[R-pkg-devel] CRAN upload and prechecking confusion - R-package-devel

Thu, Aug 24, 2017 12:28 AM #

Hello,

I'm trying to submit a new version (0.10.2) of my package
(multipanelfigure) to CRAN and have received the following email:

This is confusing. What's the deal breaker? 
The 2 Notes (which are timing issues related to drawing grid graphics)
or 
the Error on x86_64-apple-darwin15.6.0 which is based on the fact that
gridGraphics is unavailable for that platform and even more
confungsingly seems to be based on the former version (0.9.0) of the
package ...

Thanks for any hints.

Sincerely, Joh

Brian G. Peterson

Thu, Aug 24, 2017 12:59 AM #

On 08/24/2017 02:28 AM, Johannes Graumann wrote:

The URL's you've referenced have both expired.

I would suggest re-running your package checks using R-devel on RHub and 
Winbuilder first, and copying any output you receive.

Then it will be easier for others to help you.

Regards,

Brian

Brian G. Peterson
http://braverock.com/brian/
Ph: 773-459-4973
IM: bgpbraverock

Pedro J. Aphalo

Thu, Aug 24, 2017 1:39 AM #

Hello,

The version currently in CRAN fails the check on for 
r-release-osx-x86_64 with ERROR.

https://cran.r-project.org/web/checks/check_results_multipanelfigure.html 
shows this.

In general maintainers are expected to solve ERRORs when submitting a 
new version. If this is impossible, then you should explain in the 
submission message why you cannot solve the problem that you are in 
principle required to solve according to the submission form you fill-in 
in CRAN.

As the cause the ERROR is that your package depends on a package that is 
unavailable under r-release-osx-x86_64, an explanation in the submission 
message should be enough, I think.

Regards,

Pedro.

On 2017-08-24 10:59, Brian G. Peterson wrote:

------------------------------------------------------------------------
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(Office 4417, Biocenter 3, Viikinkaari 1)

Department of Biosciences
Plant Biology
P.O. Box 65
00014 University of Helsinki
Finland

e-mail: pedro.aphalo at helsinki.fi <mailto:pedro.aphalo at helsinki.fi>
Tel. (mobile) +358 50 4150623
Tel. (office) +358 2941 57897

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Web site (own teaching): http://www.helsinki.fi/people/pedro.aphalo/
Web site (using R in photobiology): http://www.r4photobiology.info/
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Johannes Graumann

Thu, Aug 24, 2017 1:45 AM #

On Thu, 2017-08-24 at 02:59 -0500, Brian G. Peterson wrote:

Thank you for that hint. I run on https://builder.r-hub.io and as on my
own arch systems, there appears to be NO issue with the package using
debian:
2591#> About to run xvfb-run R CMD check multipanelfigure_0.10.2.tar.gz
2592#> * using log directory ?/home/docker/multipanelfigure.Rcheck?
2593#> * using R Under development (unstable) (2017-08-19 r73108)
2594#> * using platform: x86_64-pc-linux-gnu (64-bit)
2595#> * using session charset: UTF-8
2596#> * checking for file ?multipanelfigure/DESCRIPTION? ... OK
2597#> * checking extension type ... Package
2598#> * this is package ?multipanelfigure? version ?0.10.2?
2599#> * checking package namespace information ... OK
2600#> * checking package dependencies ... OK
2601#> * checking if this is a source package ... OK
2602#> * checking if there is a namespace ... OK
2603#> * checking for executable files ... OK
2604#> * checking for hidden files and directories ... OK
2605#> * checking for portable file names ... OK
2606#> * checking for sufficient/correct file permissions ... OK
2607#> * checking whether package ?multipanelfigure? can be installed
... OK
2608#> * checking installed package size ... OK
2609#> * checking package directory ... OK
2610#> * checking ?build? directory ... OK
2611#> * checking DESCRIPTION meta-information ... OK
2612#> * checking top-level files ... OK
2613#> * checking for left-over files ... OK
2614#> * checking index information ... OK
2615#> * checking package subdirectories ... OK
2616#> * checking R files for non-ASCII characters ... OK
2617#> * checking R files for syntax errors ... OK
2618#> * checking whether the package can be loaded ... OK
2619#> * checking whether the package can be loaded with stated
dependencies ... OK
2620#> * checking whether the package can be unloaded cleanly ... OK
2621#> * checking whether the namespace can be loaded with stated
dependencies ... OK
2622#> * checking whether the namespace can be unloaded cleanly ... OK
2623#> * checking loading without being on the library search path ...
OK
2624#> * checking dependencies in R code ... OK
2625#> * checking S3 generic/method consistency ... OK
2626#> * checking replacement functions ... OK
2627#> * checking foreign function calls ... OK
2628#> * checking R code for possible problems ... OK
2629#> * checking Rd files ... OK
2630#> * checking Rd metadata ... OK
2631#> * checking Rd cross-references ... OK
2632#> * checking for missing documentation entries ... OK
2633#> * checking for code/documentation mismatches ... OK
2634#> * checking Rd \usage sections ... OK
2635#> * checking Rd contents ... OK
2636#> * checking for unstated dependencies in examples ... OK
2637#> * checking contents of ?data? directory ... OK
2638#> * checking data for non-ASCII characters ... OK
2639#> * checking data for ASCII and uncompressed saves ... OK
2640#> * checking installed files from ?inst/doc? ... OK
2641#> * checking files in ?vignettes? ... OK
2642#> * checking examples ... OK
2643#> * checking for unstated dependencies in vignettes ... OK
2644#> * checking package vignettes in ?inst/doc? ... OK
2645#> * checking running R code from vignettes ...
2646#> ?panel-positioning.Rmd? ... OK
2647#> ?scaling-clipping-images.Rmd? ... OK
2648#> NONE
2649#> * checking re-building of vignette outputs ... OK
2650#> * checking PDF version of manual ... OK
2651#> * DONE
2652#> Status: OK

Am rerunning on windows now ...

Sincerely, Joh

Ege Rubak

Thu, Aug 24, 2017 2:02 AM #

Hello,

Maybe you could start by writing a polite email to Paul Murrell (the 
maintainer of `gridGraphics` according to 
https://cran.r-project.org/package=gridGraphics) and ask if he is aware 
that his package fails on OSX on CRAN.

If you are lucky he might be able to quickly fix the issue and send a 
new version to CRAN.

Regards,
Ege

On 08/24/2017 10:39 AM, Pedro J. Aphalo wrote:

Hello,

The version currently in CRAN fails the check on for
r-release-osx-x86_64 with ERROR.

https://cran.r-project.org/web/checks/check_results_multipanelfigure.html
shows this.

In general maintainers are expected to solve ERRORs when submitting a
new version. If this is impossible, then you should explain in the
submission message why you cannot solve the problem that you are in
principle required to solve according to the submission form you fill-in
in CRAN.

As the cause the ERROR is that your package depends on a package that is
unavailable under r-release-osx-x86_64, an explanation in the submission
message should be enough, I think.

Regards,

Pedro.


On 2017-08-24 10:59, Brian G. Peterson wrote:

On 08/24/2017 02:28 AM, Johannes Graumann wrote:

Hello,

I'm trying to submit a new version (0.10.2) of my package
(multipanelfigure) to CRAN and have received the following email:

Dear maintainer,
   package multipanelfigure_0.10.2.tar.gz does not pass the incoming
checks automatically, please see the pre-test at:
<https://win-builder.r-project.org/incoming_pretest/170824_085724_mul
tipanelfigure_0102/00check.log>
Status: 2 NOTEs
   Current CRAN status: ERROR: 1, OK: 10
See: <https://CRAN.R-project.org/web/checks/check_results_multipanelf
igure.html>

This is confusing. What's the deal breaker?
The 2 Notes (which are timing issues related to drawing grid graphics)
or
the Error on x86_64-apple-darwin15.6.0 which is based on the fact that
gridGraphics is unavailable for that platform and even more
confungsingly seems to be based on the former version (0.9.0) of the
package ...

The URL's you've referenced have both expired.

I would suggest re-running your package checks using R-devel on RHub
and Winbuilder first, and copying any output you receive.

Then it will be easier for others to help you.

Regards,

Brian

Johannes Graumann

Thu, Aug 24, 2017 4:43 AM #

On Thu, 2017-08-24 at 02:59 -0500, Brian G. Peterson wrote:

Have a look hier:
https://builder.r-hub.io/status/multipanelfigure_0.10.2.tar.gz-7184a1dc
6654eaea5463f8cc9cac3f73
https://builder.r-hub.io/status/multipanelfigure_0.10.2.tar.gz-033531ed
74ed5a90ce66bac077293e3c
https://builder.r-hub.io/status/multipanelfigure_0.10.2.tar.gz-1c5377c9
369c4936e0c5e1a81c863275

Linux & windows work. OSX fails because gridGraphics (currently) does
not exist for the platform.

In the meantime CRAN (Uwe Ligges) got back telling me the problem is
long timing in an example ... this is based on grid speed and as the
package heavily uses that I feel uncomfortable moving the example to
'dontrun' ... thoughts.

Sincerely, Joh