Displaying 20 results from an estimated 5000 matches similar to: ""Failed to locate the 'texi2pdf' output file""
2013 Oct 08
1
"Failed to locate the 'texi2pdf' output file"
Just thought I would mention that the issue below (and in https://stat.ethz.ch/pipermail/r-devel/2013-April/066318.html) is still not resolved.
It hasn't been a big problem, but it potentially could be, if a critical package were to have this error on release day, then all its dependencies would fail to build, which would probably require us to postpone our release.
See the complete thread
2013 Mar 13
1
Failed to locate 'weave' output file / vignette product does not have a known filename extension
Hello,
I'm seeing three different vignette-related errors with recent
versions of R-3.0.0 alpha.
First, with the package BitSeq
(http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get
the following when trying to build the package:
Error: processing vignette ?BitSeq.Rnw' failed with diagnostics:
Failed to locate the ?weave? output file (by engine ?utils::Sweave?)
for
2011 Mar 22
2
R_HOME path getting munged in inst/doc/Makefile on Windows
Hello,
I have come across two separate packages that have a Makefile in inst/doc
which use the R_HOME variable.
In both cases, the path to R_HOME gets munged in such a way that commands
that include R_HOME fail on Windows:
For example, one Makefile, for the xmapcore package (
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xmapcore/username/password:
readonly) has this:
2010 Nov 12
1
installing dependencies: binary vs source
Hi,
Installing from binaries on Windows:
> install.packages("multtest")
Warning: dependency 'Biobase' is not available
trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip'
Content type 'application/zip' length 1645590 bytes (1.6 Mb)
opened URL
downloaded 1.6 Mb
package 'multtest' successfully unpacked
2011 Jun 27
1
R CMD check --force-multiarch does not install all the archs for testing
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
-----------------------------------------------------------
*
2009 Apr 24
1
Managing DLLs with the same names in an R session
I am having a problem using two DLLs with the same name, but obviously
located in different directories, in an R session. The troublesome
package is the (Bioconductor) Rgraphviz package. It relies on (3rd party
software) graphviz and imports functions from (Bioconductor) package
graph. Unfortunately, the current stable release of graphviz for Windows
2010 Sep 12
2
More strange R CMD build/check errors on Windows
Hi,
This is a follow up to:
https://stat.ethz.ch/pipermail/r-devel/2010-July/057921.html
The Bioconductor daily builds have been reporting a lot of strange
things lately on Windows using R-2.12. This started 2 or 3 months
ago and things are not getting better with recent R-2.12.
Here is a sample from today's build results. We use Windows Server
2003 R2 for the 32-bit builds, Windows
2010 Jun 10
1
R-based version of R CMD build broken on Windows
Hi,
The R-based version of R CMD build doesn't work for me on Windows:
E:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\Biobase
* checking for file 'meat\Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
Warning in shell(sprintf("%s > %s
2010 Oct 11
1
'R CMD build' not cleaning the src/ folder on Windows
Hi,
'R CMD build' (with R 2.12.0 RC) fails to clean the src/ folder
on Windows:
D:\biocbld\bbs-2.7-bioc>ls meat/BUS/src
BUS.cpp BUS.h
D:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\BUS
* checking for file 'meat\BUS/DESCRIPTION' ... OK
* preparing 'BUS':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package
2013 Aug 30
1
Problem with texi2pdf(..,clean=TRUE)
Dear all,
To create a *.pdf file from a *.Rnw file I do:
olddir <- getwd();
setwd(outdir);
tryCatch({Sweave("QAReport.Rnw");
tools::texi2pdf("QAReport.tex", clean=TRUE)
},
finally = setwd(olddir)
);
This works fine, however 'clean=TRUE' does only work when:
outdir <-
2017 Jun 27
2
texi2pdf doesn't find the correct MikTex installation due to erroneous Sys.which()
I checked after this question popped up on Stackoverflow:
https://stackoverflow.com/questions/44785961/compile-pdf-in-rstudio-works-but-knit2pdf-does-not-work-in-r-or-rstudio
On Windows, texi2pdf looks for the texify.exe of Miktex, but looks in a
very wrong place:
> Sys.which("texify")
texify
2007 Feb 05
1
Build error with last R-devel tarball
Hi,
On Windows, with last R-devel tarball (r40647) from
ftp://ftp.stat.math.ethz.ch/Software/R/R-devel_2007-02-04.tar.gz
I get the following build error:
E:\biocbld\bbs-2.0-bioc\R\src\gnuwin32> make
...
...
---------- Making package utils ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
installing R files
Error in namespaceExport(ns, exports) :
2010 Jun 09
1
Problem with library(SSPA)
Hello,
I have the fellowing problem and I am thankful for any advice!
Regards,
Samuel
################################################################
> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> biocLite("SSPA")
Using R version 2.11.0, biocinstall version 2.6.7.
Installing
2009 Dec 16
1
Rgraphviz installation
Hi,
I wanted to install Rgraphviz. From the R GUI, I downloaded the package but when I tried to load it I got the following error message:
"This application has failed to start because libcdt-4.dll was not
found. Re-installing the application may fix this problem."
The R commands and errors are:
> utils:::menuInstallPkgs()
trying URL
2010 Sep 16
1
Lack of consistent cross-platform behaviour of tools:::buildVignettes()
Hi,
On both Unix and Windows there is a mechanism to add variables
to the environment when R is started. I noticed that, on Unix,
this mechanism is not used when R is started normally at the
command line but only when it's started using the 'R CMD' syntax.
One problem with this is some lack of consistent cross-platform
behaviour. For example:
On Linux:
$ echo $TEXINPUTS
$
2016 Aug 24
1
feature request for non-sweave vignettes
Currently Makefiles for vignettes are only supported for .tex files. Could
the tools package be modified to allow file extensions to be specified for
a vignette engine? Having the pandoc pdf conversion in a Makefile rather
than through R would be tidier in some cases.
If I specify my vignette engine as
```
tools::vignetteEngine(
'myengine',
pattern = '\\.[Rr](md|nw)$',
2013 Jan 17
2
error installing KEGGSOAP
Hi, I am new to bioconductor, trying to install KEGGSOAP package, but got warnings() when installing and error message when trying to load the package, can anyone suggest what went wrong?
many thanks
John
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> biocLite("KEGGSOAP")
BioC_mirror:
2010 Nov 10
1
installed.packages Error: subscript out of bounds
Hi,
Today we've seen the following problem with the R-2.12 that we use
for our Windows builds:
> installed.packages()
Error: subscript out of bounds
After some investigation we discovered that the cause of this failure
was that 1 of the 890 packages currently installed on the machine
(Windows Server 2003 R2) had its DESCRIPTION file empty:
2014 Nov 02
1
package vignettes build in the same R process?
If I understand correctly, all vignettes in a package are built in the same R
process. Global options, loaded packages, etc., in an earlier vignette persist
in later vignettes. This can introduce user confusion (e.g., when a later
vignette builds successfully because a package is require()'ed in an earlier
vignette, but not the current one), difficult-to-identify bugs (e.g., when
a setting
2010 Nov 15
1
Cannot install packages in R 2.12.0 on Windows 7
Hi,
I am unable to install packages on my R 2.12.0 Windows 7 machine. Here are the relevant lines:
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252