Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
Dear all,
First, thank you to everyone who responded.
Let me be more specific about what I did, focusing on macOS (since I did
most of this on Windows too):
(1) I observed the problem with the Rcmdr package, including version
2.7-1, which is newly on CRAN. Presumably, it wouldn't be hard to
duplicate what I did.
(2) I previously tried both --compact-vignettes="both",
--compact-vignettes=both, and also just --compact-vignettes. R CMD build
says that it's "* compacting vignettes and other PDF files", and R CMD
check --as-cran doesn't complain, reporting "* checking sizes of PDF
files under ‘inst/doc’ ... OK."
(3) Nothing changes when, following Duncan's advice, I set GS_QUALITY=screen
In the tarball built by R CMD build, the vignette in
inst/doc/Getting-Started-with-the-Rcmdr.pdf is 1.6 MB. When I compacted
the vignette with Adobe Acrobat, it was reduced to 395 KB.
Putting all of this together, I suspect that Acrobat may just do a
better job than gs and qpdf.
Best,
John
On 2020-10-08 12:06 p.m., Duncan Murdoch wrote:
When I tried that on MacOS, it did the gs compression with gs_quality
set to "none", which does nothing. I don't know what quality CRAN uses,
but for me setting the environment variable GS_QUALITY=screen made a big
difference.
Duncan Murdoch
On 08/10/2020 11:10 a.m., John Fox wrote:
Dear Ben,
Actually, what I used was --compact-vignettes="both", with qpdf and gs
installed on my Windows and Mac machines, and that apparently didn't
work for me.
Best,
John
On 2020-10-07 10:06 p.m., Ben Bolker wrote:
OK, I think I see the problem. tl;dr use --compact-vignettes="both"
when building the vignettes.
--compact-vignettes by default only tries qpdf.
when the R CMD check --as-cran is run, it tries both qpdf and gs.
Since gs (apparently, in this case) compresses more aggressively than
qpdf, it succeeds in compressing further, and the check complains.
From R CMD build --help:
--compact-vignettes= try to compact PDF files under inst/doc:
"no" (default), "qpdf", "gs", "gs+qpdf",
"both"
--compact-vignettes same as --compact-vignettes=qpdf
I don't know if this is worth documenting somewhere, or modifying
the
behaviour to make "both" the default for --compact-vignettes ?
On 10/7/20 8:35 PM, Duncan Murdoch wrote:
On 07/10/2020 8:32 p.m., Ben Bolker wrote:
Thanks for the tip, I'll take a look.
Given that three relatively experienced package authors all
seem to
have experienced similar issues, it seems that maybe this is worth
figuring out/maybe I'm not just doing something boneheaded.
Just to clarify: I've never noticed the problem you mention. I just
know how to debug R CMD build.
Duncan
cheers
Ben
On 10/7/20 8:31 PM, Duncan Murdoch wrote:
I don't know the answer to your question, but you can debug the
--compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
where "pkgdir" is the directory of the source of your package. Add
extra options to the build as separate elements of the argument to
.build(): this function is called after args have been parsed.
When I do that, I see that it rejects the compaction, because none of
mine benefit much from it: it wants at least a 10% and 10K
reduction.
But Ben's example met those criteria. When I trick it into accepting
the compaction, it does put the compacted PDF into the tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
Dear Ben,
On 2020-10-07 5:26 p.m., Ben Bolker wrote:
I hope so too. The (annoying) workaround is to compact the
vignette
yourself (using qpdf directly or using tools::compactPDF), then use
no-build-vignettes. The problem there is whatever's supposed to
happen
with building vignette indices. The ugly workaround, I guess,
is to
build the tarball, compact the vignettes oneself, then *replace*
them in
the tarball. (Obviously I can automate that, but it seems as
though it
would be unnecessary if I knew what was going on ...)
I've used both of these workarounds and agree that it would be
nice to
avoid them. After all, what is the --compact-vignettes argument for?
Best,
John
cheers
Ben
On 10/7/20 4:10 PM, John Fox wrote:
Dear Ben,
I was hoping that someone would pick up on this problem, because
I've
experienced the same issue of --compact-vignettes apparently
ignored,
e.g., with the Rcmdr package under R 4.0.2 on both macOS and
Windows.
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or ... ?
I have qpdf installed, and am running R CMD build with
--compact-vignettes, but the PDF in the tarball doesn't seem
to be
compressed despite the fact that the output messages say
"compacting
vignettes ..."
Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
When I tried that on MacOS, it did the gs compression with gs_quality
set to "none", which does nothing. I don't know what quality CRAN uses,
but for me setting the environment variable GS_QUALITY=screen made a big
difference.
Duncan Murdoch
On 08/10/2020 11:10 a.m., John Fox wrote:
Dear Ben,
Actually, what I used was --compact-vignettes="both", with qpdf and gs
installed on my Windows and Mac machines, and that apparently didn't
work for me.
Best,
John
On 2020-10-07 10:06 p.m., Ben Bolker wrote:
OK, I think I see the problem. tl;dr use --compact-vignettes="both"
when building the vignettes.
--compact-vignettes by default only tries qpdf.
when the R CMD check --as-cran is run, it tries both qpdf and gs.
Since gs (apparently, in this case) compresses more aggressively than
qpdf, it succeeds in compressing further, and the check complains.
From R CMD build --help:
--compact-vignettes= try to compact PDF files under inst/doc:
"no" (default), "qpdf", "gs", "gs+qpdf", "both"
--compact-vignettes same as --compact-vignettes=qpdf
I don't know if this is worth documenting somewhere, or modifying the
behaviour to make "both" the default for --compact-vignettes ?
On 10/7/20 8:35 PM, Duncan Murdoch wrote:
On 07/10/2020 8:32 p.m., Ben Bolker wrote:
Thanks for the tip, I'll take a look.
Given that three relatively experienced package authors all seem to
have experienced similar issues, it seems that maybe this is worth
figuring out/maybe I'm not just doing something boneheaded.
Just to clarify: I've never noticed the problem you mention. I just
know how to debug R CMD build.
Duncan
cheers
Ben
On 10/7/20 8:31 PM, Duncan Murdoch wrote:
I don't know the answer to your question, but you can debug the
--compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
where "pkgdir" is the directory of the source of your package. Add
extra options to the build as separate elements of the argument to
.build(): this function is called after args have been parsed.
When I do that, I see that it rejects the compaction, because none of
mine benefit much from it: it wants at least a 10% and 10K reduction.
But Ben's example met those criteria. When I trick it into accepting
the compaction, it does put the compacted PDF into the tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
Dear Ben,
On 2020-10-07 5:26 p.m., Ben Bolker wrote:
I hope so too. The (annoying) workaround is to compact the
vignette
yourself (using qpdf directly or using tools::compactPDF), then use
no-build-vignettes. The problem there is whatever's supposed to
happen
with building vignette indices. The ugly workaround, I guess,
is to
build the tarball, compact the vignettes oneself, then *replace*
them in
the tarball. (Obviously I can automate that, but it seems as
though it
would be unnecessary if I knew what was going on ...)
I've used both of these workarounds and agree that it would be nice to
avoid them. After all, what is the --compact-vignettes argument for?
Best,
John
cheers
Ben
On 10/7/20 4:10 PM, John Fox wrote:
Dear Ben,
I was hoping that someone would pick up on this problem, because
I've
experienced the same issue of --compact-vignettes apparently
ignored,
e.g., with the Rcmdr package under R 4.0.2 on both macOS and
Windows.
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or ... ?
I have qpdf installed, and am running R CMD build with
--compact-vignettes, but the PDF in the tarball doesn't seem to be
compressed despite the fact that the output messages say
"compacting
vignettes ..."
$ R CMD build --compact-vignettes lme4
* checking for file ‘lme4/DESCRIPTION’ ... OK
* preparing ‘lme4’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent
rebuilding.
* compacting vignettes and other PDF files
* cleaning src
* checking for LF line-endings in source and make files and shell
scripts
* checking for empty or unneeded directories
* building ‘lme4_1.1-24.tar.gz’
The copy of lmer.pdf in the resulting tarball is 900K or so:
$ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf
-rw-r--r-- bolker/bolker 907022 2020-10-05 12:59
lme4/inst/doc/lmer.pdf
The previously built (and manually compacted) version of
lmer.pdf
in the tarball is 500K:
$ ls -l lme4/inst/doc/lmer.pdf
-rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15
lme4/ins
Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
Hi both,
I am not sure if this might be the issue here, but I think on both
Linux and Windows I need to use the both option without quotation
marks: --compact-vignettes=both
Best,
Henrik
Am Do., 8. Okt. 2020 um 17:21 Uhr schrieb Ben Bolker :
>
>Huh, weird. "both" worked for me.
>
>My debugging process involved instrumenting the compression function
> to report what it was doing (see below), rebuilding R, and running the
> build and check --as-cran processes again. (If the package you're
> experiencing problems with is public, feel free to point me to it and
> I'll try to take a look.)
>
>cheers
> Ben
>
> Index: src/library/tools/R/admin.R
> ===
> --- src/library/tools/R/admin.R (revision 79311)
> +++ src/library/tools/R/admin.R (working copy)
> @@ -1088,6 +1088,7 @@
> }
> if(!res && file.exists(tf)) {
> old <- file.size(p); new <- file.size(tf)
> +cat(sprintf("compression: old=%f, new=%f, new/old=%f,
> old-new=%f",old, new, new/old,old-new),"\n")
> if(new/old < 0.9 && new < old - 1e4) {
> file.copy(tf, p, overwrite = TRUE)
> ans[p, ] <- c(old, new)
>
>
> On 10/8/20 11:10 AM, John Fox wrote:
> > Dear Ben,
> >
> > Actually, what I used was --compact-vignettes="both", with qpdf and gs
> > installed on my Windows and Mac machines, and that apparently didn't
> > work for me.
> >
> > Best,
> > John
> >
> > On 2020-10-07 10:06 p.m., Ben Bolker wrote:
> >>OK, I think I see the problem. tl;dr use --compact-vignettes="both"
> >> when building the vignettes.
> >>
> >>--compact-vignettes by default only tries qpdf.
> >>
> >>when the R CMD check --as-cran is run, it tries both qpdf and gs.
> >> Since gs (apparently, in this case) compresses more aggressively than
> >> qpdf, it succeeds in compressing further, and the check complains.
> >>
> >> From R CMD build --help:
> >>
> >> --compact-vignettes= try to compact PDF files under inst/doc:
> >> "no" (default), "qpdf", "gs", "gs+qpdf", "both"
> >>--compact-vignettes same as --compact-vignettes=qpdf
> >>
> >>
> >>I don't know if this is worth documenting somewhere, or modifying
> >> the behaviour to make "both" the default for --compact-vignettes ?
> >>
> >>
> >> On 10/7/20 8:35 PM, Duncan Murdoch wrote:
> >>> On 07/10/2020 8:32 p.m., Ben Bolker wrote:
> Thanks for the tip, I'll take a look.
>
> Given that three relatively experienced package authors all seem to
> have experienced similar issues, it seems that maybe this is worth
> figuring out/maybe I'm not just doing something boneheaded.
> >>>
> >>> Just to clarify: I've never noticed the problem you mention. I just
> >>> know how to debug R CMD build.
> >>>
> >>> Duncan
> >>>
>
> cheers
> Ben
>
> On 10/7/20 8:31 PM, Duncan Murdoch wrote:
> > I don't know the answer to your question, but you can debug the
> > --compact-vignettes option as follows.
> >
> > debug(tools::compactPDF)
> > tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
> >
> > where "pkgdir" is the directory of the source of your package. Add
> > extra options to the build as separate elements of the argument to
> > .build(): this function is called after args have been parsed.
> >
> > When I do that, I see that it rejects the compaction, because none of
> > mine benefit much from it: it wants at least a 10% and 10K reduction.
> > But Ben's example met those criteria. When I trick it into accepting
> > the compaction, it does put the compacted PDF into the tarball.
> >
> > Duncan Murdoch
> >
> > On 07/10/2020 6:03 p.m., John Fox wrote:
> >> Dear Ben,
> >>
> >> On 2020-10-07 5:26 p.m., Ben Bolker wrote:
> >>> I hope so too. The (annoying) workaround is to compact the
> >>> vignette
> >>> yourself (using qpdf directly or using tools::compactPDF), then use
> >>> no-build-vignettes. The problem there is whatever's supposed to
> >>> happen
> >>> with building vignette indices. The ugly workaround, I
> >>> guess, is to
> >>> build the tarball, compact the vignettes oneself, then *replace*
> >>> them in
> >>> the tarball. (Obviously I can automate that, but it seems as
> >>> though it
> >>> would be unnecessary if I knew what was going on ...)
> >>
> >> I've used both of these workarounds and agree that it would be
> >> nice to
> >> avoid them. After all, what is the --compact-vignettes argument for?
> >>
> >> Best,
> >> John
> >>
> >>>
> >>> cheers
> >>> Ben
> >>>
> >>>
> >>> On 10/7/20 4:10 PM, John Fox wrote:
> Dear Ben,
>
> I was hoping that someone would pick up on this problem, because
> I've
> >>
Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
Huh, weird. "both" worked for me.
My debugging process involved instrumenting the compression function
to report what it was doing (see below), rebuilding R, and running the
build and check --as-cran processes again. (If the package you're
experiencing problems with is public, feel free to point me to it and
I'll try to take a look.)
cheers
Ben
Index: src/library/tools/R/admin.R
===
--- src/library/tools/R/admin.R (revision 79311)
+++ src/library/tools/R/admin.R (working copy)
@@ -1088,6 +1088,7 @@
}
if(!res && file.exists(tf)) {
old <- file.size(p); new <- file.size(tf)
+cat(sprintf("compression: old=%f, new=%f, new/old=%f,
old-new=%f",old, new, new/old,old-new),"\n")
if(new/old < 0.9 && new < old - 1e4) {
file.copy(tf, p, overwrite = TRUE)
ans[p, ] <- c(old, new)
On 10/8/20 11:10 AM, John Fox wrote:
Dear Ben,
Actually, what I used was --compact-vignettes="both", with qpdf and gs
installed on my Windows and Mac machines, and that apparently didn't
work for me.
Best,
John
On 2020-10-07 10:06 p.m., Ben Bolker wrote:
OK, I think I see the problem. tl;dr use --compact-vignettes="both"
when building the vignettes.
--compact-vignettes by default only tries qpdf.
when the R CMD check --as-cran is run, it tries both qpdf and gs.
Since gs (apparently, in this case) compresses more aggressively than
qpdf, it succeeds in compressing further, and the check complains.
From R CMD build --help:
--compact-vignettes= try to compact PDF files under inst/doc:
"no" (default), "qpdf", "gs", "gs+qpdf", "both"
--compact-vignettes same as --compact-vignettes=qpdf
I don't know if this is worth documenting somewhere, or modifying
the behaviour to make "both" the default for --compact-vignettes ?
On 10/7/20 8:35 PM, Duncan Murdoch wrote:
On 07/10/2020 8:32 p.m., Ben Bolker wrote:
Thanks for the tip, I'll take a look.
Given that three relatively experienced package authors all seem to
have experienced similar issues, it seems that maybe this is worth
figuring out/maybe I'm not just doing something boneheaded.
Just to clarify: I've never noticed the problem you mention. I just
know how to debug R CMD build.
Duncan
cheers
Ben
On 10/7/20 8:31 PM, Duncan Murdoch wrote:
I don't know the answer to your question, but you can debug the
--compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
where "pkgdir" is the directory of the source of your package. Add
extra options to the build as separate elements of the argument to
.build(): this function is called after args have been parsed.
When I do that, I see that it rejects the compaction, because none of
mine benefit much from it: it wants at least a 10% and 10K reduction.
But Ben's example met those criteria. When I trick it into accepting
the compaction, it does put the compacted PDF into the tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
Dear Ben,
On 2020-10-07 5:26 p.m., Ben Bolker wrote:
I hope so too. The (annoying) workaround is to compact the
vignette
yourself (using qpdf directly or using tools::compactPDF), then use
no-build-vignettes. The problem there is whatever's supposed to
happen
with building vignette indices. The ugly workaround, I
guess, is to
build the tarball, compact the vignettes oneself, then *replace*
them in
the tarball. (Obviously I can automate that, but it seems as
though it
would be unnecessary if I knew what was going on ...)
I've used both of these workarounds and agree that it would be
nice to
avoid them. After all, what is the --compact-vignettes argument for?
Best,
John
cheers
Ben
On 10/7/20 4:10 PM, John Fox wrote:
Dear Ben,
I was hoping that someone would pick up on this problem, because
I've
experienced the same issue of --compact-vignettes apparently
ignored,
e.g., with the Rcmdr package under R 4.0.2 on both macOS and
Windows.
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or ... ?
I have qpdf installed, and am running R CMD build with
--compact-vignettes, but the PDF in the tarball doesn't seem to be
compressed despite the fact that the output messages say
"compacting
vignettes ..."
$ R CMD build --compact-vignettes lme4
* checking for file ‘lme4/DESCRIPTION’ ... OK
* preparing ‘lme4’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
Dear Ben,
Actually, what I used was --compact-vignettes="both", with qpdf and gs
installed on my Windows and Mac machines, and that apparently didn't
work for me.
Best,
John
On 2020-10-07 10:06 p.m., Ben Bolker wrote:
OK, I think I see the problem. tl;dr use --compact-vignettes="both"
when building the vignettes.
--compact-vignettes by default only tries qpdf.
when the R CMD check --as-cran is run, it tries both qpdf and gs.
Since gs (apparently, in this case) compresses more aggressively than
qpdf, it succeeds in compressing further, and the check complains.
From R CMD build --help:
--compact-vignettes= try to compact PDF files under inst/doc:
"no" (default), "qpdf", "gs", "gs+qpdf", "both"
--compact-vignettes same as --compact-vignettes=qpdf
I don't know if this is worth documenting somewhere, or modifying the
behaviour to make "both" the default for --compact-vignettes ?
On 10/7/20 8:35 PM, Duncan Murdoch wrote:
On 07/10/2020 8:32 p.m., Ben Bolker wrote:
Thanks for the tip, I'll take a look.
Given that three relatively experienced package authors all seem to
have experienced similar issues, it seems that maybe this is worth
figuring out/maybe I'm not just doing something boneheaded.
Just to clarify: I've never noticed the problem you mention. I just
know how to debug R CMD build.
Duncan
cheers
Ben
On 10/7/20 8:31 PM, Duncan Murdoch wrote:
I don't know the answer to your question, but you can debug the
--compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
where "pkgdir" is the directory of the source of your package. Add
extra options to the build as separate elements of the argument to
.build(): this function is called after args have been parsed.
When I do that, I see that it rejects the compaction, because none of
mine benefit much from it: it wants at least a 10% and 10K reduction.
But Ben's example met those criteria. When I trick it into accepting
the compaction, it does put the compacted PDF into the tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
Dear Ben,
On 2020-10-07 5:26 p.m., Ben Bolker wrote:
I hope so too. The (annoying) workaround is to compact the
vignette
yourself (using qpdf directly or using tools::compactPDF), then use
no-build-vignettes. The problem there is whatever's supposed to
happen
with building vignette indices. The ugly workaround, I guess,
is to
build the tarball, compact the vignettes oneself, then *replace*
them in
the tarball. (Obviously I can automate that, but it seems as
though it
would be unnecessary if I knew what was going on ...)
I've used both of these workarounds and agree that it would be nice to
avoid them. After all, what is the --compact-vignettes argument for?
Best,
John
cheers
Ben
On 10/7/20 4:10 PM, John Fox wrote:
Dear Ben,
I was hoping that someone would pick up on this problem, because
I've
experienced the same issue of --compact-vignettes apparently
ignored,
e.g., with the Rcmdr package under R 4.0.2 on both macOS and
Windows.
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or ... ?
I have qpdf installed, and am running R CMD build with
--compact-vignettes, but the PDF in the tarball doesn't seem to be
compressed despite the fact that the output messages say
"compacting
vignettes ..."
$ R CMD build --compact-vignettes lme4
* checking for file ‘lme4/DESCRIPTION’ ... OK
* preparing ‘lme4’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent
rebuilding.
* compacting vignettes and other PDF files
* cleaning src
* checking for LF line-endings in source and make files and shell
scripts
* checking for empty or unneeded directories
* building ‘lme4_1.1-24.tar.gz’
The copy of lmer.pdf in the resulting tarball is 900K or so:
$ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf
-rw-r--r-- bolker/bolker 907022 2020-10-05 12:59
lme4/inst/doc/lmer.pdf
The previously built (and manually compacted) version of
lmer.pdf
in the tarball is 500K:
$ ls -l lme4/inst/doc/lmer.pdf
-rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15
lme4/inst/doc/lmer.pdf
Is 'R CMD build' confused by the presence of a pre-built
PDF in
the inst/doc directory? Or am I somehow mistaken about how this is
supposed to work?
I would just use --no-build-vignettes and submit the
tarball with
the previously built/compressed PDF, but
Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
> Ben Bolker
> on Wed, 7 Oct 2020 20:42:08 -0400 writes:
> On 10/7/20 8:35 PM, Duncan Murdoch wrote:
>> On 07/10/2020 8:32 p.m., Ben Bolker wrote:
>>> Thanks for the tip, I'll take a look.
>>>
>>> Given that three relatively experienced package
>>> authors all seem to have experienced similar issues, it
>>> seems that maybe this is worth figuring out/maybe I'm
>>> not just doing something boneheaded.
>>
>> Just to clarify: I've never noticed the problem you
>> mention. I just know how to debug R CMD build.
>I wasn't saying you had. My count of three was Bolker
> (me), Fox, Nash.
>cheers Ben
>>
>> Duncan
Thank you, Ben, John (2x), and Duncan.
I agree this should be investigated and fixed if/where needed.
My personal experience is that PDF compaction "has worked for
me" mostly, but not always; I think I never had looked closely
when it did not work, and yes, I know I also had used manual
compaction when I was unhappy with the automatic one.
Given that lme4 takes relatively long, and also given Duncan
Murdoch's precise instruction on how to debug,
could you try to find a as small as "possible" repr.example?
Of course it needs a vignette whose pdf is relatively large or
rather "well compactable", but otherwise could also be an
artificial package.
Martin
>>>
>>> cheers Ben
>>>
>>> On 10/7/20 8:31 PM, Duncan Murdoch wrote:
I don't know the answer to your question, but you can
debug the --compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes",
"pkgdir"))
where "pkgdir" is the directory of the source of your
package. Add extra options to the build as separate
elements of the argument to .build(): this function is
called after args have been parsed.
When I do that, I see that it rejects the compaction,
because none of mine benefit much from it: it wants at
least a 10% and 10K reduction. But Ben's example met
those criteria. When I trick it into accepting the
compaction, it does put the compacted PDF into the
tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
> Dear Ben,
>
> On 2020-10-07 5:26 p.m., Ben Bolker wrote:
> I hope so too. The (annoying) workaround is to
> compact the
> vignette
> yourself (using qpdf directly or using tools::compactPDF),
> then use
> no-build-vignettes. The problem there is whatever's
> supposed to
> happen
> with building vignette indices. The ugly workaround,
> I guess,
> is to
> build the tarball, compact the vignettes oneself, then
> *replace*
> them in
> the tarball. (Obviously I can automate that, but it seems
> as
> though it
> would be unnecessary if I knew what was going on ...)
>
> I've used both of these workarounds and agree that it
> would be nice to avoid them. After all, what is the
> --compact-vignettes argument for?
>
> Best, John
>
>>
> cheers
> Ben
>>
>>
> On 10/7/20 4:10 PM, John Fox wrote:
>>> Dear Ben,
>>>
>>> I was hoping that someone would pick up on this
>>> problem, because I've experienced the same issue of
>>> --compact-vignettes apparently ignored, e.g., with
>>> the Rcmdr package under R 4.0.2 on both macOS and
>>> Windows.
>>>
>>> Best, John
>>>
>>> John Fox, Professor Emeritus McMaster University
>>> Hamilton, Ontario, Canada web:
>>> https://socialsciences.mcmaster.ca/jfox/
>>>
>>> On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or
... ?
I have qpdf installed, and am running R CMD
build with --compact-vignettes, but the PDF in the
tarball doesn't seem to be compressed despite the
fact that the output messages say "compacting
vignettes ..."
$ R CMD build --compact-vignettes lme4 *
checking for file ‘lme4/DESCRIPTION’ ... OK *
preparing ‘lme4’: * checking DESCRIPTION
meta-information ... OK * cleaning src * installing
the package to process help pages * saving partial
Rd database * creating vignettes ... OK Warning:
‘inst/doc’ files ‘lmerperf.html’,
‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
ignored as vignettes have been rebuilt. Run R
CMD build with --no-buil
Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
OK, I think I see the problem. tl;dr use --compact-vignettes="both"
when building the vignettes.
--compact-vignettes by default only tries qpdf.
when the R CMD check --as-cran is run, it tries both qpdf and gs.
Since gs (apparently, in this case) compresses more aggressively than
qpdf, it succeeds in compressing further, and the check complains.
From R CMD build --help:
--compact-vignettes= try to compact PDF files under inst/doc:
"no" (default), "qpdf", "gs", "gs+qpdf", "both"
--compact-vignettes same as --compact-vignettes=qpdf
I don't know if this is worth documenting somewhere, or modifying the
behaviour to make "both" the default for --compact-vignettes ?
On 10/7/20 8:35 PM, Duncan Murdoch wrote:
On 07/10/2020 8:32 p.m., Ben Bolker wrote:
Thanks for the tip, I'll take a look.
Given that three relatively experienced package authors all seem to
have experienced similar issues, it seems that maybe this is worth
figuring out/maybe I'm not just doing something boneheaded.
Just to clarify: I've never noticed the problem you mention. I just
know how to debug R CMD build.
Duncan
cheers
Ben
On 10/7/20 8:31 PM, Duncan Murdoch wrote:
I don't know the answer to your question, but you can debug the
--compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
where "pkgdir" is the directory of the source of your package. Add
extra options to the build as separate elements of the argument to
.build(): this function is called after args have been parsed.
When I do that, I see that it rejects the compaction, because none of
mine benefit much from it: it wants at least a 10% and 10K reduction.
But Ben's example met those criteria. When I trick it into accepting
the compaction, it does put the compacted PDF into the tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
Dear Ben,
On 2020-10-07 5:26 p.m., Ben Bolker wrote:
I hope so too. The (annoying) workaround is to compact the
vignette
yourself (using qpdf directly or using tools::compactPDF), then use
no-build-vignettes. The problem there is whatever's supposed to
happen
with building vignette indices. The ugly workaround, I guess,
is to
build the tarball, compact the vignettes oneself, then *replace*
them in
the tarball. (Obviously I can automate that, but it seems as
though it
would be unnecessary if I knew what was going on ...)
I've used both of these workarounds and agree that it would be nice to
avoid them. After all, what is the --compact-vignettes argument for?
Best,
John
cheers
Ben
On 10/7/20 4:10 PM, John Fox wrote:
Dear Ben,
I was hoping that someone would pick up on this problem, because I've
experienced the same issue of --compact-vignettes apparently ignored,
e.g., with the Rcmdr package under R 4.0.2 on both macOS and Windows.
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or ... ?
I have qpdf installed, and am running R CMD build with
--compact-vignettes, but the PDF in the tarball doesn't seem to be
compressed despite the fact that the output messages say "compacting
vignettes ..."
$ R CMD build --compact-vignettes lme4
* checking for file ‘lme4/DESCRIPTION’ ... OK
* preparing ‘lme4’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent
rebuilding.
* compacting vignettes and other PDF files
* cleaning src
* checking for LF line-endings in source and make files and shell
scripts
* checking for empty or unneeded directories
* building ‘lme4_1.1-24.tar.gz’
The copy of lmer.pdf in the resulting tarball is 900K or so:
$ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf
-rw-r--r-- bolker/bolker 907022 2020-10-05 12:59
lme4/inst/doc/lmer.pdf
The previously built (and manually compacted) version of
lmer.pdf
in the tarball is 500K:
$ ls -l lme4/inst/doc/lmer.pdf
-rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15
lme4/inst/doc/lmer.pdf
Is 'R CMD build' confused by the presence of a pre-built
PDF in
the inst/doc directory? Or am I somehow mistaken about how this is
supposed to work?
I would just use --no-build-vignettes and submit the
tarball with
the previously built/compressed PDF, but I'm trying to avoid a
"Package has a VignetteBuilder field but no prebuilt vignette index"
NOTE, which I assume is missing because I built without building
vignettes ... ?
As always, enlightenment is welcome.
cheers
Ben B
Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
On 10/7/20 8:35 PM, Duncan Murdoch wrote:
On 07/10/2020 8:32 p.m., Ben Bolker wrote:
Thanks for the tip, I'll take a look.
Given that three relatively experienced package authors all seem to
have experienced similar issues, it seems that maybe this is worth
figuring out/maybe I'm not just doing something boneheaded.
Just to clarify: I've never noticed the problem you mention. I just
know how to debug R CMD build.
I wasn't saying you had. My count of three was Bolker (me), Fox, Nash.
cheers
Ben
Duncan
cheers
Ben
On 10/7/20 8:31 PM, Duncan Murdoch wrote:
I don't know the answer to your question, but you can debug the
--compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
where "pkgdir" is the directory of the source of your package. Add
extra options to the build as separate elements of the argument to
.build(): this function is called after args have been parsed.
When I do that, I see that it rejects the compaction, because none of
mine benefit much from it: it wants at least a 10% and 10K reduction.
But Ben's example met those criteria. When I trick it into accepting
the compaction, it does put the compacted PDF into the tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
Dear Ben,
On 2020-10-07 5:26 p.m., Ben Bolker wrote:
I hope so too. The (annoying) workaround is to compact the
vignette
yourself (using qpdf directly or using tools::compactPDF), then use
no-build-vignettes. The problem there is whatever's supposed to
happen
with building vignette indices. The ugly workaround, I guess,
is to
build the tarball, compact the vignettes oneself, then *replace*
them in
the tarball. (Obviously I can automate that, but it seems as
though it
would be unnecessary if I knew what was going on ...)
I've used both of these workarounds and agree that it would be nice to
avoid them. After all, what is the --compact-vignettes argument for?
Best,
John
cheers
Ben
On 10/7/20 4:10 PM, John Fox wrote:
Dear Ben,
I was hoping that someone would pick up on this problem, because I've
experienced the same issue of --compact-vignettes apparently ignored,
e.g., with the Rcmdr package under R 4.0.2 on both macOS and Windows.
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or ... ?
I have qpdf installed, and am running R CMD build with
--compact-vignettes, but the PDF in the tarball doesn't seem to be
compressed despite the fact that the output messages say "compacting
vignettes ..."
$ R CMD build --compact-vignettes lme4
* checking for file ‘lme4/DESCRIPTION’ ... OK
* preparing ‘lme4’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent
rebuilding.
* compacting vignettes and other PDF files
* cleaning src
* checking for LF line-endings in source and make files and shell
scripts
* checking for empty or unneeded directories
* building ‘lme4_1.1-24.tar.gz’
The copy of lmer.pdf in the resulting tarball is 900K or so:
$ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf
-rw-r--r-- bolker/bolker 907022 2020-10-05 12:59
lme4/inst/doc/lmer.pdf
The previously built (and manually compacted) version of
lmer.pdf
in the tarball is 500K:
$ ls -l lme4/inst/doc/lmer.pdf
-rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15
lme4/inst/doc/lmer.pdf
Is 'R CMD build' confused by the presence of a pre-built
PDF in
the inst/doc directory? Or am I somehow mistaken about how this is
supposed to work?
I would just use --no-build-vignettes and submit the
tarball with
the previously built/compressed PDF, but I'm trying to avoid a
"Package has a VignetteBuilder field but no prebuilt vignette index"
NOTE, which I assume is missing because I built without building
vignettes ... ?
As always, enlightenment is welcome.
cheers
Ben Bolker
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Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
On 07/10/2020 8:32 p.m., Ben Bolker wrote:
Thanks for the tip, I'll take a look.
Given that three relatively experienced package authors all seem to
have experienced similar issues, it seems that maybe this is worth
figuring out/maybe I'm not just doing something boneheaded.
Just to clarify: I've never noticed the problem you mention. I just
know how to debug R CMD build.
Duncan
cheers
Ben
On 10/7/20 8:31 PM, Duncan Murdoch wrote:
I don't know the answer to your question, but you can debug the
--compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
where "pkgdir" is the directory of the source of your package. Add
extra options to the build as separate elements of the argument to
.build(): this function is called after args have been parsed.
When I do that, I see that it rejects the compaction, because none of
mine benefit much from it: it wants at least a 10% and 10K reduction.
But Ben's example met those criteria. When I trick it into accepting
the compaction, it does put the compacted PDF into the tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
Dear Ben,
On 2020-10-07 5:26 p.m., Ben Bolker wrote:
I hope so too. The (annoying) workaround is to compact the vignette
yourself (using qpdf directly or using tools::compactPDF), then use
no-build-vignettes. The problem there is whatever's supposed to happen
with building vignette indices. The ugly workaround, I guess, is to
build the tarball, compact the vignettes oneself, then *replace* them in
the tarball. (Obviously I can automate that, but it seems as though it
would be unnecessary if I knew what was going on ...)
I've used both of these workarounds and agree that it would be nice to
avoid them. After all, what is the --compact-vignettes argument for?
Best,
John
cheers
Ben
On 10/7/20 4:10 PM, John Fox wrote:
Dear Ben,
I was hoping that someone would pick up on this problem, because I've
experienced the same issue of --compact-vignettes apparently ignored,
e.g., with the Rcmdr package under R 4.0.2 on both macOS and Windows.
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or ... ?
I have qpdf installed, and am running R CMD build with
--compact-vignettes, but the PDF in the tarball doesn't seem to be
compressed despite the fact that the output messages say "compacting
vignettes ..."
$ R CMD build --compact-vignettes lme4
* checking for file ‘lme4/DESCRIPTION’ ... OK
* preparing ‘lme4’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent rebuilding.
* compacting vignettes and other PDF files
* cleaning src
* checking for LF line-endings in source and make files and shell
scripts
* checking for empty or unneeded directories
* building ‘lme4_1.1-24.tar.gz’
The copy of lmer.pdf in the resulting tarball is 900K or so:
$ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf
-rw-r--r-- bolker/bolker 907022 2020-10-05 12:59
lme4/inst/doc/lmer.pdf
The previously built (and manually compacted) version of lmer.pdf
in the tarball is 500K:
$ ls -l lme4/inst/doc/lmer.pdf
-rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15 lme4/inst/doc/lmer.pdf
Is 'R CMD build' confused by the presence of a pre-built PDF in
the inst/doc directory? Or am I somehow mistaken about how this is
supposed to work?
I would just use --no-build-vignettes and submit the tarball with
the previously built/compressed PDF, but I'm trying to avoid a
"Package has a VignetteBuilder field but no prebuilt vignette index"
NOTE, which I assume is missing because I built without building
vignettes ... ?
As always, enlightenment is welcome.
cheers
Ben Bolker
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https://stat.ethz.ch/mailman/listinfo/r-package-devel
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Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
Thanks for the tip, I'll take a look.
Given that three relatively experienced package authors all seem to
have experienced similar issues, it seems that maybe this is worth
figuring out/maybe I'm not just doing something boneheaded.
cheers
Ben
On 10/7/20 8:31 PM, Duncan Murdoch wrote:
I don't know the answer to your question, but you can debug the
--compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
where "pkgdir" is the directory of the source of your package. Add
extra options to the build as separate elements of the argument to
.build(): this function is called after args have been parsed.
When I do that, I see that it rejects the compaction, because none of
mine benefit much from it: it wants at least a 10% and 10K reduction.
But Ben's example met those criteria. When I trick it into accepting
the compaction, it does put the compacted PDF into the tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
Dear Ben,
On 2020-10-07 5:26 p.m., Ben Bolker wrote:
I hope so too. The (annoying) workaround is to compact the vignette
yourself (using qpdf directly or using tools::compactPDF), then use
no-build-vignettes. The problem there is whatever's supposed to happen
with building vignette indices. The ugly workaround, I guess, is to
build the tarball, compact the vignettes oneself, then *replace* them in
the tarball. (Obviously I can automate that, but it seems as though it
would be unnecessary if I knew what was going on ...)
I've used both of these workarounds and agree that it would be nice to
avoid them. After all, what is the --compact-vignettes argument for?
Best,
John
cheers
Ben
On 10/7/20 4:10 PM, John Fox wrote:
Dear Ben,
I was hoping that someone would pick up on this problem, because I've
experienced the same issue of --compact-vignettes apparently ignored,
e.g., with the Rcmdr package under R 4.0.2 on both macOS and Windows.
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or ... ?
I have qpdf installed, and am running R CMD build with
--compact-vignettes, but the PDF in the tarball doesn't seem to be
compressed despite the fact that the output messages say "compacting
vignettes ..."
$ R CMD build --compact-vignettes lme4
* checking for file ‘lme4/DESCRIPTION’ ... OK
* preparing ‘lme4’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent rebuilding.
* compacting vignettes and other PDF files
* cleaning src
* checking for LF line-endings in source and make files and shell
scripts
* checking for empty or unneeded directories
* building ‘lme4_1.1-24.tar.gz’
The copy of lmer.pdf in the resulting tarball is 900K or so:
$ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf
-rw-r--r-- bolker/bolker 907022 2020-10-05 12:59
lme4/inst/doc/lmer.pdf
The previously built (and manually compacted) version of lmer.pdf
in the tarball is 500K:
$ ls -l lme4/inst/doc/lmer.pdf
-rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15 lme4/inst/doc/lmer.pdf
Is 'R CMD build' confused by the presence of a pre-built PDF in
the inst/doc directory? Or am I somehow mistaken about how this is
supposed to work?
I would just use --no-build-vignettes and submit the tarball with
the previously built/compressed PDF, but I'm trying to avoid a
"Package has a VignetteBuilder field but no prebuilt vignette index"
NOTE, which I assume is missing because I built without building
vignettes ... ?
As always, enlightenment is welcome.
cheers
Ben Bolker
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https://stat.ethz.ch/mailman/listinfo/r-package-devel
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Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
I don't know the answer to your question, but you can debug the
--compact-vignettes option as follows.
debug(tools::compactPDF)
tools:::.build_packages(c("--compact-vignettes", "pkgdir"))
where "pkgdir" is the directory of the source of your package. Add
extra options to the build as separate elements of the argument to
.build(): this function is called after args have been parsed.
When I do that, I see that it rejects the compaction, because none of
mine benefit much from it: it wants at least a 10% and 10K reduction.
But Ben's example met those criteria. When I trick it into accepting
the compaction, it does put the compacted PDF into the tarball.
Duncan Murdoch
On 07/10/2020 6:03 p.m., John Fox wrote:
Dear Ben,
On 2020-10-07 5:26 p.m., Ben Bolker wrote:
I hope so too. The (annoying) workaround is to compact the vignette
yourself (using qpdf directly or using tools::compactPDF), then use
no-build-vignettes. The problem there is whatever's supposed to happen
with building vignette indices. The ugly workaround, I guess, is to
build the tarball, compact the vignettes oneself, then *replace* them in
the tarball. (Obviously I can automate that, but it seems as though it
would be unnecessary if I knew what was going on ...)
I've used both of these workarounds and agree that it would be nice to
avoid them. After all, what is the --compact-vignettes argument for?
Best,
John
cheers
Ben
On 10/7/20 4:10 PM, John Fox wrote:
Dear Ben,
I was hoping that someone would pick up on this problem, because I've
experienced the same issue of --compact-vignettes apparently ignored,
e.g., with the Rcmdr package under R 4.0.2 on both macOS and Windows.
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-10-05 1:09 p.m., Ben Bolker wrote:
Am I confused, or doing something wrong, or ... ?
I have qpdf installed, and am running R CMD build with
--compact-vignettes, but the PDF in the tarball doesn't seem to be
compressed despite the fact that the output messages say "compacting
vignettes ..."
$ R CMD build --compact-vignettes lme4
* checking for file ‘lme4/DESCRIPTION’ ... OK
* preparing ‘lme4’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent rebuilding.
* compacting vignettes and other PDF files
* cleaning src
* checking for LF line-endings in source and make files and shell
scripts
* checking for empty or unneeded directories
* building ‘lme4_1.1-24.tar.gz’
The copy of lmer.pdf in the resulting tarball is 900K or so:
$ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf
-rw-r--r-- bolker/bolker 907022 2020-10-05 12:59 lme4/inst/doc/lmer.pdf
The previously built (and manually compacted) version of lmer.pdf
in the tarball is 500K:
$ ls -l lme4/inst/doc/lmer.pdf
-rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15 lme4/inst/doc/lmer.pdf
Is 'R CMD build' confused by the presence of a pre-built PDF in
the inst/doc directory? Or am I somehow mistaken about how this is
supposed to work?
I would just use --no-build-vignettes and submit the tarball with
the previously built/compressed PDF, but I'm trying to avoid a
"Package has a VignetteBuilder field but no prebuilt vignette index"
NOTE, which I assume is missing because I built without building
vignettes ... ?
As always, enlightenment is welcome.
cheers
Ben Bolker
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R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?
Dear Ben, On 2020-10-07 5:26 p.m., Ben Bolker wrote: I hope so too. The (annoying) workaround is to compact the vignette yourself (using qpdf directly or using tools::compactPDF), then use no-build-vignettes. The problem there is whatever's supposed to happen with building vignette indices. The ugly workaround, I guess, is to build the tarball, compact the vignettes oneself, then *replace* them in the tarball. (Obviously I can automate that, but it seems as though it would be unnecessary if I knew what was going on ...) I've used both of these workarounds and agree that it would be nice to avoid them. After all, what is the --compact-vignettes argument for? Best, John cheers Ben On 10/7/20 4:10 PM, John Fox wrote: Dear Ben, I was hoping that someone would pick up on this problem, because I've experienced the same issue of --compact-vignettes apparently ignored, e.g., with the Rcmdr package under R 4.0.2 on both macOS and Windows. Best, John John Fox, Professor Emeritus McMaster University Hamilton, Ontario, Canada web: https://socialsciences.mcmaster.ca/jfox/ On 2020-10-05 1:09 p.m., Ben Bolker wrote: Am I confused, or doing something wrong, or ... ? I have qpdf installed, and am running R CMD build with --compact-vignettes, but the PDF in the tarball doesn't seem to be compressed despite the fact that the output messages say "compacting vignettes ..." $ R CMD build --compact-vignettes lme4 * checking for file ‘lme4/DESCRIPTION’ ... OK * preparing ‘lme4’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to process help pages * saving partial Rd database * creating vignettes ... OK Warning: ‘inst/doc’ files ‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’ ignored as vignettes have been rebuilt. Run R CMD build with --no-build-vignettes to prevent rebuilding. * compacting vignettes and other PDF files * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘lme4_1.1-24.tar.gz’ The copy of lmer.pdf in the resulting tarball is 900K or so: $ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf -rw-r--r-- bolker/bolker 907022 2020-10-05 12:59 lme4/inst/doc/lmer.pdf The previously built (and manually compacted) version of lmer.pdf in the tarball is 500K: $ ls -l lme4/inst/doc/lmer.pdf -rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15 lme4/inst/doc/lmer.pdf Is 'R CMD build' confused by the presence of a pre-built PDF in the inst/doc directory? Or am I somehow mistaken about how this is supposed to work? I would just use --no-build-vignettes and submit the tarball with the previously built/compressed PDF, but I'm trying to avoid a "Package has a VignetteBuilder field but no prebuilt vignette index" NOTE, which I assume is missing because I built without building vignettes ... ? As always, enlightenment is welcome. cheers Ben Bolker __ 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] is R CMD build --compact-vignettes working as expected?
I hope so too. The (annoying) workaround is to compact the vignette yourself (using qpdf directly or using tools::compactPDF), then use no-build-vignettes. The problem there is whatever's supposed to happen with building vignette indices. The ugly workaround, I guess, is to build the tarball, compact the vignettes oneself, then *replace* them in the tarball. (Obviously I can automate that, but it seems as though it would be unnecessary if I knew what was going on ...) cheers Ben On 10/7/20 4:10 PM, John Fox wrote: Dear Ben, I was hoping that someone would pick up on this problem, because I've experienced the same issue of --compact-vignettes apparently ignored, e.g., with the Rcmdr package under R 4.0.2 on both macOS and Windows. Best, John John Fox, Professor Emeritus McMaster University Hamilton, Ontario, Canada web: https://socialsciences.mcmaster.ca/jfox/ On 2020-10-05 1:09 p.m., Ben Bolker wrote: Am I confused, or doing something wrong, or ... ? I have qpdf installed, and am running R CMD build with --compact-vignettes, but the PDF in the tarball doesn't seem to be compressed despite the fact that the output messages say "compacting vignettes ..." $ R CMD build --compact-vignettes lme4 * checking for file ‘lme4/DESCRIPTION’ ... OK * preparing ‘lme4’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to process help pages * saving partial Rd database * creating vignettes ... OK Warning: ‘inst/doc’ files ‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’ ignored as vignettes have been rebuilt. Run R CMD build with --no-build-vignettes to prevent rebuilding. * compacting vignettes and other PDF files * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘lme4_1.1-24.tar.gz’ The copy of lmer.pdf in the resulting tarball is 900K or so: $ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf -rw-r--r-- bolker/bolker 907022 2020-10-05 12:59 lme4/inst/doc/lmer.pdf The previously built (and manually compacted) version of lmer.pdf in the tarball is 500K: $ ls -l lme4/inst/doc/lmer.pdf -rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15 lme4/inst/doc/lmer.pdf Is 'R CMD build' confused by the presence of a pre-built PDF in the inst/doc directory? Or am I somehow mistaken about how this is supposed to work? I would just use --no-build-vignettes and submit the tarball with the previously built/compressed PDF, but I'm trying to avoid a "Package has a VignetteBuilder field but no prebuilt vignette index" NOTE, which I assume is missing because I built without building vignettes ... ? As always, enlightenment is welcome. cheers Ben Bolker __ 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] is R CMD build --compact-vignettes working as expected?
Dear Ben, I was hoping that someone would pick up on this problem, because I've experienced the same issue of --compact-vignettes apparently ignored, e.g., with the Rcmdr package under R 4.0.2 on both macOS and Windows. Best, John John Fox, Professor Emeritus McMaster University Hamilton, Ontario, Canada web: https://socialsciences.mcmaster.ca/jfox/ On 2020-10-05 1:09 p.m., Ben Bolker wrote: Am I confused, or doing something wrong, or ... ? I have qpdf installed, and am running R CMD build with --compact-vignettes, but the PDF in the tarball doesn't seem to be compressed despite the fact that the output messages say "compacting vignettes ..." $ R CMD build --compact-vignettes lme4 * checking for file ‘lme4/DESCRIPTION’ ... OK * preparing ‘lme4’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to process help pages * saving partial Rd database * creating vignettes ... OK Warning: ‘inst/doc’ files ‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’ ignored as vignettes have been rebuilt. Run R CMD build with --no-build-vignettes to prevent rebuilding. * compacting vignettes and other PDF files * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘lme4_1.1-24.tar.gz’ The copy of lmer.pdf in the resulting tarball is 900K or so: $ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf -rw-r--r-- bolker/bolker 907022 2020-10-05 12:59 lme4/inst/doc/lmer.pdf The previously built (and manually compacted) version of lmer.pdf in the tarball is 500K: $ ls -l lme4/inst/doc/lmer.pdf -rw-r--r-- 1 bolker bolker 495199 Oct 3 22:15 lme4/inst/doc/lmer.pdf Is 'R CMD build' confused by the presence of a pre-built PDF in the inst/doc directory? Or am I somehow mistaken about how this is supposed to work? I would just use --no-build-vignettes and submit the tarball with the previously built/compressed PDF, but I'm trying to avoid a "Package has a VignetteBuilder field but no prebuilt vignette index" NOTE, which I assume is missing because I built without building vignettes ... ? As always, enlightenment is welcome. cheers Ben Bolker __ 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
