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paternogbc / sensiPhy

R package to perform sensitivity analysis for comparative methods
http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12990/full
GNU General Public License v2.0
12 stars 4 forks source link

CRAN check: v0.7 #161

Closed paternogbc closed 7 years ago

paternogbc commented 7 years ago

Heys guys, I have solved most of the things. These still missing to be solved. Just keeping track.

Undocumented arguments in documentation object 'intra_clade_phyglm'
  ‘Vy’ ‘y.transf’ ‘model’

Documented arguments not in \usage in documentation object 'intra_samp_phyglm':
  ‘model’ ‘y.transf’

Undocumented arguments in documentation object 'intra_samp_phylm'
  ‘Vy’

Undocumented arguments in documentation object 'sensi_plot.influ.physig'
  ‘...’

Undocumented arguments in documentation object 'sensi_plot.sensiIntra_Clade'
  ‘graphs’

Documented arguments not in \usage in documentation object 'sensi_plot.sensiIntra_Influ':
  ‘param’

Documented arguments not in \usage in documentation object 'sensi_plot.sensiIntra_Samp':
  ‘param’

Undocumented arguments in documentation object 'sensi_plot.sensiTree_Clade'
  ‘graphs’

Documented arguments not in \usage in documentation object 'sensi_plot.sensiTree_Influ':
  ‘param’

Undocumented arguments in documentation object 'tree_intra_phyglm'
  ‘btol’
Documented arguments not in \usage in documentation object 'tree_intra_phyglm':
  ‘Vy’ ‘model’
caterinap commented 7 years ago

Ok are you working on it now? If not, I'm on it!

paternogbc commented 7 years ago

I have just pushed some changes. would go back to that later. But if you can go on it would be great! ;)

It would be good to run checks also in your computer and see if something else show up. Then update here =)

Thanks

caterinap commented 7 years ago

All good (fixed commit ee0127c). Concerning the check I still have two warnings that will be fixed when you will rebuild the documentation. No errrors but 1 note:

checking package dependencies ... NOTE
Package suggested but not available for checking: 'rmarkdown'
paternogbc commented 7 years ago

You are right!

deepinscreenshot_20170902000707

@caterinap and @gijsbertwerner could you please run CRAN checks on your computers, after updating R and Rstudio to the last version, and report the results here? Also, could you please add the details of your system ('field using plataform') from the output.

* using platform: x86_64-pc-linux-gnu (64-bit)
caterinap commented 7 years ago

Sure @paternogbc ! Can you just push the new documentation to master so we are all on the same page?

paternogbc commented 7 years ago

sorry. it is update now =)

caterinap commented 7 years ago

SUCCESS!

* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)

image

(some examples are still a bit long to run, we could reduce the number of iterations but I guess it's also ok as it is)

Well done everybody 🥇

gijsbertwerner commented 7 years ago

Running mine now!

Dr. Gijsbert Werner Newton Fellow, Department of Zoology Junior Research Fellow, Balliol College University of Oxford

Balliol College Broad Street Oxford OX1 3BJ United Kingdom

On 1 Sep 2017, at 15:48, Caterina Penone notifications@github.com<mailto:notifications@github.com> wrote:

SUCCESS!

[image]https://user-images.githubusercontent.com/6351295/29975034-3ff0cd40-8f35-11e7-8354-8115628c9e08.png

(some examples are still a bit long to run, we could reduce the number of iterations but I guess it's also ok as it is)

Well done everybody 🥇

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/paternogbc/sensiPhy/issues/161#issuecomment-326600473, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGauyNzqf86IMPhNc9rBzlOcWyVJzitbks5seBkigaJpZM4PJxFS.

gijsbertwerner commented 7 years ago

YES SUCCESS TOO!!!!!

Status: OK

R CMD check results 0 errors | 0 warnings | 0 notes

My computer is clearly quite a bit slower than yours, Caterina, but this is my slow laptop so no worries.

Systems stuff:

We did it!!!

Dr. Gijsbert Werner Newton Fellow, Department of Zoology Junior Research Fellow, Balliol College University of Oxford

Balliol College Broad Street Oxford OX1 3BJ United Kingdom

On 1 Sep 2017, at 15:48, Caterina Penone notifications@github.com<mailto:notifications@github.com> wrote:

SUCCESS!

[image]https://user-images.githubusercontent.com/6351295/29975034-3ff0cd40-8f35-11e7-8354-8115628c9e08.png

(some examples are still a bit long to run, we could reduce the number of iterations but I guess it's also ok as it is)

Well done everybody 🥇

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/paternogbc/sensiPhy/issues/161#issuecomment-326600473, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGauyNzqf86IMPhNc9rBzlOcWyVJzitbks5seBkigaJpZM4PJxFS.

paternogbc commented 7 years ago

Very nice guys =) It is wierd but TRAVIS still gives the following error:

checking PDF version of manual without hyperrefs or index ... ERRORchecking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Something's wrong--perhaps a missing \item.
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
caterinap commented 7 years ago

Looks that you fixed it! Well done!

paternogbc commented 7 years ago

There still some small problems with CRAN check. I am not sure if it is system dependent or something else, but working on it. But I should finish today together with the online tutorial. Then you can have a look on that before I submit the manuscript =) Lets say tonight or Tuesday morning!

paternogbc commented 7 years ago

Found the problem! =) Submitting to CRAN right now.