Listening on http://127.0.0.1:42893
Loading required package: bfabricShiny

Attaching package: 'bfabricShiny'

The following object is masked from 'package:base':

    save

saving 'login and webservicepassword' ...
In function read_workflowid
read bfabricposturl https://fgcz-c-072.uzh.ch:5000/.
Request started from user tobiasko
Bfabric query: workflow containerid = 33
Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(),  :
  query failed.
Warning: Error in $: $ operator is invalid for atomic vectors
  121: append
  120: <reactive:read_workflowid> [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125]
  104: read_workflowid
   97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#135]
   96: func
   83: renderFunc
   82: output$workflow
    1: runApp
In function read_workflowid
Bfabric query: workflow containerid = 331
Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(),  :
  query failed.
Warning: Error in $: $ operator is invalid for atomic vectors
  121: append [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125]
  120: <reactive:read_workflowid> [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125]
  104: read_workflowid
   97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#135]
   96: func
   83: renderFunc
   82: output$workflow
    1: runApp
In function read_workflowid
Bfabric query: workflow containerid = 33122
saving 'login and webservicepassword' ...
In function read_templatefile
Bfabric query: dataset id
Selected workflows ids: 4461

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4461
workflowtemplate step id  239 
workflowtemplate step id  271 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 57
workflowtemplate name: Proteomics Sample Preparation

Selected workflows ids: 4461
Selected workflows ids: 4481

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4461
workflowtemplate step id  239 
workflowtemplate step id  271 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 57
workflowtemplate name: Proteomics Sample Preparation

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4481
workflowtemplate step id  244 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 58
workflowtemplate name: Proteomics Data acquisition

Selected workflows ids: 4461
Selected workflows ids: 4481
Selected workflows ids: 4522

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4461
workflowtemplate step id  239 
workflowtemplate step id  271 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 57
workflowtemplate name: Proteomics Sample Preparation

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4481
workflowtemplate step id  244 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 58
workflowtemplate name: Proteomics Data acquisition

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4522
workflowtemplate step id  274 
workflowtemplate step id  273 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 59
workflowtemplate name: Proteomics Data analysis

Selected workflows ids: 4461
Selected workflows ids: 4481
Selected workflows ids: 4522
Selected workflows ids: 4524

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4461
workflowtemplate step id  239 
workflowtemplate step id  271 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 57
workflowtemplate name: Proteomics Sample Preparation

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4481
workflowtemplate step id  244 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 58
workflowtemplate name: Proteomics Data acquisition

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4522
workflowtemplate step id  274 
workflowtemplate step id  273 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 59
workflowtemplate name: Proteomics Data analysis

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4524
workflowtemplate step id  257 

In function read_workflowtemplate
Bfabric query: workflowtemplate workflowtemplateid = 60
workflowtemplate name: Proteomics Results

saving 'login and webservicepassword' ...
saving 'login and webservicepassword' ...
saving 'login and webservicepassword' ...
saving 'login and webservicepassword' ...
generateReport
In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4461
workflowtemplate step id  239 
workflowtemplate step id  271 

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4481
workflowtemplate step id  244 

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4522
workflowtemplate step id  274 
workflowtemplate step id  273 

In function read_steptemplateid
Bfabric query: workflowstep workflowid = 4524
workflowtemplate step id  257 



processing file: report.Rmd
output file: report.knit.md


Output created: fgcz_order_report-33122.pdf
bfabricUpload
bfabricUpload


Execution halted