Missing y label

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Missing y label

Therneau, Terry M., Ph.D.
My on-screen plots with the latest build are acting strange.  If the y label is longer
than some small value it is not shown.

Here is the script of a job.  A pdf graph is fine.  I use xubuntu as the windowing system.


tmt-local1334% R --vanilla

R Under development (unstable) (2017-08-31 r73172) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

 > sessionInfo()
R Under development (unstable) (2017-08-31 r73172)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/local/src/R-devel/lib/libRblas.so
LAPACK: /usr/local/src/R-devel/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] compiler_3.5.0
 > plot(1:5, 1:5, ylab="abcde")  # has a y label
 > plot(1:5, 1:5, ylab="abcdefghi")  # no label

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Re: Missing y label

Martin Maechler
>>>>> Therneau, Terry M , Ph D <[hidden email]>
>>>>>     on Thu, 31 Aug 2017 16:08:24 -0500 writes:

    > My on-screen plots with the latest build are acting
    > strange.  If the y label is longer than some small value it is not shown.

[MM: moved the important part of the script up here:]

    plot(1:5, 1:5, ylab="abcde")  # has a y label

    plot(1:5, 1:5, ylab="abcdefghi")  # no label

That is amazing.
I don't see a problem here (Linux Fedora F24, or F26, in both
case using GNOME as windowing system),
also with this, both interactive or pdf :

plot(1:5, 1:5, ylab="abcdefghi or even quite an order of magnitude longer")

pdf("long-ylab.pdf")
plot(1:5, 1:5, ylab="abcdefghi or even quite an order of magnitude longer")
dev.off(); system("evince long-ylab.pdf &")

I have no further idea but guess this must be specific to your platform.

Did you try the same thing with R 3.4.1?
Did you install both in the same way -- from the sources ??

Best,
Martin


    > Here is the script of a job.  A pdf graph is fine.  I use xubuntu as the windowing system.


    > tmt-local1334% R --vanilla

    > R Under development (unstable) (2017-08-31 r73172) -- "Unsuffered Consequences"
    > Copyright (C) 2017 The R Foundation for Statistical Computing
    > Platform: x86_64-pc-linux-gnu (64-bit)

    [.........]
    >> sessionInfo()
    > R Under development (unstable) (2017-08-31 r73172)
    > Platform: x86_64-pc-linux-gnu (64-bit)
    > Running under: Ubuntu 16.04.2 LTS

    > Matrix products: default
    > BLAS: /usr/local/src/R-devel/lib/libRblas.so
    > LAPACK: /usr/local/src/R-devel/lib/libRlapack.so

    > locale:
    > [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    > [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
    > [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    > [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    > [9] LC_ADDRESS=C               LC_TELEPHONE=C
    > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

    > loaded via a namespace (and not attached):
    > [1] compiler_3.5.0

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Re: Missing y label

Therneau, Terry M., Ph.D.
Martin,
   Thanks for taking a quick look.  Yes it looks like it must be something local.
I've done the following to make sure I have a clean box:
   reboot
   sudo apt-get update
   sudo apt-get upgrade

Rerun the "svn up" command and do a
    make distclean
    svn up
    tools/rsync-recommended
    ./configure
    make

The problem persists in 2017-09-01 r73179
I pulled the source code for 3.4-1 and compiled it, the problem persists.

I then did sudo apt-get install R, which installs version 3.2.3 on the machine.  The plots
work as expected there.

The new plots are the same size, same layout and margins, but the text and lines are
definitely thinner.  According to the package manager I have the latest version of
texlive-fonts-extra.

I don't see how to get it to pull a newer compiled version than 3.2.

Anything else that would help?

Terry T.




On 09/01/2017 02:37 AM, Martin Maechler wrote:

>      > My on-screen plots with the latest build are acting
>      > strange.  If the y label is longer than some small value it is not shown.
>
> [MM: moved the important part of the script up here:]
>
>      plot(1:5, 1:5, ylab="abcde")  # has a y label
>
>      plot(1:5, 1:5, ylab="abcdefghi")  # no label
>
> That is amazing.
> I don't see a problem here (Linux Fedora F24, or F26, in both
> case using GNOME as windowing system),
> also with this, both interactive or pdf :
>
> plot(1:5, 1:5, ylab="abcdefghi or even quite an order of magnitude longer")
>
> pdf("long-ylab.pdf")
> plot(1:5, 1:5, ylab="abcdefghi or even quite an order of magnitude longer")
> dev.off(); system("evince long-ylab.pdf &")
>
> I have no further idea but guess this must be specific to your platform.
>
> Did you try the same thing with R 3.4.1?
> Did you install both in the same way -- from the sources ??

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Re: Missing y label

Dirk Eddelbuettel

On 1 September 2017 at 14:28, Therneau, Terry M., Ph.D. wrote:
| Martin,
|    Thanks for taking a quick look.  Yes it looks like it must be something local.
| I've done the following to make sure I have a clean box:
|    reboot
|    sudo apt-get update
|    sudo apt-get upgrade
|
| Rerun the "svn up" command and do a
|     make distclean
|     svn up
|     tools/rsync-recommended
|     ./configure
|     make
|
| The problem persists in 2017-09-01 r73179
| I pulled the source code for 3.4-1 and compiled it, the problem persists.
|
| I then did sudo apt-get install R, which installs version 3.2.3 on the machine.  The plots
| work as expected there.

Read the fine README here:  https://cloud.r-project.org/bin/linux/ubuntu/README.html
Similar one for Debian at   https://cloud.r-project.org/bin/linux/debian/

Many of us have been using R from CRAN on Ubuntu and Debian for many years,
and many update cycles.  I try hard to get new R versions into Debian the
morning of the release [1] and Michael and Johannes usually produce binary
for the mirrors within a day or two too. On this box still running 16.10:

edd@bud:~$ apt-cache policy r-base-core
r-base-core:
  Installed: 3.4.1-2yakkety0
  Candidate: 3.4.1-2yakkety0
  Version table:
 *** 3.4.1-2yakkety0 500
        500 https://cloud.r-project.org/bin/linux/ubuntu yakkety/ Packages
        100 /var/lib/dpkg/status
     3.4.1-1yakkety0 500
        500 https://cloud.r-project.org/bin/linux/ubuntu yakkety/ Packages
     3.4.0-1yakkety0 500
        500 https://cloud.r-project.org/bin/linux/ubuntu yakkety/ Packages
     3.3.3-1yakkety0 500
        500 https://cloud.r-project.org/bin/linux/ubuntu yakkety/ Packages
     3.3.2-1yakkety0 500
        500 https://cloud.r-project.org/bin/linux/ubuntu yakkety/ Packages
     3.3.1-1build1 500
        500 http://us.archive.ubuntu.com/ubuntu yakkety/universe amd64 Packages
edd@bud:~$


Dirk

[1] And once every couple of years I get to do it on a high-speed train...


--
http://dirk.eddelbuettel.com | @eddelbuettel | [hidden email]

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Re: Missing y label

Therneau, Terry M., Ph.D.
I did read that fine file.
I added the following line to my /etc/apt/sources.list file:

tmt-local2023% tail -2 /etc/apt/sources.list
# R sources
deb https://mirror.las.iastate.edu/bin/linux/ubuntu xenial/

Here is what apt says on my machine

tmt-local2024% apt-cache policy r-base-core r-base-core: Installed: 3.2.3-4 Candidate:
3.2.3-4 Version table: *** 3.2.3-4 500 500 http://us.archive.ubuntu.com/ubuntu 
xenial/universe amd64 Packages 100 /var/lib/dpkg/status My long term habit is to stick to
LTS versions, which currently is 16.04: "still running 16.10" is a different outlook. The
system admins here tend to be more conservative than me. Again, thanks for any input.
Getting this particular box straightened out quickly isn't critical, but I would like to
understand the root of the issue. Terry T.

On 09/01/2017 02:58 PM, Dirk Eddelbuettel wrote:

> Read the fine README here:https://cloud.r-project.org/bin/linux/ubuntu/README.html
> Similar one for Debian athttps://cloud.r-project.org/bin/linux/debian/
>
> Many of us have been using R from CRAN on Ubuntu and Debian for many years,
> and many update cycles.  I try hard to get new R versions into Debian the
> morning of the release [1] and Michael and Johannes usually produce binary
> for the mirrors within a day or two too. On this box still running 16.10:
>
> edd@bud:~$ apt-cache policy r-base-core
> r-base-core:
>    Installed: 3.4.1-2yakkety0
>    Candidate: 3.4.1-2yakkety0
>    Version table:
>   *** 3.4.1-2yakkety0 500
>    


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Re: Missing y label

Dirk Eddelbuettel

On 1 September 2017 at 15:50, Therneau, Terry M., Ph.D. wrote:
| The system admins here ...

I suggest you get these local admins to help you.

These CRAN repos for Ubuntu are used by thousands of people every day, and
they "just work", for both the recent releases and the most recent LTS.

Dirk

--
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