Listening on http://127.0.0.1:40769
Loading required package: bfabricShiny

Attaching package: 'bfabricShiny'

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

    save

Loading required package: protViz
Loading required package: rawDiag
Loading required package: parallel
Loading required package: tidyr
Loading required package: rmarkdown
Loading required package: base64enc
Loading required package: ggplot2
Loading required package: lattice
Loading required package: PKI


#rows are 0
saving 'login and webservicepassword' ...
output$employee <- renderUI({
read bfabricposturl https://fgcz-c-072.uzh.ch:5000/.
Warning in .read(login = login, webservicepassword = webservicepassword,  :
  query failed.
bfabricConnectionWorking FALSE
output$employee <- renderUI({
Warning in .read(login = login, webservicepassword = webservicepassword,  :
  query failed.
bfabricConnectionWorking FALSE
output$employee <- renderUI({
bfabricConnectionWorking TRUE
'empdegree' found.
Warning in shinyStore::updateStore(session, "login", isolate(input$login),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "project", isolate(input$project),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "login", isolate(input$login),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "project", isolate(input$project),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "login", isolate(input$login),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "project", isolate(input$project),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "login", isolate(input$login),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "project", isolate(input$project),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_006_S588817_NCI-H1975_UTR_1to10_Group_1.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_007_S588818_NCI-H1975_PJ34_1to10_Group_2.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_008_S588819_NCI-H1975_RBN-2397_1to10_Group_3.raw qc ...
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed AGCPSMode to PrescanMode
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
#rows are 124126
output$tic.basepeak <- renderPlot({
#rows are 124126
output$download 2...
Warning in shinyStore::updateStore(session, "login", isolate(input$login),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "project", isolate(input$project),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
ggsave to file /tmp/Rtmp8btH1R/rawDiag-2d3a398d594b.pdf
generated pdf
/tmp/Rtmp8btH1R/rawDiag-2d3a398d594b.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 295912, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:05:16", createdby = "tobiasko", description = "input files:\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_007_S588818_NCI-H1975_PJ34_1to10_Group_2.raw \np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_008_S588819_NCI-H1975_RBN-2397_1to10_Group_3.raw\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_006_S588817_NCI-H1975_UTR_1to10_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", 
    exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2388450), list(`_classname` = "resource", `_id` = 2388449), list(`_classname` = "resource", `_id` = 2388448)), modified = "2023-11-10 16:05:16", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2390127, container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:05:17", createdby = "tobiasko", filechecksum = "90e194921e7227cdedbca8c734719324", junk = "false", modified = "2023-11-10 16:05:17", modifiedby = "tobiasko", name = "WU295912-20231110-1605-rawDiag.pdf", relativepath = "container_33066/workunit_295912/WU295912-20231110-1605-rawDiag.pdf", size = "140544", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33066/workunit_295912/WU295912-20231110-1605-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33066/workunit_295912/WU295912-20231110-1605-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295912)))
The current plot is available as workunit 295912
#rows are 124126
output$download 1...
Warning in shinyStore::updateStore(session, "login", isolate(input$login),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "project", isolate(input$project),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
output$scan.frequency <- renderPlot
Warning: Removed 29 rows containing missing values (`geom_line()`).
#rows are 124126
output$download 2...
ggsave to file /tmp/Rtmp8btH1R/rawDiag-2d3a394fec5a3.pdf
Warning: Removed 29 rows containing missing values (`geom_line()`).
generated pdf
/tmp/Rtmp8btH1R/rawDiag-2d3a394fec5a3.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 295913, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:05:28", createdby = "tobiasko", description = "input files:\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_007_S588818_NCI-H1975_PJ34_1to10_Group_2.raw \np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_008_S588819_NCI-H1975_RBN-2397_1to10_Group_3.raw\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_006_S588817_NCI-H1975_UTR_1to10_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", 
    exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2388450), list(`_classname` = "resource", `_id` = 2388449), list(`_classname` = "resource", `_id` = 2388448)), modified = "2023-11-10 16:05:28", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2390128, container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:05:30", createdby = "tobiasko", filechecksum = "ebba2e0c1206f2c6befef3f464b5281b", junk = "false", modified = "2023-11-10 16:05:30", modifiedby = "tobiasko", name = "WU295913-20231110-1605-rawDiag.pdf", relativepath = "container_33066/workunit_295913/WU295913-20231110-1605-rawDiag.pdf", size = "139073", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33066/workunit_295913/WU295913-20231110-1605-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33066/workunit_295913/WU295913-20231110-1605-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295913)))
The current plot is available as workunit 295913
#rows are 124126
output$download 1...
`geom_smooth()` using formula = 'y ~ x'
#rows are 124126
output$download 2...
ggsave to file /tmp/Rtmp8btH1R/rawDiag-2d3a393bf5da10.pdf
`geom_smooth()` using formula = 'y ~ x'
generated pdf
/tmp/Rtmp8btH1R/rawDiag-2d3a393bf5da10.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 295914, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:05:45", createdby = "tobiasko", description = "input files:\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_007_S588818_NCI-H1975_PJ34_1to10_Group_2.raw \np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_008_S588819_NCI-H1975_RBN-2397_1to10_Group_3.raw\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_006_S588817_NCI-H1975_UTR_1to10_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", 
    exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2388450), list(`_classname` = "resource", `_id` = 2388449), list(`_classname` = "resource", `_id` = 2388448)), modified = "2023-11-10 16:05:45", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2390129, container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:05:46", createdby = "tobiasko", filechecksum = "109ff113612386ba0d7bb7f6a63f44de", junk = "false", modified = "2023-11-10 16:05:46", modifiedby = "tobiasko", name = "WU295914-20231110-1605-rawDiag.pdf", relativepath = "container_33066/workunit_295914/WU295914-20231110-1605-rawDiag.pdf", size = "109244", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33066/workunit_295914/WU295914-20231110-1605-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33066/workunit_295914/WU295914-20231110-1605-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295914)))
The current plot is available as workunit 295914
#rows are 124126
output$download 1...
Warning: Removed 43 rows containing non-finite values (`stat_smooth()`).
Warning: Removed 43 rows containing missing values (`geom_line()`).
#rows are 124126
output$download 2...
ggsave to file /tmp/Rtmp8btH1R/rawDiag-2d3a3945839c3c.pdf
Warning: Removed 43 rows containing non-finite values (`stat_smooth()`).
Warning: Removed 43 rows containing missing values (`geom_line()`).
generated pdf
/tmp/Rtmp8btH1R/rawDiag-2d3a3945839c3c.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 295915, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:05:55", createdby = "tobiasko", description = "input files:\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_007_S588818_NCI-H1975_PJ34_1to10_Group_2.raw \np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_008_S588819_NCI-H1975_RBN-2397_1to10_Group_3.raw\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_006_S588817_NCI-H1975_UTR_1to10_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", 
    exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2388450), list(`_classname` = "resource", `_id` = 2388449), list(`_classname` = "resource", `_id` = 2388448)), modified = "2023-11-10 16:05:55", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2390130, container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:05:56", createdby = "tobiasko", filechecksum = "919ec30624bc440e618aaf677101a3c3", junk = "false", modified = "2023-11-10 16:05:56", modifiedby = "tobiasko", name = "WU295915-20231110-1605-rawDiag.pdf", relativepath = "container_33066/workunit_295915/WU295915-20231110-1605-rawDiag.pdf", size = "78567", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33066/workunit_295915/WU295915-20231110-1605-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33066/workunit_295915/WU295915-20231110-1605-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295915)))
The current plot is available as workunit 295915
#rows are 124126
output$download 1...
#rows are 124126
output$download 2...
ggsave to file /tmp/Rtmp8btH1R/rawDiag-2d3a39294fd70d.pdf
generated pdf
/tmp/Rtmp8btH1R/rawDiag-2d3a39294fd70d.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 295916, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:06:16", createdby = "tobiasko", description = "input files:\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_007_S588818_NCI-H1975_PJ34_1to10_Group_2.raw \np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_008_S588819_NCI-H1975_RBN-2397_1to10_Group_3.raw\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_006_S588817_NCI-H1975_UTR_1to10_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", 
    exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2388450), list(`_classname` = "resource", `_id` = 2388449), list(`_classname` = "resource", `_id` = 2388448)), modified = "2023-11-10 16:06:16", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2390131, container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:06:17", createdby = "tobiasko", filechecksum = "76e8d8f4bee79ef55ad596cf3bf91c23", junk = "false", modified = "2023-11-10 16:06:17", modifiedby = "tobiasko", name = "WU295916-20231110-1606-rawDiag.pdf", relativepath = "container_33066/workunit_295916/WU295916-20231110-1606-rawDiag.pdf", size = "660177", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33066/workunit_295916/WU295916-20231110-1606-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33066/workunit_295916/WU295916-20231110-1606-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295916)))
The current plot is available as workunit 295916
#rows are 124126
output$download 1...
#rows are 124126
output$download 2...
ggsave to file /tmp/Rtmp8btH1R/rawDiag-2d3a396c9d7e1c.pdf
generated pdf
/tmp/Rtmp8btH1R/rawDiag-2d3a396c9d7e1c.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 295917, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:06:33", createdby = "tobiasko", description = "input files:\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_007_S588818_NCI-H1975_PJ34_1to10_Group_2.raw \np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_008_S588819_NCI-H1975_RBN-2397_1to10_Group_3.raw\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_006_S588817_NCI-H1975_UTR_1to10_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", 
    exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2388450), list(`_classname` = "resource", `_id` = 2388449), list(`_classname` = "resource", `_id` = 2388448)), modified = "2023-11-10 16:06:33", modifiedby = "tobiasko", name = "precursor heatmap plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2390132, container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:06:35", createdby = "tobiasko", filechecksum = "a3a6b72adafa573623559b160fa5ed61", junk = "false", modified = "2023-11-10 16:06:35", modifiedby = "tobiasko", name = "WU295917-20231110-1606-rawDiag.pdf", relativepath = "container_33066/workunit_295917/WU295917-20231110-1606-rawDiag.pdf", size = "198401", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33066/workunit_295917/WU295917-20231110-1606-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33066/workunit_295917/WU295917-20231110-1606-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295917)))
The current plot is available as workunit 295917
#rows are 124126
output$download 1...
#rows are 124126
output$download 2...
ggsave to file /tmp/Rtmp8btH1R/rawDiag-2d3a394ee499a5.pdf
generated pdf
/tmp/Rtmp8btH1R/rawDiag-2d3a394ee499a5.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 295918, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:06:44", createdby = "tobiasko", description = "input files:\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_007_S588818_NCI-H1975_PJ34_1to10_Group_2.raw \np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_008_S588819_NCI-H1975_RBN-2397_1to10_Group_3.raw\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_006_S588817_NCI-H1975_UTR_1to10_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", 
    exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2388450), list(`_classname` = "resource", `_id` = 2388449), list(`_classname` = "resource", `_id` = 2388448)), modified = "2023-11-10 16:06:44", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2390133, container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:06:45", createdby = "tobiasko", filechecksum = "cb1cb5be15c9477fc7f17f8c8c4ecf4f", junk = "false", modified = "2023-11-10 16:06:45", modifiedby = "tobiasko", name = "WU295918-20231110-1606-rawDiag.pdf", relativepath = "container_33066/workunit_295918/WU295918-20231110-1606-rawDiag.pdf", size = "91081", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33066/workunit_295918/WU295918-20231110-1606-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33066/workunit_295918/WU295918-20231110-1606-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295918)))
The current plot is available as workunit 295918
#rows are 124126
output$download 1...
#rows are 124126
output$download 2...
ggsave to file /tmp/Rtmp8btH1R/rawDiag-2d3a39758c7612.pdf
generated pdf
/tmp/Rtmp8btH1R/rawDiag-2d3a39758c7612.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 295919, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:06:53", createdby = "tobiasko", description = "input files:\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_007_S588818_NCI-H1975_PJ34_1to10_Group_2.raw \np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_008_S588819_NCI-H1975_RBN-2397_1to10_Group_3.raw\np33066/Proteomics/EXPLORIS_1/pmanet_20231109/20231109_006_S588817_NCI-H1975_UTR_1to10_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", 
    exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2388450), list(`_classname` = "resource", `_id` = 2388449), list(`_classname` = "resource", `_id` = 2388448)), modified = "2023-11-10 16:06:53", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2390134, container = list(`_classname` = "project", `_id` = 33066), created = "2023-11-10 16:06:54", createdby = "tobiasko", filechecksum = "8dc159811ef7e20689afbdb7f2e1db4e", junk = "false", modified = "2023-11-10 16:06:54", modifiedby = "tobiasko", name = "WU295919-20231110-1606-rawDiag.pdf", relativepath = "container_33066/workunit_295919/WU295919-20231110-1606-rawDiag.pdf", size = "6478", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33066/workunit_295919/WU295919-20231110-1606-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33066/workunit_295919/WU295919-20231110-1606-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295919)))
The current plot is available as workunit 295919
#rows are 124126
output$download 1...
DEBUG queryMass
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
#rows are 124126
output$download 2...
DEBUG renderPlot
plotQCs
#rows are 124126
output$download 2...
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning in mclapply(rf, function(file) { :
  all scheduled cores encountered errors in user code
Warning: Error in : All inputs to rbind.fill must be data.frames
  123: stop
  122: plyr::rbind.fill
  121: <reactive:rawXICAUCData> [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424]
  105: rawXICAUCData
  104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860]
  103: widgetFunc
  102: ::
htmlwidgets
shinyRenderWidget
  101: func
   88: renderFunc
   87: renderFunc
   83: renderFunc
   82: output$tableXICAUC
    1: runApp
Warning in shinyStore::updateStore(session, "login", isolate(input$login),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
Warning in shinyStore::updateStore(session, "project", isolate(input$project),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.


Execution halted