Listening on http://127.0.0.1:41961
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({
bfabricConnectionWorking TRUE
'empdegree' found.
saving 'login and webservicepassword' ...
saving 'login and webservicepassword' ...
saving 'login and webservicepassword' ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_009_S517545_NegCtrl_R2_negative_control.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_004_S517547_mGFP_BAZ2A_wt_R1_DropletPellet_WT.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_014_S517552_mGFP_BAZ2A_dTAM_R3_DropletPellet_mutant.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_010_S517544_NegCtrl_R1_negative_control.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_005_S517546_NegCtrl_R3_negative_control.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_011_S517549_mGFP_BAZ2A_wt_R3_DropletPellet_WT.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_008_S517551_mGFP_BAZ2A_dTAM_R2_DropletPellet_mutant.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_003_S517548_mGFP_BAZ2A_wt_R2_DropletPellet_WT.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_002_S517550_mGFP_BAZ2A_dTAM_R1_DropletPellet_mutant.raw qc ...
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
renamed LMmZCorrectionppm to LMCorrection
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
renamed AGCPSMode to PrescanMode
renamed AGCPSMode to PrescanMode
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
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
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
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 241089
output$tic.basepeak <- renderPlot({
#rows are 241089
output$download 2...
saving 'login and webservicepassword' ...
ggsave to file /tmp/RtmpWWZHXL/rawDiag-f30645ad626c4.pdf
generated pdf
/tmp/RtmpWWZHXL/rawDiag-f30645ad626c4.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 289982, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:29:26", createdby = "tobiasko", deletable = "true", description = "input files:\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_004_S517547_mGFP_BAZ2A_wt_R1_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_011_S517549_mGFP_BAZ2A_wt_R3_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_003_S517548_mGFP_BAZ2A_wt_R2_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_010_S517544_NegCtrl_R1_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_005_S517546_NegCtrl_R3_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_008_S517551_mGFP_BAZ2A_dTAM_R2_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_002_S517550_mGFP_BAZ2A_dTAM_R1_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_009_S517545_NegCtrl_R2_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_014_S517552_mGFP_BAZ2A_dTAM_R3_DropletPellet_mutant.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2308146), list(`_classname` = "resource", `_id` = 2308145), list(`_classname` = "resource", `_id` = 2308144), list(`_classname` = "resource", `_id` = 2308143), list(`_classname` = "resource", `_id` = 2308142), list(`_classname` = "resource", `_id` = 2308141), list(`_classname` = "resource", `_id` = 2308140), list(`_classname` = "resource", `_id` = 2308139), list(`_classname` = "resource", `_id` = 2308138)), modified = "2023-06-12 09:29:26", 
    modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2308162, container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:29:28", createdby = "tobiasko", deletable = "true", filechecksum = "79e790074f2af5be6e38279d61ffa850", junk = "false", modified = "2023-06-12 09:29:28", modifiedby = "tobiasko", name = "WU289982-20230612-0929-rawDiag.pdf", relativepath = "container_31940/workunit_289982/WU289982-20230612-0929-rawDiag.pdf", size = "325876", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31940/workunit_289982/WU289982-20230612-0929-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31940/workunit_289982/WU289982-20230612-0929-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289982)))
The current plot is available as workunit 289982
#rows are 241089
output$download 1...
saving 'login and webservicepassword' ...
output$scan.frequency <- renderPlot
Warning: Removed 29 rows containing missing values (`geom_line()`).
#rows are 241089
output$download 2...
ggsave to file /tmp/RtmpWWZHXL/rawDiag-f306418b58f6d.pdf
Warning: Removed 29 rows containing missing values (`geom_line()`).
generated pdf
/tmp/RtmpWWZHXL/rawDiag-f306418b58f6d.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 289983, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:30:29", createdby = "tobiasko", deletable = "true", description = "input files:\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_004_S517547_mGFP_BAZ2A_wt_R1_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_011_S517549_mGFP_BAZ2A_wt_R3_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_003_S517548_mGFP_BAZ2A_wt_R2_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_010_S517544_NegCtrl_R1_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_005_S517546_NegCtrl_R3_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_008_S517551_mGFP_BAZ2A_dTAM_R2_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_002_S517550_mGFP_BAZ2A_dTAM_R1_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_009_S517545_NegCtrl_R2_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_014_S517552_mGFP_BAZ2A_dTAM_R3_DropletPellet_mutant.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2308146), list(`_classname` = "resource", `_id` = 2308145), list(`_classname` = "resource", `_id` = 2308144), list(`_classname` = "resource", `_id` = 2308143), list(`_classname` = "resource", `_id` = 2308142), list(`_classname` = "resource", `_id` = 2308141), list(`_classname` = "resource", `_id` = 2308140), list(`_classname` = "resource", `_id` = 2308139), list(`_classname` = "resource", `_id` = 2308138)), modified = "2023-06-12 09:30:29", 
    modifiedby = "tobiasko", name = "scan frequency plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2308163, container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:30:31", createdby = "tobiasko", deletable = "true", filechecksum = "de2ca6395962c47bf5819107c161dfb5", junk = "false", modified = "2023-06-12 09:30:31", modifiedby = "tobiasko", name = "WU289983-20230612-0930-rawDiag.pdf", relativepath = "container_31940/workunit_289983/WU289983-20230612-0930-rawDiag.pdf", size = "280701", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31940/workunit_289983/WU289983-20230612-0930-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31940/workunit_289983/WU289983-20230612-0930-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289983)))
The current plot is available as workunit 289983
#rows are 241089
output$download 1...
`geom_smooth()` using formula = 'y ~ x'
#rows are 241089
output$download 2...
ggsave to file /tmp/RtmpWWZHXL/rawDiag-f3064594afb73.pdf
`geom_smooth()` using formula = 'y ~ x'
generated pdf
/tmp/RtmpWWZHXL/rawDiag-f3064594afb73.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 289984, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:31:08", createdby = "tobiasko", deletable = "true", description = "input files:\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_004_S517547_mGFP_BAZ2A_wt_R1_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_011_S517549_mGFP_BAZ2A_wt_R3_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_003_S517548_mGFP_BAZ2A_wt_R2_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_010_S517544_NegCtrl_R1_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_005_S517546_NegCtrl_R3_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_008_S517551_mGFP_BAZ2A_dTAM_R2_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_002_S517550_mGFP_BAZ2A_dTAM_R1_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_009_S517545_NegCtrl_R2_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_014_S517552_mGFP_BAZ2A_dTAM_R3_DropletPellet_mutant.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2308146), list(`_classname` = "resource", `_id` = 2308145), list(`_classname` = "resource", `_id` = 2308144), list(`_classname` = "resource", `_id` = 2308143), list(`_classname` = "resource", `_id` = 2308142), list(`_classname` = "resource", `_id` = 2308141), list(`_classname` = "resource", `_id` = 2308140), list(`_classname` = "resource", `_id` = 2308139), list(`_classname` = "resource", `_id` = 2308138)), modified = "2023-06-12 09:31:08", 
    modifiedby = "tobiasko", name = "cycle load plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2308164, container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:31:10", createdby = "tobiasko", deletable = "true", filechecksum = "fac6d24b90a2e8a7c195b6bf17370ea5", junk = "false", modified = "2023-06-12 09:31:10", modifiedby = "tobiasko", name = "WU289984-20230612-0931-rawDiag.pdf", relativepath = "container_31940/workunit_289984/WU289984-20230612-0931-rawDiag.pdf", size = "769996", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31940/workunit_289984/WU289984-20230612-0931-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31940/workunit_289984/WU289984-20230612-0931-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289984)))
The current plot is available as workunit 289984
#rows are 241089
output$download 1...
#rows are 241089
output$download 2...
ggsave to file /tmp/RtmpWWZHXL/rawDiag-f30645abc50ae.pdf
generated pdf
/tmp/RtmpWWZHXL/rawDiag-f30645abc50ae.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 289985, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:31:34", createdby = "tobiasko", deletable = "true", description = "input files:\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_004_S517547_mGFP_BAZ2A_wt_R1_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_011_S517549_mGFP_BAZ2A_wt_R3_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_003_S517548_mGFP_BAZ2A_wt_R2_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_010_S517544_NegCtrl_R1_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_005_S517546_NegCtrl_R3_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_008_S517551_mGFP_BAZ2A_dTAM_R2_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_002_S517550_mGFP_BAZ2A_dTAM_R1_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_009_S517545_NegCtrl_R2_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_014_S517552_mGFP_BAZ2A_dTAM_R3_DropletPellet_mutant.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2308146), list(`_classname` = "resource", `_id` = 2308145), list(`_classname` = "resource", `_id` = 2308144), list(`_classname` = "resource", `_id` = 2308143), list(`_classname` = "resource", `_id` = 2308142), list(`_classname` = "resource", `_id` = 2308141), list(`_classname` = "resource", `_id` = 2308140), list(`_classname` = "resource", `_id` = 2308139), list(`_classname` = "resource", `_id` = 2308138)), modified = "2023-06-12 09:31:34", 
    modifiedby = "tobiasko", name = "injection time plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2308165, container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:31:35", createdby = "tobiasko", deletable = "true", filechecksum = "5a56071a5826456ad438ca9e73ac6e44", junk = "false", modified = "2023-06-12 09:31:35", modifiedby = "tobiasko", name = "WU289985-20230612-0931-rawDiag.pdf", relativepath = "container_31940/workunit_289985/WU289985-20230612-0931-rawDiag.pdf", size = "1012681", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31940/workunit_289985/WU289985-20230612-0931-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31940/workunit_289985/WU289985-20230612-0931-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289985)))
The current plot is available as workunit 289985
#rows are 241089
output$download 1...
Warning: Removed 40 rows containing non-finite values (`stat_smooth()`).
#rows are 241089
output$download 2...
ggsave to file /tmp/RtmpWWZHXL/rawDiag-f30647bbb3429.pdf
Warning: Removed 40 rows containing non-finite values (`stat_smooth()`).
generated pdf
/tmp/RtmpWWZHXL/rawDiag-f30647bbb3429.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 289986, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:31:52", createdby = "tobiasko", deletable = "true", description = "input files:\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_004_S517547_mGFP_BAZ2A_wt_R1_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_011_S517549_mGFP_BAZ2A_wt_R3_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_003_S517548_mGFP_BAZ2A_wt_R2_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_010_S517544_NegCtrl_R1_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_005_S517546_NegCtrl_R3_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_008_S517551_mGFP_BAZ2A_dTAM_R2_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_002_S517550_mGFP_BAZ2A_dTAM_R1_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_009_S517545_NegCtrl_R2_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_014_S517552_mGFP_BAZ2A_dTAM_R3_DropletPellet_mutant.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2308146), list(`_classname` = "resource", `_id` = 2308145), list(`_classname` = "resource", `_id` = 2308144), list(`_classname` = "resource", `_id` = 2308143), list(`_classname` = "resource", `_id` = 2308142), list(`_classname` = "resource", `_id` = 2308141), list(`_classname` = "resource", `_id` = 2308140), list(`_classname` = "resource", `_id` = 2308139), list(`_classname` = "resource", `_id` = 2308138)), modified = "2023-06-12 09:31:52", 
    modifiedby = "tobiasko", name = "lock mass correction plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2308166, container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:31:53", createdby = "tobiasko", deletable = "true", filechecksum = "d763fc101df9b985e82607243266cdc9", junk = "false", modified = "2023-06-12 09:31:53", modifiedby = "tobiasko", name = "WU289986-20230612-0931-rawDiag.pdf", relativepath = "container_31940/workunit_289986/WU289986-20230612-0931-rawDiag.pdf", size = "170178", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31940/workunit_289986/WU289986-20230612-0931-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31940/workunit_289986/WU289986-20230612-0931-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289986)))
The current plot is available as workunit 289986
#rows are 241089
output$download 1...
#rows are 241089
output$download 2...
ggsave to file /tmp/RtmpWWZHXL/rawDiag-f306433cf9158.pdf
generated pdf
/tmp/RtmpWWZHXL/rawDiag-f306433cf9158.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 289987, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:32:14", createdby = "tobiasko", deletable = "true", description = "input files:\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_004_S517547_mGFP_BAZ2A_wt_R1_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_011_S517549_mGFP_BAZ2A_wt_R3_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_003_S517548_mGFP_BAZ2A_wt_R2_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_010_S517544_NegCtrl_R1_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_005_S517546_NegCtrl_R3_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_008_S517551_mGFP_BAZ2A_dTAM_R2_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_002_S517550_mGFP_BAZ2A_dTAM_R1_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_009_S517545_NegCtrl_R2_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_014_S517552_mGFP_BAZ2A_dTAM_R3_DropletPellet_mutant.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2308146), list(`_classname` = "resource", `_id` = 2308145), list(`_classname` = "resource", `_id` = 2308144), list(`_classname` = "resource", `_id` = 2308143), list(`_classname` = "resource", `_id` = 2308142), list(`_classname` = "resource", `_id` = 2308141), list(`_classname` = "resource", `_id` = 2308140), list(`_classname` = "resource", `_id` = 2308139), list(`_classname` = "resource", `_id` = 2308138)), modified = "2023-06-12 09:32:14", 
    modifiedby = "tobiasko", name = "cycle time plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2308167, container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:32:15", createdby = "tobiasko", deletable = "true", filechecksum = "716d36d0ba9cfe1489f21717e1e12471", junk = "false", modified = "2023-06-12 09:32:15", modifiedby = "tobiasko", name = "WU289987-20230612-0932-rawDiag.pdf", relativepath = "container_31940/workunit_289987/WU289987-20230612-0932-rawDiag.pdf", size = "208926", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31940/workunit_289987/WU289987-20230612-0932-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31940/workunit_289987/WU289987-20230612-0932-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289987)))
The current plot is available as workunit 289987
#rows are 241089
output$download 1...
#rows are 241089
output$download 2...
ggsave to file /tmp/RtmpWWZHXL/rawDiag-f3064368a4193.pdf
generated pdf
/tmp/RtmpWWZHXL/rawDiag-f3064368a4193.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 289988, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:32:30", createdby = "tobiasko", deletable = "true", description = "input files:\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_004_S517547_mGFP_BAZ2A_wt_R1_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_011_S517549_mGFP_BAZ2A_wt_R3_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_003_S517548_mGFP_BAZ2A_wt_R2_DropletPellet_WT.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_010_S517544_NegCtrl_R1_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_005_S517546_NegCtrl_R3_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_008_S517551_mGFP_BAZ2A_dTAM_R2_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_002_S517550_mGFP_BAZ2A_dTAM_R1_DropletPellet_mutant.raw\np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_009_S517545_NegCtrl_R2_negative_control.raw \np31940/Proteomics/EXPLORIS_2/analytic_20230609/20230609_C31940_014_S517552_mGFP_BAZ2A_dTAM_R3_DropletPellet_mutant.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2308146), list(`_classname` = "resource", `_id` = 2308145), list(`_classname` = "resource", `_id` = 2308144), list(`_classname` = "resource", `_id` = 2308143), list(`_classname` = "resource", `_id` = 2308142), list(`_classname` = "resource", `_id` = 2308141), list(`_classname` = "resource", `_id` = 2308140), list(`_classname` = "resource", `_id` = 2308139), list(`_classname` = "resource", `_id` = 2308138)), modified = "2023-06-12 09:32:30", 
    modifiedby = "tobiasko", name = "charge state plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2308168, container = list(`_classname` = "order", `_id` = 31940), created = "2023-06-12 09:32:31", createdby = "tobiasko", deletable = "true", filechecksum = "2cbe036116bc691b7485f06a77fcc58e", junk = "false", modified = "2023-06-12 09:32:31", modifiedby = "tobiasko", name = "WU289988-20230612-0932-rawDiag.pdf", relativepath = "container_31940/workunit_289988/WU289988-20230612-0932-rawDiag.pdf", size = "9906", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31940/workunit_289988/WU289988-20230612-0932-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31940/workunit_289988/WU289988-20230612-0932-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289988)))
The current plot is available as workunit 289988
#rows are 241089
output$download 1...
DEBUG renderPlot
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: '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: '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")
plotQCs
#rows are 241089
output$download 1...
DEBUG renderPlot
plotQCs
#rows are 241089
output$download 1...


Execution halted