Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
Oops, sorry for the noise but after looking at today's BioC build/check results, I realize the problem is still here. At least for some of the 8 packages that had an 'R CMD build' timeout because of the Sweave.sty file not being found. I just happened to run 'R CMD build' by hands yesterday on a package for which the problem is gone so I went ahead and started to sing victory... not so fast! I'm gonna post with a new subject and give more details. H. On 09/14/2010 11:48 AM, Duncan Murdoch wrote: On 14/09/2010 2:46 PM, Hervé Pagès wrote: Duncan, On 09/13/2010 11:47 AM, Duncan Murdoch wrote: On 13/09/2010 2:38 PM, Hervé Pagès wrote: [...] Thanks for suggesting workarounds but don't you think there is a real problem? As I said, we don't use TEXINPUTS on Windows, we use the command line version. I didn't write the code, so I don't know why there's the difference, but I assume there's a reason for it, and presumably the reason is that relying on TEXINPUTS doesn't work. This is fixed in current R-devel. That explains my confusion. Duncan Murdoch -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
Duncan, On 09/13/2010 11:47 AM, Duncan Murdoch wrote: On 13/09/2010 2:38 PM, Hervé Pagès wrote: [...] Thanks for suggesting workarounds but don't you think there is a real problem? As I said, we don't use TEXINPUTS on Windows, we use the command line version. I didn't write the code, so I don't know why there's the difference, but I assume there's a reason for it, and presumably the reason is that relying on TEXINPUTS doesn't work. This is fixed in current R-devel. Cheers, H. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
On 14/09/2010 2:46 PM, Hervé Pagès wrote: Duncan, On 09/13/2010 11:47 AM, Duncan Murdoch wrote: On 13/09/2010 2:38 PM, Hervé Pagès wrote: [...] Thanks for suggesting workarounds but don't you think there is a real problem? As I said, we don't use TEXINPUTS on Windows, we use the command line version. I didn't write the code, so I don't know why there's the difference, but I assume there's a reason for it, and presumably the reason is that relying on TEXINPUTS doesn't work. This is fixed in current R-devel. That explains my confusion. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
Hervé Pagès wrote:
Hi Duncan,
On 09/12/2010 05:07 AM, Duncan Murdoch wrote:
On 12/09/2010 12:49 AM, Hervé Pagès wrote:
Hi Duncan,
On 09/11/2010 03:56 AM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignett
creation for packages that have a Makefile in pkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
This sounds like a problem that only the package maintainer could
address. Presumably it will be temporary: once they adjust to the new
organization of the share/texmf directory, things will be fine again.
The reorg is described in this NEWS item:
* Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
Before this reorg, the package maintainer didn't have to care about
where to find things in R_HOME/share/texmf. 'R CMD build' would just
find them by setting the TEXINPUTS envir variable appropriately (and
then commands in the inst/doc/Makefile file would find them too).
This reorg was checked in svn as rev 52256. I see the following
adjustments to TEXINPUTS:
** On Unix (src/scripts/Rcmd.in file):
-## Append 'share/texmf' to TeX's input search path.
-if test -z $TEXINPUTS}; then
- TEXINPUTS=.:${R_SHARE_DIR}/texmf:
+## Append 'share/texmf/...' to TeX's input search path.
+if test -z ${TEXINPUTS}; then
+ TEXINPUTS=.:${R_SHARE_DIR}/texmf/tex/latex:
else
- TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf:
+ TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf/tex/latex:
fi
export TEXINPUTS
** On Windows (src/gnuwin32/fixed/etc/Rcmd_environ file):
-TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf;
+TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf/tex/latex;
The path seems to have been adjusted correctly. So my question is:
why isn't this working on Windows for packages that use a Makefile?
I don't know. My first assumption would that something in the Makefile
is wrong, but since you don't give any examples, I can't check.
There are 8 Bioconductor packages failing to build on Windows
because of this problem. They have a Makefile in inst/doc/ that
calls 'pdflatex' or 'texi2dvi --pdf' on some_vignette to convert
some_vignette.tex into some_vignette.pdf. They don't
have Sweave.sty in inst/doc/ (other packages use the same kind of
Makefile and are building ok because they have a copy of Sweave.sty
in inst/doc/).
For example, here is the content of adSplit/inst/doc/Makefile:
all:pdf clean
pdf:tr_2005_02.tex
epstopdf splitSet.eps
pdflatex tr_2005_02
pdflatex tr_2005_02
pdflatex tr_2005_02
clean:
rm -f *.aux *.eps *.log *.out *.tex *.toc
rm -f Rplots.ps splitSet.pdf tr_2005_02-*
The 7 other packages use similar Makefile. As I said before, they
all used to build ok before the R_HOME/share/texmf reorg. They still
build ok on non-Windows machines. Thanks!
H.
On Windows using MikTeX, we put a -I option on the command line to point
to the input directory. If you don't want to do that, you can use R
CMD texify --pdf instead of pdflatex; it will try to determine the
appropriate command line based on the platform.
Duncan Murdoch
__
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Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
On 13/09/2010 2:38 PM, Hervé Pagès wrote:
On 09/13/2010 03:34 AM, Duncan Murdoch wrote:
Hervé Pagès wrote:
Hi Duncan,
On 09/12/2010 05:07 AM, Duncan Murdoch wrote:
On 12/09/2010 12:49 AM, Hervé Pagès wrote:
Hi Duncan,
On 09/11/2010 03:56 AM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD buildpkg' gets stalled during vignett
creation for packages that have a Makefile inpkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
This sounds like a problem that only the package maintainer could
address. Presumably it will be temporary: once they adjust to the new
organization of the share/texmf directory, things will be fine again.
The reorg is described in this NEWS item:
* Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
Before this reorg, the package maintainer didn't have to care about
where to find things in R_HOME/share/texmf. 'R CMD build' would just
find them by setting the TEXINPUTS envir variable appropriately (and
then commands in the inst/doc/Makefile file would find them too).
This reorg was checked in svn as rev 52256. I see the following
adjustments to TEXINPUTS:
** On Unix (src/scripts/Rcmd.in file):
-## Append 'share/texmf' to TeX's input search path.
-if test -z $TEXINPUTS}; then
- TEXINPUTS=.:${R_SHARE_DIR}/texmf:
+## Append 'share/texmf/...' to TeX's input search path.
+if test -z ${TEXINPUTS}; then
+ TEXINPUTS=.:${R_SHARE_DIR}/texmf/tex/latex:
else
- TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf:
+ TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf/tex/latex:
fi
export TEXINPUTS
** On Windows (src/gnuwin32/fixed/etc/Rcmd_environ file):
-TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf;
+TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf/tex/latex;
The path seems to have been adjusted correctly. So my question is:
why isn't this working on Windows for packages that use a Makefile?
I don't know. My first assumption would that something in the Makefile
is wrong, but since you don't give any examples, I can't check.
There are 8 Bioconductor packages failing to build on Windows
because of this problem. They have a Makefile in inst/doc/ that
calls 'pdflatex' or 'texi2dvi --pdf' onsome_vignette to convert
some_vignette.tex intosome_vignette.pdf. They don't
have Sweave.sty in inst/doc/ (other packages use the same kind of
Makefile and are building ok because they have a copy of Sweave.sty
in inst/doc/).
For example, here is the content of adSplit/inst/doc/Makefile:
all: pdf clean
pdf: tr_2005_02.tex
epstopdf splitSet.eps
pdflatex tr_2005_02
pdflatex tr_2005_02
pdflatex tr_2005_02
clean:
rm -f *.aux *.eps *.log *.out *.tex *.toc
rm -f Rplots.ps splitSet.pdf tr_2005_02-*
The 7 other packages use similar Makefile. As I said before, they
all used to build ok before the R_HOME/share/texmf reorg. They still
build ok on non-Windows machines. Thanks!
H.
On Windows using MikTeX, we put a -I option on the command line to point
to the input directory. If you don't want to do that, you can use R CMD
texify --pdf instead of pdflatex; it will try to determine the
appropriate command line based on the platform.
Yes I can use 'R CMD some_command' instead of just 'some_command' in the
Makefile so 'some_command' sees the TEXINPUTS variable and that solves
the problem. But when I call 'R CMD build', shouldn't 'make' and its
child processes ('pdflatex', 'texify', etc...) already see TEXINPUTS?
Why do I need to call the commands in the Makefile thru R CMD again
in order to see TEXINPUTS?
Thanks for suggesting workarounds but don't you think there is a real
problem?
As I said, we don't use TEXINPUTS on Windows, we use the command line
version. I didn't write the code, so I don't know why there's the
difference, but I assume there's a reason for it, and presumably the
reason is that relying on TEXINPUTS doesn't work.
Duncan Murdoch
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
On 09/13/2010 03:34 AM, Duncan Murdoch wrote:
Hervé Pagès wrote:
Hi Duncan,
On 09/12/2010 05:07 AM, Duncan Murdoch wrote:
On 12/09/2010 12:49 AM, Hervé Pagès wrote:
Hi Duncan,
On 09/11/2010 03:56 AM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignett
creation for packages that have a Makefile in pkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
This sounds like a problem that only the package maintainer could
address. Presumably it will be temporary: once they adjust to the new
organization of the share/texmf directory, things will be fine again.
The reorg is described in this NEWS item:
* Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
Before this reorg, the package maintainer didn't have to care about
where to find things in R_HOME/share/texmf. 'R CMD build' would just
find them by setting the TEXINPUTS envir variable appropriately (and
then commands in the inst/doc/Makefile file would find them too).
This reorg was checked in svn as rev 52256. I see the following
adjustments to TEXINPUTS:
** On Unix (src/scripts/Rcmd.in file):
-## Append 'share/texmf' to TeX's input search path.
-if test -z $TEXINPUTS}; then
- TEXINPUTS=.:${R_SHARE_DIR}/texmf:
+## Append 'share/texmf/...' to TeX's input search path.
+if test -z ${TEXINPUTS}; then
+ TEXINPUTS=.:${R_SHARE_DIR}/texmf/tex/latex:
else
- TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf:
+ TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf/tex/latex:
fi
export TEXINPUTS
** On Windows (src/gnuwin32/fixed/etc/Rcmd_environ file):
-TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf;
+TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf/tex/latex;
The path seems to have been adjusted correctly. So my question is:
why isn't this working on Windows for packages that use a Makefile?
I don't know. My first assumption would that something in the Makefile
is wrong, but since you don't give any examples, I can't check.
There are 8 Bioconductor packages failing to build on Windows
because of this problem. They have a Makefile in inst/doc/ that
calls 'pdflatex' or 'texi2dvi --pdf' on some_vignette to convert
some_vignette.tex into some_vignette.pdf. They don't
have Sweave.sty in inst/doc/ (other packages use the same kind of
Makefile and are building ok because they have a copy of Sweave.sty
in inst/doc/).
For example, here is the content of adSplit/inst/doc/Makefile:
all: pdf clean
pdf: tr_2005_02.tex
epstopdf splitSet.eps
pdflatex tr_2005_02
pdflatex tr_2005_02
pdflatex tr_2005_02
clean:
rm -f *.aux *.eps *.log *.out *.tex *.toc
rm -f Rplots.ps splitSet.pdf tr_2005_02-*
The 7 other packages use similar Makefile. As I said before, they
all used to build ok before the R_HOME/share/texmf reorg. They still
build ok on non-Windows machines. Thanks!
H.
On Windows using MikTeX, we put a -I option on the command line to point
to the input directory. If you don't want to do that, you can use R CMD
texify --pdf instead of pdflatex; it will try to determine the
appropriate command line based on the platform.
Yes I can use 'R CMD some_command' instead of just 'some_command' in the
Makefile so 'some_command' sees the TEXINPUTS variable and that solves
the problem. But when I call 'R CMD build', shouldn't 'make' and its
child processes ('pdflatex', 'texify', etc...) already see TEXINPUTS?
Why do I need to call the commands in the Makefile thru R CMD again
in order to see TEXINPUTS?
Thanks for suggesting workarounds but don't you think there is a real
problem?
H.
Duncan Murdoch
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
On 12/09/2010 12:49 AM, Hervé Pagès wrote:
Hi Duncan,
On 09/11/2010 03:56 AM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignett
creation for packages that have a Makefile in pkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
This sounds like a problem that only the package maintainer could
address. Presumably it will be temporary: once they adjust to the new
organization of the share/texmf directory, things will be fine again.
The reorg is described in this NEWS item:
* Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
Before this reorg, the package maintainer didn't have to care about
where to find things in R_HOME/share/texmf. 'R CMD build' would just
find them by setting the TEXINPUTS envir variable appropriately (and
then commands in the inst/doc/Makefile file would find them too).
This reorg was checked in svn as rev 52256. I see the following
adjustments to TEXINPUTS:
** On Unix (src/scripts/Rcmd.in file):
-## Append 'share/texmf' to TeX's input search path.
-if test -z $TEXINPUTS}; then
- TEXINPUTS=.:${R_SHARE_DIR}/texmf:
+## Append 'share/texmf/...' to TeX's input search path.
+if test -z ${TEXINPUTS}; then
+ TEXINPUTS=.:${R_SHARE_DIR}/texmf/tex/latex:
else
- TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf:
+ TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf/tex/latex:
fi
export TEXINPUTS
** On Windows (src/gnuwin32/fixed/etc/Rcmd_environ file):
-TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf;
+TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf/tex/latex;
The path seems to have been adjusted correctly. So my question is:
why isn't this working on Windows for packages that use a Makefile?
I don't know. My first assumption would that something in the Makefile
is wrong, but since you don't give any examples, I can't check.
Duncan Murdoch
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
Hi Duncan
wouldn't it be possible that by default the Sweave.sty in share/texmf is
found by 'R CMD build' for use by package vignettes without manual
intervention?
AfaIcs this is also how it worked in the past.
Best wishes
Wolfgang
On Sep/11/10 12:56 PM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignette
creation for packages that have a Makefile in pkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
This sounds like a problem that only the package maintainer could
address. Presumably it will be temporary: once they adjust to the new
organization of the share/texmf directory, things will be fine again.
The reorg is described in this NEWS item:
* Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
Duncan Murdoch
I noticed that the location of Sweave.sty shipped with
R has changed recently (moved from ${R_HOME}/share/texmf
to ${R_HOME}/share/texmf/tex/latex/). Could that be related
to the problem?
I don't see that problem on platforms other than Windows or
with R 2.12
Thanks,
H.
__
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--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
On 12/09/2010 12:04 PM, Wolfgang Huber wrote:
Hi Duncan
wouldn't it be possible that by default the Sweave.sty in share/texmf is
found by 'R CMD build' for use by package vignettes without manual
intervention?
Yes, it does work that way. What Hervé is talking about are cases where
people use Makefiles to bypass the normal process.
Duncan Murdoch
AfaIcs this is also how it worked in the past.
Best wishes
Wolfgang
On Sep/11/10 12:56 PM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignette
creation for packages that have a Makefile in pkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
This sounds like a problem that only the package maintainer could
address. Presumably it will be temporary: once they adjust to the new
organization of the share/texmf directory, things will be fine again.
The reorg is described in this NEWS item:
* Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
Duncan Murdoch
I noticed that the location of Sweave.sty shipped with
R has changed recently (moved from ${R_HOME}/share/texmf
to ${R_HOME}/share/texmf/tex/latex/). Could that be related
to the problem?
I don't see that problem on platforms other than Windows or
with R 2.12
Thanks,
H.
__
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__
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Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
Hi Duncan,
On 09/12/2010 05:07 AM, Duncan Murdoch wrote:
On 12/09/2010 12:49 AM, Hervé Pagès wrote:
Hi Duncan,
On 09/11/2010 03:56 AM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignett
creation for packages that have a Makefile in pkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
This sounds like a problem that only the package maintainer could
address. Presumably it will be temporary: once they adjust to the new
organization of the share/texmf directory, things will be fine again.
The reorg is described in this NEWS item:
* Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
Before this reorg, the package maintainer didn't have to care about
where to find things in R_HOME/share/texmf. 'R CMD build' would just
find them by setting the TEXINPUTS envir variable appropriately (and
then commands in the inst/doc/Makefile file would find them too).
This reorg was checked in svn as rev 52256. I see the following
adjustments to TEXINPUTS:
** On Unix (src/scripts/Rcmd.in file):
-## Append 'share/texmf' to TeX's input search path.
-if test -z $TEXINPUTS}; then
- TEXINPUTS=.:${R_SHARE_DIR}/texmf:
+## Append 'share/texmf/...' to TeX's input search path.
+if test -z ${TEXINPUTS}; then
+ TEXINPUTS=.:${R_SHARE_DIR}/texmf/tex/latex:
else
- TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf:
+ TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf/tex/latex:
fi
export TEXINPUTS
** On Windows (src/gnuwin32/fixed/etc/Rcmd_environ file):
-TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf;
+TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf/tex/latex;
The path seems to have been adjusted correctly. So my question is:
why isn't this working on Windows for packages that use a Makefile?
I don't know. My first assumption would that something in the Makefile
is wrong, but since you don't give any examples, I can't check.
There are 8 Bioconductor packages failing to build on Windows
because of this problem. They have a Makefile in inst/doc/ that
calls 'pdflatex' or 'texi2dvi --pdf' on some_vignette to convert
some_vignette.tex into some_vignette.pdf. They don't
have Sweave.sty in inst/doc/ (other packages use the same kind of
Makefile and are building ok because they have a copy of Sweave.sty
in inst/doc/).
For example, here is the content of adSplit/inst/doc/Makefile:
all:pdf clean
pdf:tr_2005_02.tex
epstopdf splitSet.eps
pdflatex tr_2005_02
pdflatex tr_2005_02
pdflatex tr_2005_02
clean:
rm -f *.aux *.eps *.log *.out *.tex *.toc
rm -f Rplots.ps splitSet.pdf tr_2005_02-*
The 7 other packages use similar Makefile. As I said before, they
all used to build ok before the R_HOME/share/texmf reorg. They still
build ok on non-Windows machines. Thanks!
H.
Duncan Murdoch
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignette
creation for packages that have a Makefile in pkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
This sounds like a problem that only the package maintainer could
address. Presumably it will be temporary: once they adjust to the new
organization of the share/texmf directory, things will be fine again.
The reorg is described in this NEWS item:
* Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
Duncan Murdoch
I noticed that the location of Sweave.sty shipped with
R has changed recently (moved from ${R_HOME}/share/texmf
to ${R_HOME}/share/texmf/tex/latex/). Could that be related
to the problem?
I don't see that problem on platforms other than Windows or
with R 2.12
Thanks,
H.
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Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used
Hi Duncan,
On 09/11/2010 03:56 AM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignett
creation for packages that have a Makefile in pkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
This sounds like a problem that only the package maintainer could
address. Presumably it will be temporary: once they adjust to the new
organization of the share/texmf directory, things will be fine again.
The reorg is described in this NEWS item:
* Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
Before this reorg, the package maintainer didn't have to care about
where to find things in R_HOME/share/texmf. 'R CMD build' would just
find them by setting the TEXINPUTS envir variable appropriately (and
then commands in the inst/doc/Makefile file would find them too).
This reorg was checked in svn as rev 52256. I see the following
adjustments to TEXINPUTS:
** On Unix (src/scripts/Rcmd.in file):
-## Append 'share/texmf' to TeX's input search path.
-if test -z $TEXINPUTS}; then
- TEXINPUTS=.:${R_SHARE_DIR}/texmf:
+## Append 'share/texmf/...' to TeX's input search path.
+if test -z ${TEXINPUTS}; then
+ TEXINPUTS=.:${R_SHARE_DIR}/texmf/tex/latex:
else
- TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf:
+ TEXINPUTS=.:${TEXINPUTS}:${R_SHARE_DIR}/texmf/tex/latex:
fi
export TEXINPUTS
** On Windows (src/gnuwin32/fixed/etc/Rcmd_environ file):
-TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf;
+TEXINPUTS=.;${TEXINPUTS};${R_SHARE_DIR}/texmf/tex/latex;
The path seems to have been adjusted correctly. So my question is:
why isn't this working on Windows for packages that use a Makefile?
Thanks,
H.
Duncan Murdoch
I noticed that the location of Sweave.sty shipped with
R has changed recently (moved from ${R_HOME}/share/texmf
to ${R_HOME}/share/texmf/tex/latex/). Could that be related
to the problem?
I don't see that problem on platforms other than Windows or
with R 2.12
Thanks,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
__
R-devel@r-project.org mailing list
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[Rd] R CMD build cannot create vignettes on Windows if Makefile is used
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignette
creation for packages that have a Makefile in pkg/inst/doc.
It seems that the problem is that the commands used in the
Makefile for converting .tex to .pdf are not able to locate
the Sweave.sty file anymore (if I drop this file to
pkg/inst/doc, then the problem goes away).
I noticed that the location of Sweave.sty shipped with
R has changed recently (moved from ${R_HOME}/share/texmf
to ${R_HOME}/share/texmf/tex/latex/). Could that be related
to the problem?
I don't see that problem on platforms other than Windows or
with R 2.12
Thanks,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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