Re: [R-pkg-devel] Static PDF Vignette
Hi, I am trying to add a PDF file (perfectphyloR.pdf) as the vignette of my R package (perfectphyloR). When I check my package using win-builder, I am getting the following warning message: * checking re-building of vignette outputs ... [2s] WARNING Error in re-building vignettes: ... Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", : running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "perfectphyloR.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.3/share/texmf/bibtex/bst"' had status 1 Error: running 'texi2dvi' on 'perfectphyloR.tex' failed LaTeX errors: !pdfTeX error: pdflatex.EXE (file ./perfectphyloR.pdf): reading image file fail ed ==> Fatal error occurred, no output PDF file produced! Execution halted Could someone help me fix this issue? Thank you! Charith. From: I�aki Ucar Sent: Wednesday, December 4, 2019 2:46:25 PM To: Charith Karunarathna Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] Static PDF Vignette On Wed, 4 Dec 2019 at 22:54, Charith Karunarathna wrote: > > Hi, > > I followed these instructions, > (https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/), > to add a pdf (perfectphyloR.pdf) as the vignette of my package > (perfectphyloR). However, I am getting the following Warning message and > NOTE from the win-builder: > > Warning messge: > > * checking files in 'vignettes' ... WARNING > Files in the 'vignettes' directory but no files in 'inst/doc': > 'perfectphyloR.pdf' > > NOTE: > > * checking for hidden files and directories ... NOTE > Found the following hidden files and directories: > vignettes/.Rnw > These were most likely included in error. See section 'Package > structure' in the 'Writing R Extensions' manual. > > CRAN-pack does not know about > vignettes/.Rnw > > I am having a hardship to fix those two. Could someone direct me to fix those > issue? The post doesn't mean ".Rnw" literally. Give it a filename instead of just .Rnw: perfectphyloR.Rnw seems appropriate. I�aki [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] New Package olr 4 NOTES
I have not had good luck building packages for final delivery using devtools...
use the command line, Luke!
On December 5, 2019 7:40:46 AM PST, Mat Fok via R-package-devel
wrote:
>Hi Max,
>Following your comment about, ".Rbuildignore is used by R CMD build to
>exclude some files from the bundled package. If you created the tar.gz
>file manually, then .Rbuildignore was, well, ignored. And .Rproj.user
>would then have been included in the tarball."
>I assume that if I create the tar.gz file "automatically" through R and
>not 7zip, then the .Rbuildignore is not ignored and I won't have the
>problem of .Rproj.user being included in the tarball:
>
>devtools::build(pkg = "C:/Rstuff/olr", path = NULL, binary = FALSE,
>vignettes = TRUE, manual = FALSE, args = NULL, quiet = FALSE)
>
>√ checking for file 'C:\Rstuff\olr/DESCRIPTION' ...- preparing
>'olr':√ checking DESCRIPTION meta-information ...- checking for LF
>line-endings in source and make files and shell scripts- checking for
>empty or unneeded directories- building 'olr_1.0.0.2000.tar.gz' [1]
>"C:/Rstuff/olr_1.0.0.2000.tar.gz"
>Thank you very much!
>
>
>
>
>
>On Thursday, December 5, 2019, 9:25 AM, Max Turgeon
> wrote:
>
>#yiv7416260906 -- P {margin-top:0;margin-bottom:0;}#yiv7416260906
>.Rbuildignore is used by R CMD build to exclude some files from the
>bundled package. If you created the tar.gz file manually, then
>.Rbuildignore was, well, ignored. And .Rproj.user would then have been
>included in the tarball.
>
>
>
>
>
>Max Turgeon
>Assistant ProfessorDepartment of Statistics
>Department of Computer Science
>University of Manitobamaxturgeon.ca
>
>
>
>
>
>From: R-package-devel on behalf
>of Mat Fok via R-package-devel
>Sent: December 5, 2019 8:17 AM
>To: Martin Maechler
>Cc: R-package-devel
>Subject: Re: [R-pkg-devel] New Package olr 4 NOTES I meant
>.Rbuildignore.
>
>
>Sent from Yahoo Mail for iPhone
>
>
>On Thursday, December 5, 2019, 3:19 AM, Martin Maechler
> wrote:
>
>> Mat Fok via R-package-devel
>> on Wed, 4 Dec 2019 22:25:47 + writes:
>
> > Hi,
> > Thank you. I am wondering why the log would output .Rproj.user
>when it was already in the .Rignorefile. Hope the .Rignore file is
>correct anyways as I have mentioned below.
>
>If you really use .Rignore then no wonder you have problems.
>The correct file name is .Rbuildignore
>
>Martin
>
> > Thanks,
> > Mathew
>
>
>
>
> [[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>
>
> [[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
Sent from my phone. Please excuse my brevity.
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] New Package olr 4 NOTES
Hi Max,
Following your comment about, ".Rbuildignore is used by R CMD build to exclude
some files from the bundled package. If you created the tar.gz file manually,
then .Rbuildignore was, well, ignored. And .Rproj.user would then have been
included in the tarball."
I assume that if I create the tar.gz file "automatically" through R and not
7zip, then the .Rbuildignore is not ignored and I won't have the problem of
.Rproj.user being included in the tarball:
devtools::build(pkg = "C:/Rstuff/olr", path = NULL, binary = FALSE, vignettes =
TRUE, manual = FALSE, args = NULL, quiet = FALSE)
√ checking for file 'C:\Rstuff\olr/DESCRIPTION' ...- preparing 'olr':√
checking DESCRIPTION meta-information ...- checking for LF line-endings in
source and make files and shell scripts- checking for empty or unneeded
directories- building 'olr_1.0.0.2000.tar.gz' [1]
"C:/Rstuff/olr_1.0.0.2000.tar.gz"
Thank you very much!
On Thursday, December 5, 2019, 9:25 AM, Max Turgeon
wrote:
#yiv7416260906 -- P {margin-top:0;margin-bottom:0;}#yiv7416260906
.Rbuildignore is used by R CMD build to exclude some files from the bundled
package. If you created the tar.gz file manually, then .Rbuildignore was, well,
ignored. And .Rproj.user would then have been included in the tarball.
Max Turgeon
Assistant ProfessorDepartment of Statistics
Department of Computer Science
University of Manitobamaxturgeon.ca
From: R-package-devel on behalf of Mat
Fok via R-package-devel
Sent: December 5, 2019 8:17 AM
To: Martin Maechler
Cc: R-package-devel
Subject: Re: [R-pkg-devel] New Package olr 4 NOTES I meant .Rbuildignore.
Sent from Yahoo Mail for iPhone
On Thursday, December 5, 2019, 3:19 AM, Martin Maechler
wrote:
> Mat Fok via R-package-devel
> on Wed, 4 Dec 2019 22:25:47 + writes:
> Hi,
> Thank you. I am wondering why the log would output .Rproj.user when it
was already in the .Rignorefile. Hope the .Rignore file is correct anyways as I
have mentioned below.
If you really use .Rignore then no wonder you have problems.
The correct file name is .Rbuildignore
Martin
> Thanks,
> Mathew
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] New Package olr 4 NOTES
I meant .Rbuildignore. Sent from Yahoo Mail for iPhone On Thursday, December 5, 2019, 3:19 AM, Martin Maechler wrote: > Mat Fok via R-package-devel > on Wed, 4 Dec 2019 22:25:47 + writes: > Hi, > Thank you. I am wondering why the log would output .Rproj.user when it was already in the .Rignorefile. Hope the .Rignore file is correct anyways as I have mentioned below. If you really use .Rignore then no wonder you have problems. The correct file name is .Rbuildignore Martin > Thanks, > Mathew [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Issue with Biostrings-- can't find the base rgb function on r-devel
That was a bug in Biostrings that has been fixed in the meantime.
Best,
Uwe Ligges
On 05.12.2019 05:19, Hugh Parsonage wrote:
rgb is from package grDevices not package base.
On Thu, 5 Dec 2019 at 2:48 pm, Dalgleish, James (NIH/NCI) [V] via
R-package-devel wrote:
Question:
NIPTeR is experiencing new warnings when loading Biostrings. I have the
exact same warnings with my package, CNVScope.
It seems a little odd that the base function rgb cannot be found. What can
cause a base package to not be found? I can't replicate this issue on
either of my linux or windows machines or on winbuilder.
I have already asked the Bioconductor community, but didn't get a response
(https://support.bioconductor.org/p/126878/).
Thanks,
James Dalgleish
Maintainer, CNVScope
NIH/NCI
Source: https://cran.r-project.org/web/checks/check_results_NIPTeR.html
Check Details
Version: 1.0.2
Check: whether the package can be unloaded cleanly
Result: WARN
Error: package or namespace load failed for 'NIPTeR':
.onLoad failed in loadNamespace() for 'Biostrings', details:
call: rgb(1, 1, 1)
error: could not find function "rgb"
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: whether the namespace can be loaded with stated dependencies
Result: WARN
Error: .onLoad failed in loadNamespace() for 'Biostrings', details:
call: rgb(1, 1, 1)
error: could not find function "rgb"
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: dependencies in R code
Result: NOTE
Error: package or namespace load failed for 'NIPTeR':
.onLoad failed in loadNamespace() for 'Biostrings', details:
call: rgb(1, 1, 1)
error: could not find function "rgb"
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc, character.only = T
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: R code for possible problems
Result: NOTE
Error: .onLoad failed in loadNamespace() for 'Biostrings', details:
call: rgb(1, 1, 1)
error: could not find function "rgb"
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] New Package olr 4 NOTES
> Mat Fok via R-package-devel > on Wed, 4 Dec 2019 22:25:47 + writes: > Hi, > Thank you. I am wondering why the log would output .Rproj.user when it was already in the .Rignorefile. Hope the .Rignore file is correct anyways as I have mentioned below. If you really use .Rignore then no wonder you have problems. The correct file name is .Rbuildignore Martin > Thanks, > Mathew __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
