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How to create vignette.pdf for R-2.13.0?

19 messages · Orin Richards, Kasper Daniel Hansen, Uwe Ligges +2 more

Original
cstrato
# 
Dear all,

While R CMD check and R CMD INSTALL have always created the vignettes on 
R-2.12.1 or any earlier versions of R, I am no longer able to build the 
vignettes on R-2.13.0.

Instead R CMD check gives me the following output:

* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
    APTvsXPS.Rnw
    xps.Rnw
    xpsClasses.Rnw
    xpsPreprocess.Rnw

* checking running R code from vignettes ... OK
* checking re-building of vignettes ... OK
* checking PDF version of manual ... OK


Does someone know what the reason might be?

(R64 CMD check --help says that be default rebuild-vignettes is turned on.)

Interestingly, R CMD check still creates the file "xps-manual.pdf".

Here is my sessionInfo:

 > sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] xps_1.13.1

loaded via a namespace (and not attached):
[1] Biobase_2.12.1        Biostrings_2.20.0     IRanges_1.10.0
[4] affy_1.30.0           affyPLM_1.28.5        affyio_1.20.0
[7] preprocessCore_1.14.0

Thank you in advance.
Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._
Orin Richards
# 
Hello All,
I heard of the First() function in R. but am not sure entirely how it is used. 
 I would like to load an R package at startup, instead of having to manually 
load each time I run R. How is the first() function used to achieve this .

Specifically I would like to tell R at startup to look in a specific folder for 
the package and load it.

Is there a way to do this, and is there any code sample code avail for this.


Thanks for your help.

Orin
Uwe Ligges
#
On 23.04.2011 21:50, cstrato wrote:
No, it does for me for other packages.
Perhaps an error when processing the vignettes? Have you tried to build 
them manually?
That is the collection of help pages, unrelated to the vignette.


Uwe Ligges
Uwe Ligges
# 
See ?Startup

Uwe Ligges
On 24.04.2011 16:08, Orin Richards wrote:
Kasper Daniel Hansen
#
On Sun, Apr 24, 2011 at 10:08 AM, Orin Richards <oowar at yahoo.com> wrote:
Orin

Is this for a package (in which case you solve it by using Depends) or
is it in general for your usage?  If the later, you can put code into
~/.Rprofile which is essentially an R script that gets run every time
you start R.  The code in the file would be something like
  library(PKGNAME, lib.loc = "DIR")

Kasper
cstrato
# 
Dear Uwe,

Thank you for your reply.

ad 2, Yes, i know that "xps-manual.pdf" is the collection of help pages, 
I have mentioned it only to show that creating pdf-files does work for 
R-2.13.0.

ad 1, Could it be that this is a Mac-specific problem since I see it on 
both my old MacBook Pro and my new Mac Mini.

Using R CMD check with R-2.12.2 I get:

$ R64 CMD check xps_1.13.1.tar.gz
* using log directory '/Volumes/CoreData/CRAN/xps.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-apple-darwin9.8.0 (64-bit)
* using session charset: ASCII
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '1.13.1'
...
...
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF:

/Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/APTvsXPS.Rnw
/Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xps.Rnw
/Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xpsClasses.Rnw
/Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xpsPreprocess.Rnw
* checking PDF version of manual ... OK


Using "RSwitch.app" I switch to R-2.13.0, but now I get:

$ R64 CMD check xps_1.13.1.tar.gz
* using log directory '/Volumes/CoreData/CRAN/xps.Rcheck'
* using R version 2.13.0 (2011-04-13)
* using platform: x86_64-apple-darwin9.8.0 (64-bit)
* using session charset: ASCII
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '1.13.1'
...
...
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
    APTvsXPS.Rnw
    xps.Rnw
    xpsClasses.Rnw
    xpsPreprocess.Rnw

* checking running R code from vignettes ... OK
* checking re-building of vignettes ... OK
* checking PDF version of manual ... OK


I must admit that I have never built the vignettes manually, and I 
cannot find a hint how I can do it from the command line. Is this possible?

However, building the vignettes within R-2.13.0 I get:
 > library(tools)
 > buildVignettes("xps", dir="/Volumes/CoreData/CRAN/xps", quiet=F)

Overfull \vbox (21.68121pt too high) has occurred while \output is 
Writing to file xps.tex
Processing code chunks with options ...
  1 : term verbatim
  2 : echo term hide
  3 : echo term verbatim
  4 : echo term verbatim
  5 : echo term verbatim
SysError in <TFile::TFile>: file 
/tmpdt_DataTest3_cel.root/tmpdt_DataTest3_cel_20110424_201301.root can 
not be opened (No such file or directory)
Error: Could not create file </tmpdt_DataTest3_cel.root>


Here are the two important chunks 4 and 5, which work fine with R-2.12.2 
and earlier versions:

###################################################
### chunk number 4:
###################################################
#line 132 "xps.Rnw"
scheme.test3 <- root.scheme(file.path(.path.package("xps"), "schemes", 
"SchemeTest3.root"))


###################################################
### chunk number 5:
###################################################
#line 137 "xps.Rnw"
celfiles <- c("TestA1.CEL","TestA2.CEL")
data.test3 <- import.data(scheme.test3, "tmpdt_DataTest3", 
celdir=celdir, celfiles=celfiles, verbose=FALSE)


However, in R-2.13.0 chunk 5 crashes!!!
It works only when replacing chunk 5 with:

###################################################
### chunk number 5:
###################################################
#line 137 "xps.Rnw"
celfiles <- c("TestA1.CEL","TestA2.CEL")
scheme.test3 <- root.scheme(file.path(.path.package("xps"), "schemes", 
"SchemeTest3.root"))
data.test3 <- import.data(scheme.test3, "tmpdt_DataTest3", 
celdir=celdir, celfiles=celfiles, verbose=FALSE)


As you see R-2.13.0 does no longer remember the result of chunk 4, i.e. 
"scheme.test3". Now I have to include the line defining "scheme.test3" 
also in chunk 5.

Do you have any idea for this behavior?


An example, which does work in R-2.13.0 are the following two chunks:

#################################################
### chunk number 20:
###################################################
#line 300 "xps.Rnw"
library(xps)
scheme.test3 <- root.scheme(file.path(.path.package("xps"), "schemes", 
"SchemeTest3.root"))
data.test3 <- root.data(scheme.test3, 
file.path(.path.package("xps"),"rootdata", "DataTest3_cel.root"))


###################################################
### chunk number 21:
###################################################
#line 318 "xps.Rnw"
data.rma <- rma(data.test3, "tmpdt_Test3RMA", verbose=FALSE)


In summary it is not quite clear to me what has changed in R-2.13.0 so 
that chunk 5 no longer works.

BTW, the error:
SysError in <TFile::TFile>: file 
/tmpdt_DataTest3_cel.root/tmpdt_DataTest3_cel_20110424_201301.root can 
not be opened
is not clear to me since "/tmpdt_DataTest3_cel.root/" is definitively 
NOT a directory.

Do you have any ideas?

Please note that the vignette "xps.Rnw" did work for the last two years 
w/o problem. Furthermore, the Bioconductor servers are able to build the 
vignette, see:
http://www.bioconductor.org/packages/release/bioc/html/xps.html

Best regards
Christian
On 4/24/11 4:12 PM, Uwe Ligges wrote:
Uwe Ligges
#
On 24.04.2011 20:59, cstrato wrote:
Have you tried on any other OS? I did not since installing root is a bit 
too much effort.
I thought we are talking about R-2.13.0?

Where is the R CMD build output (since R CMD build is supposed to 
prepare the vignette).
How objects generated in one chunk can be reused later on is explained 
in the Sweave manual.
Time to debug what root.scheme is doing with the supplied path.
See 
http://bioconductor.org/checkResults/2.8/bioc-20110225/xps/liverpool-checksrc.html 
and find that their Mac Servers are also fine with it. So maybe it is 
your setup that is corrupted?

Best wishes,
Uwe
cstrato
# 
Dear Uwe,
On 4/24/11 10:37 PM, Uwe Ligges wrote:
No, until now I did not try another OS, but I will, since xps has to 
work on all three OSes.
I showed you the output of R-2.12.2 first and then the output of 
R-2.13.0, so that you can see that on the same machine with the same 
file it works with one version but not the other.
Is it possible to build the vignettes from the command line?
Sorry, I do not understand what you mean. root.scheme does not change 
the path, otherwise it would not work on all older versions of R.
Maybe, you are right that my setup is corrupted, but on two independent 
machines?

Maybe the download of "R-2.13.0.pkg" is corrupted, but then nothing 
should work, or am I wrong?

How can I check if my setup is corrupted?

Best regards
Christian
Uwe Ligges
#
On 24.04.2011 23:10, cstrato wrote:
But you got a Warning in both cases:
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF: ........
R --help suggests there is
R CMD Sweave .....
Right, but since something changed obviously, and you tell us the path 
is not a path, it might be a function used by root.scheme .... That's 
why I said time to debug the code in your vignette!
By debugging the code in your package's vignette.

Uwe Ligges
cstrato
# 
Dear Uwe,

Your suggestion to look at the Sweave manual helped me to solve the 
problem. It seems that in R-2.13.0 every chunk can use the code from the 
chunk before but not from an earlier chunk.

Concretely, the following does not work since chunk 5 needs the code 
from chunk 3 and 4:

###################################################
### chunk number 3:
###################################################
#line 126 "xps.Rnw"
celdir <- file.path(.path.package("xps"), "raw")

###################################################
### chunk number 4:
###################################################
#line 132 "xps.Rnw"
scheme.test3 <- root.scheme(file.path(.path.package("xps"), "schemes", 
"SchemeTest3.root"))

###################################################
### chunk number 5:
###################################################
#line 137 "xps.Rnw"
celfiles <- c("TestA1.CEL","TestA2.CEL")
data.test3 <- import.data(scheme.test3, "tmpdt_DataTest3", 
celdir=celdir, celfiles=celfiles, verbose=FALSE)


However, when I add "celdir" to chunk 5 then everything works since now 
chunk 5 needs only the code from chunk 4 but not from chunk 3:

###################################################
### chunk number 5:
###################################################
#line 137 "xps.Rnw"
celdir   <- file.path(.path.package("xps"), "raw")
celfiles <- c("TestA1.CEL","TestA2.CEL")
data.test3 <- import.data(scheme.test3, "tmpdt_DataTest3", 
celdir=celdir, celfiles=celfiles, verbose=FALSE)


Now buildVignettes() is able to create the vignettes, however R CMD 
check still does not build the vignettes.


Yes, I get a Warning in both cases:
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF: ........

However, with R-2.12.2 the following lines are added:

/Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/APTvsXPS.Rnw
/Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xps.Rnw
/Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xpsClasses.Rnw
/Volumes/CoreData/CRAN/xps.Rcheck/00_pkg_src/xps/inst/doc/xpsPreprocess.Rnw

and in xps.Rcheck the subdirectory "inst/doc" will be created which 
contains the vignette data such as xps.Rnw, but also xps.tex and xps.pdf.

In contrast, R-2.13.0 does not create the subdirectory "inst/doc" and no 
vignettes are built.

One more issue:
In contrast to my former believe R CMD INSTALL does not build the 
vignettes, neither in R-2.12.2 nor in R-2.13.0. I have to run 
buildVignettes() after installation. Is this the usual case?

Best regards
Christian
On 4/25/11 4:00 PM, Uwe Ligges wrote:
Duncan Murdoch
#
cstrato wrote:
I'm either misreading what you wrote, or it's wrong.  If I have this in 
a Sweave file:

<<>>=
x <- 1
@

<<>>=
y <- 2
@

<<>>=
print(x)
@

I will see the value of x getting printed, even though it came from two 
chunks earlier.

I think Uwe is right:  there is some bug in the code you're running. 
Sweave isn't the problem.

Duncan Murdoch
cstrato
# 
Dear Duncan,

Thank you for your example, however it is different since it does not 
use x and y. What about print(x+y)?

Sorry, I do not believe that there is a bug in my code, since:
1, it worked in all versions from R starting with R-2.6.0 till R-2.12.2.
2, the identical code works in the examples
3, this code (or a similar code) is the starting code which all users of 
xps have to use, and there was never a problem.

Maybe the reason could be that my code has to import
- the CEL-files from the package dir
- the file SchemeTest3.root from the package dir
??

Best regards
Christian
On 4/25/11 8:00 PM, Duncan Murdoch wrote:
Duncan Murdoch
#
cstrato wrote:
Try it.
This might be a problem in R, or might be a problem in your code.  As 
far as I know, it has only shown up in your code, so I'd guess that's 
where the problem is.  In any case, you're the one in the best position 
to isolate it and debug it.

If it turns out to be a problem in R, put together an example 
illustrating the problem that doesn't involve your code, and I'll take a 
look.

Duncan Murdoch
cstrato
# 
Thank you.

My problem seems to be that at the moment the problem can be seen only 
on my Mac, since e.g. the Bioconductor servers have no problems creating 
the vignettes.

Best regards
Christian
On 4/25/11 8:55 PM, Duncan Murdoch wrote:
Duncan Murdoch
#
On 25/04/2011 3:16 PM, cstrato wrote:
Then you are definitely the one in the best position to diagnose the 
problem.  Use the usual approach:  simplify it by cutting out everything 
that looks unrelated.  Verify that the problem still exists, then cut 
some more.  Eventually you'll have isolated the error to a particular 
small snippet of code, and then you can add print() statements, or use 
trace(), or do whatever is necessary to see what's so special about your 
system.

I suspect it will turn out to be an assumption in the code that is not 
true on your system.

If the assumption is being made by code you wrote, then fix it.  If it's 
being made by R, let us know.

Duncan Murdoch
cstrato
# 
Thank you, I will try. Christian
On 4/25/11 9:31 PM, Duncan Murdoch wrote:
1 day later
cstrato
# 
Dear Duncan, dear Uwe,

Just now I have re-run everything, and today xps.Rnw can be converted to 
a vignette w/o any problems using:
a, buildVignettes("xps", dir="/Volumes/CoreData/CRAN/xps", quiet=F)
b, R CMD Sweave xps.Rnw

In both cases the vignette xps.pdf is created (maybe my Mac did not like 
to work during eastern holidays).

However, one issue remains:
"R64 CMD check xps_1.13.1.tar.gz" no longer creates any pdf files for 
the vignettes.

Best regards
Christian
On 4/25/11 9:31 PM, Duncan Murdoch wrote:
Uwe Ligges
#
On 26.04.2011 21:58, cstrato wrote:
Dioes it give an error or warning? It should check the code. R CMD build 
creates the pdf files.

Uwe Ligges
cstrato
# 
Dear Uwe,

As I have already mentioned R CMD check gives the following output:

* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
    APTvsXPS.Rnw
    xps.Rnw
    xpsClasses.Rnw
    xpsPreprocess.Rnw

* checking running R code from vignettes ... OK
* checking re-building of vignettes ... OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
   '/Volumes/CoreData/CRAN/xps.Rcheck/00check.log'
for details


Although the output says "checking PDF version of manual ... OK" I 
cannot find any result in "xps.Rcheck".


When I run "R64 CMD build xps" I get:

* checking for file 'xps/DESCRIPTION' ... OK
* preparing 'xps':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'xps_1.13.1.tar.gz'

However, the resulting file "xps_1.13.1.tgz" does also not contain any 
vignettes.

Best regards
Christian
On 4/27/11 10:16 AM, Uwe Ligges wrote: