Report generation fails

[cbielow]

from @hugoagno3

Hi Chris, nice R package, I am somehow new in R, I got these errors. I do not know how to see the code in the package to try to fix those problems by myself. I did BSA digestion with two different buffers after the desalting step. Then I run max quant. I used a TRipletof Sciex for DDA. I got the following errors. I copy the TXT folder + the mqpar.xml. I run the example txt_20 minutes and it works well. But my experiment not. My code to run was:

library(PTXQC)
require(PTXQC)
require(methods)
txt_folder = "/home/hugo/Documents/QC hugo/Complexome dist tris Hepes"
r = createReport(txt_folder)
Errors (3 to 6- I think it is ggplot related). 1 and 2, I do not know these are the most important.
r = createReport(txt_folder)
#############################
Error in if (last > x[i] && up) { : missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In (function (parents, id = names(parents), name = id, obsolete = setNames(nm = id, :
Some parent terms not found: MS:1001456
2: In (function (parents, id = names(parents), name = id, obsolete = setNames(nm = id, :
Some parent terms not found: UO:0000000
3: guides(<scale> = FALSE) is deprecated. Please use guides(<scale> = "none") instead.
4: guides(<scale> = FALSE) is deprecated. Please use guides(<scale> = "none") instead.
5: guides(<scale> = FALSE) is deprecated. Please use guides(<scale> = "none") instead.
6: guides(<scale> = FALSE) is deprecated. Please use guides(<scale> = "none") instead.
############################################
Unfortunately, It did not create the pdf report.
Best,

[cbielow]

Hi @hugoagno3

mhh.. this is a bug on PTXQC-side. Could you please upload the txt folder+mqpar file somewhere. I will have a look. Thanks for reporting!

[hugoagno3]

Hi there, Thank you very much for your help. I upload this in my google drive link ( https://drive.google.com/file/d/1RC8kTG-gI8CAbX6ATI0yqh8_LH5-0D-V/view?usp=sharing ) I am Ph.D. student working in the proteomic facility of UMG (Göttingen, Germany), I find interesting your R package for QC.

Experiment: The sample is BSA digested in two different buffers. I expect to see the same pattern within buffers... and compare which is best. The BSA is a quality standard (high purity) in addition there are blanks for each buffer. The reads of spectra by peak view were between 3000 and the highest 7000. Please let me know if the zip works if not I can send it by wetransfer.

An extra detail I try in R Linux and R windows and the problems 3 to 6 disappears (scale="none" ) is a problem related to my R Linux about dplyr or ggplot . It happened before when I plotted Venn diagram by ggvenn package. When that happens it will plot things but in grey color, anyways I still can use another computer to run it with colors...

Thanks, best regards,

          Hugo.

https://drive.google.com/file/d/1RC8kTG-gI8CAbX6ATI0yqh8_LH5-0D-V/view?usp=sharing

El vie, 29 oct 2021 a las 16:46, Chris Bielow @.***>) escribió:

Hi @hugoagno3 https://github.com/hugoagno3

mhh.. this is a bug on PTXQC-side. Could you please upload the txt folder+mqpar file somewhere. I will have a look. Thanks for reporting!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/cbielow/PTXQC/issues/110#issuecomment-954803245, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATWQURDUPI6QFVEHR62FC4LUJK6T3ANCNFSM5G7P677A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[cbielow]

The bug is fixed, see #112.

The other things you see are 'just' warnings. Some of them are already fixed in the most recent version of PTXQC (which will become v1.0.12)

You can pull the latest changes by installing PTXQC from Github. Or wait a few days until the new version is published on CRAN.

Hope this helps.

cheers Chris