[BioC] Gviz output extra empty page on pdf device

[Hahne, Florian]

Hi Dan,
I introduced a bug in one of the development commits that called
grid.newpage() two times instead of only once. I may have fixed that bug
in a later commit but forgot to bump the version number, which is the
trigger for the build system in Seattle to recompile the package. So I
assume that a working version was committed to the svn but not made
available via the Bioconductor server.
Florian

On 2/24/14 3:28 PM, "Dan Du" <tooyoung at gmail.com> wrote:

>Hi Florian,
>
>Thanks for the commit. I also noticed that the new update magically
>eliminates the empty page.
>
>But it leaves me wonder, what is the actual cause... I can see from the
>svn, there is no real change to the package itself other than the
>version number bump. And from my test, it seems that it is indeed this
>version number change and probably the re-installation which did the
>trick I guess. 
>
>I think probably it is the way how I handle multiple R-devel versions
>and how libraries are shared that is causing the problem. Sorry for the
>noises and any time you have wasted.
>
>Best regards,
>Dan
>
>On Mon, 2014-02-24 at 10:55 +0000, Hahne, Florian wrote:
>> Hi Dan,
>> Thanks for the heads up. I think this issue is resolved in the latest
>> development version (1.7.8)
>> At least on the build machines in Seattle the vignette has been built
>> properly.
>> Florian
>> 
>> On 2/19/14 5:04 PM, "Dan Du" <tooyoung at gmail.com> wrote:
>> 
>> >Hi Florian and others,
>> >
>> >I have been testing some functions and parameters, and noticed
>>something
>> >odd when plotting tracks on a pdf device (postscript turns out fine),
>> >this only happens to some recent R-devel versions (tested on three
>> >r-devel builds Feb.3, Feb.14 and Feb.18), apparently the build machine
>> >in Seattle is not yet affected, which has a devel build on Jan.15. This
>> >happens to the most recent devel version of Gviz 1.7.7.
>> >
>> >Here is an example, can't really figure it why,
>> >#########################################
>> ># say using the 1st example of plotTracks, I will get one empty page
>> >before the real deal.
>> >#########################################
>> >pdf('test.Gviz.pdf')
>> >#postscript('test.Gviz.eps', fonts='sans') # this is ok...
>> >st <- c(2000000, 2070000, 2100000, 2160000)
>> >ed <- c(2050000, 2130000, 2150000, 2170000)
>> >str <- c("-", "+", "-", "-")
>> >gr <- c("Group1","Group2","Group1", "Group3")
>> >annTrack <- AnnotationTrack(start=st, end=ed, strand=str, chromosome=7,
>> >                            genome="hg19", feature="test", group=gr,
>> >                            id=paste("annTrack item", 1:4),
>> >                            name="annotation track foo",
>> >                            stacking="squish")
>> >ax <- GenomeAxisTrack()
>> >dt <- DataTrack(start=seq(min(st), max(ed), len=10), width=18000,
>> >data=matrix(runif(40), nrow=4), genome="hg19", chromosome=7,
>> >type="histogram", name="data track bar")
>> >## Now plot the tracks
>> >res <- plotTracks(list(ax, annTrack, dt))
>> >dev.off()
>> >#########################################
>> >
>> >#########################################
>> ># while it turns out fine for a normal multipage grid viewport, say the
>> >viewport clipping example of viewport()
>> >#########################################
>> >pdf('test.viewport.pdf')
>> >clip.demo <- function(i, j, clip1, clip2) {
>> >  pushViewport(viewport(layout.pos.col=i,
>> >                         layout.pos.row=j))
>> >  pushViewport(viewport(width=0.6, height=0.6, clip=clip1))
>> >  grid.rect(gp=gpar(fill="white"))
>> >  grid.circle(r=0.55, gp=gpar(col="red", fill="pink"))
>> >  popViewport()
>> >  pushViewport(viewport(width=0.6, height=0.6, clip=clip2))
>> >  grid.polygon(x=c(0.5, 1.1, 0.6, 1.1, 0.5, -0.1, 0.4, -0.1),
>> >               y=c(0.6, 1.1, 0.5, -0.1, 0.4, -0.1, 0.5, 1.1),
>> >               gp=gpar(col="blue", fill="light blue"))
>> >  popViewport(2)
>> >}
>> >
>> >grid.newpage()
>> >grid.rect(gp=gpar(fill="grey"))
>> >pushViewport(viewport(layout=grid.layout(2, 2)))
>> >clip.demo(1, 1, FALSE, FALSE)
>> >clip.demo(1, 2, TRUE, FALSE)
>> >clip.demo(2, 1, FALSE, TRUE)
>> >clip.demo(2, 2, TRUE, TRUE)
>> >popViewport()
>> ># Demonstrate turning clipping off
>> >grid.newpage()
>> >pushViewport(viewport(w=.5, h=.5, clip="on"))
>> >grid.rect()
>> >grid.circle(r=.6, gp=gpar(lwd=10))
>> >pushViewport(viewport(clip="inherit"))
>> >grid.circle(r=.6, gp=gpar(lwd=5, col="grey"))
>> >pushViewport(viewport(clip="off"))
>> >grid.circle(r=.6)
>> >popViewport(3)
>> ># Demonstrate vpList, vpStack, and vpTree
>> >grid.newpage()
>> >tree <- vpTree(viewport(w=0.8, h=0.8, name="A"),
>> >               vpList(vpStack(viewport(x=0.1, y=0.1, w=0.5, h=0.5,
>> >                                       just=c("left", "bottom"),
>> >name="B"),
>> >                              viewport(x=0.1, y=0.1, w=0.5, h=0.5,
>> >                                       just=c("left", "bottom"),
>> >name="C"),
>> >                              viewport(x=0.1, y=0.1, w=0.5, h=0.5,
>> >                                       just=c("left", "bottom"),
>> >name="D")),
>> >                      viewport(x=0.5, w=0.4, h=0.9,
>> >                               just="left", name="E")))
>> >pushViewport(tree)
>> >for (i in LETTERS[1:5]) {
>> >  seekViewport(i)
>> >  grid.rect()
>> >  grid.text(current.vpTree(FALSE),
>> >            x=unit(1, "mm"), y=unit(1, "npc") - unit(1, "mm"),
>> >            just=c("left", "top"),
>> >            gp=gpar(fontsize=8))
>> >}
>> >dev.off()
>> >#########################################
>> >
>> >I found that there has been a bug fix introduced in R-devel on Feb 2,
>>not
>> >sure if this is the cause. Also noticed some very recent commit
>>(r65013)
>> >to r-devel, will see if this changes anything.
>> >
>> ># R-devel news
>> >"Bug fix for pushing viewports in Œgrid¹ (reported by JJ Allaire and
>> >Kevin Ushey).
>> >NOTE for anyone poking around within the graphics engine display list
>> >(despite the warnings not to) that this changes what is recorded by
>> >Œgrid¹ on the graphics engine display list."
>> >
>> ># R-devel svn log
>> >r64901 | murrell | 2014-01-31 00:45:44 +0100 (Fri, 31 Jan 2014) | 1
>>line
>> >Changed paths:
>> >   M /trunk/doc/NEWS.Rd
>> >   M /trunk/src/library/grid/R/grid.R
>> >   M /trunk/src/library/grid/R/util.R
>> >   M /trunk/src/library/grid/R/viewport.R
>> >   M /trunk/src/library/grid/inst/doc/changes.txt
>> >   M /trunk/src/library/grid/src/grid.c
>> >   M /trunk/src/library/grid/src/grid.h
>> >
>> >bug fix for pushing grid viewports (only record viewport, NOT pushedvp,
>> >on graphics engine display list)
>> >
>> >Best regards,
>> >Dan
>> >
>> 
>
>