to the CXX line solved the problem. I had, CC=cc -xc99 -m64 -xarch=sparcvis2 CXX=CC -library=stlport4 And now I have (the working version), CC=cc -xc99 -m64 -xarch=sparcvis2 CXX=CC -m64 -library=stlport4 Thank you! Jun Zhang System Analyst III Division of Quantitative Science FCT4.6109 713-792-2606 -Original Message- From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk] Sent: Thursday, December 02, 2010 12:30 AM To: Zhang,Jun Cc: 'r-devel@r-project.org' Subject: Re: [Rd] Install package 'Matrix' problem We need more information, at the minimum the line which compiled CHMfactor.o. Can you make the install log (you may need to run this again) and your etc/Makeconf available on-line? At first sight your C++ compiler is missing -m64: the R-admin manual says 'For a 64-bit target add -m64 to the compiler macros and use something like LDFLAGS=-L/opt/csw/lib/sparcv9 or LDFLAGS=-L/usr/local/lib/amd64 as appropriate.' I see I used CC=cc -xc99 -m64 CFLAGS=-O -xlibmieee F77=f95 -m64 FFLAGS=-O4 CXX=CC -m64 -library=stlport4 CXXFLAGS=-O FC=$F77 FCFLAGS=$FFLAGS LDFLAGS=-L/usr/local/lib/sparcv9 FCLIBS=-lfai -lfsu -lfai2 in config.site. And BTW, it is always worth checking the manuals of current R-patched: your compiler postdates the pre-release period for R 2.12.0. On Wed, 1 Dec 2010, Zhang,Jun wrote: 64-bit R-2.12.0 was installed on Sun SPARC Solaris 10. Compiler used is solstudio12.2. Attached is the configure script. I then tried to install a recommended package called Matrix. The compilation failed with the following messages, ... CC -library=stlport4 -G -L/opt/csw/lib/sparcv9 -L/opt/solstudio12.2/prod/lib/v9 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a -L/apps/sparcv9/R-2.12.0/lib/R/lib -lRlapack -L/apps/sparcv9/R-2.12.0/lib/R/lib -lRblas -lifai -lsunimath -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai -lfminvai -lfmaxvai -lfui -lfsu -lsunmath -lmtsk -lm ld: fatal: file CHMfactor.o: wrong ELF class: ELFCLASS64 ld: fatal: File processing errors. No output written to Matrix.so make: *** [Matrix.so] Error 2 ERROR: compilation failed for package 'Matrix' * removing '/apps/sparcv9/R-2.12.0/lib/R/library/Matrix' Some article suggests theorectically that ld or compiler driver You need to give references for what you are quoting here (there is much misinformation on the Internet). I suspect it is simply that you didn't specify the C++ compiler correctly. first sees a component .o file which is 32-bit (don't know which one here), and decides that other components should be 32-bit, too, hence the error message, since CHMfactor.o must be a 64-bit object. I just don't know what is the practical way to avoid this situation. I guess I'm posting in the right list, can somebody help? Maybe, but really your local IT support is there to help your use of your OS: this is a Solaris issue, not an R one. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] FW: [R] R-2.12.0 problem on Solaris 10
I used solstutio12.2 to compile a 32-bit R-2.12.0 CC=cc -xc99 CPPFLAGS=-I/opt/csw/include CFLAGS=-O -xlibmieee F77=f95 FFLAGS=-O4 CXX=CC -library=stlport4 CXXFLAGS=-O FC=f95 FCFLAGS=$FFLAGS LDFLAGS=-L/opt/csw/lib export CC CPPFLAGS CFLAGS F77 FFLAGS CXX CXXFLAGS FC FCFLAGS LDFLAGS ./configure --prefix=/apps/R-2.12.0 --with-tcl-config=/opt/csw/lib/tclConfig.sh --with-tk-config=/opt/csw/lib/tkConfig.sh --disable-nls --with-recommended-packages=no Make Make install R Platform: sparc-sun-solaris2.10 (32-bit) install.packages(Matrix) Loading required package: Matrix *** caught segfault *** address 300, cause 'memory not mapped' Segmentation Fault - core dumped The downloaded packages are in '/tmp/Rtmp10h8f8/downloaded_packages' Updating HTML index of packages in '.Library' Warning message: In install.packages(Matrix) : installation of package 'Matrix' had non-zero exit status I then removed all the optimization options and compiled again, got same results. The require(Matrix) will cause 'memory not mapped' error each time with a different address. Please help. Jun __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
