ver 0.2.2 about survminer HOT 12 CLOSED

@kassambara

from survminer.

staticdocs is now updated: http://www.sthda.com/english/rpkgs/survminer/

from survminer.

Great, we can close the issue after submision to CRAN
https://cran.r-project.org/web/packages/survminer/index.html

from survminer.

Have you considered uploading this on CRAN? I am planning another blog post about new functions in survminer where I would create flexdashboard with full cox ph analysis with diagnostic plots from survminer :)

from survminer.

Hi Marcin,

I'm trying to do some checks before submitting v0.2.2.

I received the following message, after using devtools::build_win(), mentioning 2 errors:

Dear package maintainer,

this notification has been generated automatically.
Your package survminer_0.2.2.tar.gz has been built (if working) and checked for Windows.
Please check the log files and (if working) the binary package at:
http://win-builder.r-project.org/7eGnVpf7iT51
The files will be removed after roughly 72 hours.
Installation time in seconds: 11
Check time in seconds: 143
Status: 2 ERRORs, 1 WARNING, 3 NOTEs
R version 3.3.1 (2016-06-21)

All the best,
Uwe Ligges
(CRAN maintainer of binary packages for Windows)

Please check the log file at http://win-builder.r-project.org/7eGnVpf7iT51. The errors concerns particularly the example section of the function 'ggcoxdiagnostics()' as well as the vignette file (Informative_Survival_Plots.Rmd).

Question: Should we change the examples in these files to fix CRAN check errors?

For the function 'ggcoxdiagnostics()', we can use the function \donttest{} around the example section to avoid CRAN check.

Do you have any suggestion for the vignette file?

Best,
A.

from survminer.

I have seen such a topic on stackoverflow where one solution is to
http://stackoverflow.com/a/38577486/3857701
http://stackoverflow.com/questions/14343817/cran-package-depends-on-bioconductor-package-installing-error
add

This is not documented anywhere but the trick is that you add a line that
says biocViews: in your DESCRIPTION file (yes, it ends with a colon and
then no need to list anything, you can keep it blank). Then R will know to
check bioconductor repositories for the package requirements.

So I'll maybe add this to DESCRIPTION and you can configure AppVeyor (
https://ci.appveyor.com/projects/new) for windows checks (this is travis
for windows ) to let us know if checks passes on windows?

2016-07-27 14:37 GMT+02:00 Alboukadel KASSAMBARA [email protected]:

Hi Marcin,

I'm trying to do some checks before submitting v0.2.2.

I received the following message, after using devtools::build_win(),
mentioning 2 errors:

Dear package maintainer,

this notification has been generated automatically.
Your package survminer_0.2.2.tar.gz has been built (if working) and checked for Windows.
Please check the log files and (if working) the binary package at:http://win-builder.r-project.org/7eGnVpf7iT51
The files will be removed after roughly 72 hours.
Installation time in seconds: 11
Check time in seconds: 143
Status: 2 ERRORs, 1 WARNING, 3 NOTEs
R version 3.3.1 (2016-06-21)

All the best,
Uwe Ligges
(CRAN maintainer of binary packages for Windows)

Please check the log file at http://win-builder.r-project.org/7eGnVpf7iT51.
The errors concerns particularly the example section of the function
'ggcoxdiagnostics()' as well as the vignette file
(Informative_Survival_Plots.Rmd).

Question: Should we change the examples in these files to fix CRAN check
errors?

For the function 'ggcoxdiagnostics()', we can use the function \donttest{}
around the example section to avoid CRAN check.

Do you have any suggestion for the vignette file?

Best,
A.

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from survminer.

adding biocViews: in DESCRIPTION file doesn't seem to work (http://win-builder.r-project.org/hh21OsuUs8D4)

from survminer.

That's weird. I have added AppVeyor to my fork and it lists that cran-check checks for bioconductor package https://ci.appveyor.com/project/MarcinKosinski/survminer/build/1.0.2#L133 but I also receive a message that RTCGA.clinical can not be found, because was not installed.

Why this fails only for windows? Maybe we should contact cran-windows maintainers direclty? It has passed for Linux and Mac OS.

from survminer.

mail sent:-)!

from survminer.

The answer from Uwe Ligges:

On 27.07.2016 17:17, Alboukadel Kassambara wrote:
Dear Uwe Ligges,

Before submitting the update version (v0.2.2) of survminer, I did a
check on win-bulder that generated the following error:

"there is no package called 'RTCGA.clinical". (RTCGA.clinical is a bioconductor package.)

I'm wondering, why the check fails only for windows? It has passed for
Linux (Travis) and Mac OSX (local). Do you have any suggestion to fix
this error?

It is just not installed on winbuilder.
I will do that once you submit the new version, please write it in the sumission comments.

Anyway, you should also change inn your package that the checks do not require a suggested package: Please run code that requires the package only conditionally on its availability.

Best,
Uwe Ligges

from survminer.

So it should normally pass, if she'll add a binary to winbuilder repository
:)
Thanks Alboukadel.

2016-07-28 7:43 GMT+02:00 Alboukadel KASSAMBARA [email protected]:

The answer from Uwe Ligges:

On 27.07.2016 17:17, Alboukadel Kassambara wrote:
Dear Uwe Ligges,

Before submitting the update version (v0.2.2) of survminer, I did a
check on win-bulder that generated the following error:

"there is no package called 'RTCGA.clinical". (RTCGA.clinical is a
bioconductor package.)

I'm wondering, why the check fails only for windows? It has passed for
Linux (Travis) and Mac OSX (local). Do you have any suggestion to fix
this error?

It is just not installed on winbuilder.
I will do that once you submit the new version, please write it in the sumission comments.

Anyway, you should also change inn your package that the checks do not require a suggested package: Please run code that requires the package only conditionally on its availability.

Best,
Uwe Ligges

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You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
#48 (comment),
or mute the thread
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from survminer.

v0.2.2 on CRAN now... Thanks!!

from survminer.