Error in reading the report format

[Vy5HAGit]

Hello I am trying to upload my report into pavian and it;s saying it can read the file format

it's a .txt file

[SilasK]

I aslo tried to upload a kraken2 report with a custom database. I don't know do you only suport default db or only bracken reports?

[emi-panzetta]

Hi! I installed Pavian and I'm trying to use Metaphlan3 output files which are .txt. But I get this : "The following files did not conform the report format". Were you able to find a solution?

Error message:
Warning: File C:/Users/MARIAE~1/AppData/Local/Temp/Rtmpa04HKP/d5cbd7a481490ec0ee8c0a05/X.profile.txt does not have the required format
'data.frame': 5 obs. of 4 variables:
$ k__Bacteria: chr "k__Bacteria|p__Firmicutes" "k__Bacteria|p__Bacteroidetes" "k__Bacteria|p__Proteobacteria" "k__Bacteria|p__Verrucomicrobia" ...
$ 2 : chr "2|1239" "2|976" "2|1224" "2|74201" ...
$ 100.0 : num 61.963 33.352 3.213 1.016 0.456
$ : logi NA NA NA NA NA

[emi-panzetta]

Hi! I installed Pavian and I'm trying to use Metaphlan3 output files which are .txt. But I get this : "The following files did not conform the report format". Were you able to find a solution?

Error message:
Warning: File C:/Users/MARIAE~1/AppData/Local/Temp/Rtmpa04HKP/d5cbd7a481490ec0ee8c0a05/X.profile.txt does not have the required format
'data.frame': 5 obs. of 4 variables:
$ k__Bacteria: chr "k__Bacteria|p__Firmicutes" "k__Bacteria|p__Bacteroidetes" "k__Bacteria|p__Proteobacteria" "k__Bacteria|p__Verrucomicrobia" ...
$ 2 : chr "2|1239" "2|976" "2|1224" "2|74201" ...
$ 100.0 : num 61.963 33.352 3.213 1.016 0.456
$ : logi NA NA NA NA NA

I also tried this : #48

[evezeyl]

Same problem here.
Tested with a file that previously worked. This file does not work anymore.
Seems that this occurred after dependencies for the shiny app were updated

[fbreitwieser]

Hi @Vy5HAGit , @SilasK , @evezeyl , can you provide example files that don't work? Thanks!

[evezeyl]

61225_report.txt
I previously could make report with this file. Because I encountered a problem with a new run, I used it to test if it was a problem with my new run (with kraken2 output) or with pavian. It is not read anymore.
Some package have been updated, unfortunately I do not have session Info when it worked.

Screenshot of the error message I get when trying to upload the report file, and current R session Info bellow. I hope this helps.
All the best. Eve

Here is R session info
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS: /home/evezeyl/bin/R/4.0.0_GWAS/lib/R/lib/libRblas.so
LAPACK: /home/evezeyl/bin/R/4.0.0_GWAS/lib/R/lib/libRlapack.so

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

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

other attached packages:
[1] shiny_1.6.0 pavian_1.0.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 jquerylib_0.1.3 bslib_0.2.4 pillar_1.6.0 compiler_4.0.0
[6] later_1.1.0.1 shinyWidgets_0.6.0 shinyjs_2.0.0 tools_4.0.0 digest_0.6.27
[11] jsonlite_1.7.2 lifecycle_1.0.0 tibble_3.1.0 gtable_0.3.0 pkgconfig_2.0.3
[16] rlang_0.4.10 DBI_1.1.1 crosstalk_1.1.1 yaml_2.2.1 fastmap_1.1.0
[21] dplyr_1.0.5 sass_0.3.1 generics_0.1.0 vctrs_0.3.7 htmlwidgets_1.5.3
[26] DT_0.17 shinydashboard_0.7.1 grid_4.0.0 tidyselect_1.1.0 shinyFileTree_0.0.0.9000
[31] glue_1.4.2 R6_2.5.0 fansi_0.4.2 ggplot2_3.3.3 purrr_0.3.4
[36] magrittr_2.0.1 sankeyD3_0.3.2 scales_1.1.1 promises_1.2.0.1 ellipsis_0.3.1
[41] htmltools_0.5.1.1 assertthat_0.2.1 xtable_1.8-4 rhandsontable_0.3.7 mime_0.10
[46] colorspace_2.0-0 httpuv_1.5.5 utf8_1.2.1 munsell_0.5.0 cachem_1.0.4
[51] crayon_1.4.1

[fbreitwieser]

Hi @evezeyl , can you try updating once more? Pavian v1.1.0 should fix your issue again. Thanks!

[evezeyl]

Thanks! This is updated and working fine. Tested with large number of samples, no problem. All the best Eve

…

On Wed, Apr 14, 2021 at 9:17 AM Florian Breitwieser < ***@***.***> wrote: Hi @evezeyl <https://github.com/evezeyl> , can you try updating once more? Pavian v1.1.0 should fix your issue again. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#68 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK3TRDNSAU7EJ4NIPEUR5TTTIU6Q5ANCNFSM4QEAED6A> .

-- *Med vennlig hilsen/ best regards* Eve Zeyl Fiskebeck

--------------------------------------------------------------- Mobil: +47 45 41 56 90 email: ***@***.*** <https://no.linkedin.com/in/eve-fiskebeck-73a29bb>

[fbreitwieser]

Thanks for the info @evezeyl .

@SilasK , @Vy5HAGit , I'll close this issue , but please feel free to open a new one with a sample file if it doesn't work for you