Listening on http://127.0.0.1:42803
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
/scratch/cpanse/
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$employee <- renderUI({
bfabricConnectionWorking TRUE
'empdegree' found.
saving 'login and webservicepassword' ...
saving 'login and webservicepassword' ...
saving 'login and webservicepassword' ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_002_S588449_ExpB_2D_12Y_mIgG_37C_1h_negative_control.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_004_S588450_ExpB_2D_12Y_AK23_4C_1h_Untreated.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_006_S588451_ExpB_2D_12Y_AK23_37C_1h_Treated.raw qc ...
missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
MasterScanNumber calculated
missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
MasterScanNumber calculated
renamed LMmZCorrectionppm to LMCorrection
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
renamed AGCPSMode to PrescanMode
missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
MasterScanNumber calculated
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
#rows are 57555
output$tic.basepeak <- renderPlot({
#rows are 57555
output$download 2...
saving 'login and webservicepassword' ...
output$tic.basepeak <- renderPlot({
#rows are 57555
output$download 2...
ggsave to file /tmp/Rtmp31Ldkj/rawDiag-36ac5361fc3ed8.pdf
generated pdf
/tmp/Rtmp31Ldkj/rawDiag-36ac5361fc3ed8.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 296368, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:32:13", createdby = "tobiasko", description = "input files:\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_002_S588449_ExpB_2D_12Y_mIgG_37C_1h_negative_control.raw\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_006_S588451_ExpB_2D_12Y_AK23_37C_1h_Treated.raw \np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_004_S588450_ExpB_2D_12Y_AK23_4C_1h_Untreated.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` = 2396982), list(`_classname` = "resource", `_id` = 2396981), list(`_classname` = "resource", `_id` = 2396980)), modified = "2023-11-21 11:32:13", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2397672, container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:32:14", createdby = "tobiasko", filechecksum = "e703ef8dfaf8fb0a3f7c3d24bc91f4af", junk = "false", modified = "2023-11-21 11:32:14", modifiedby = "tobiasko", name = "WU296368-20231121-1132-rawDiag.pdf", relativepath = "container_33379/workunit_296368/WU296368-20231121-1132-rawDiag.pdf", size = "135812", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33379/workunit_296368/WU296368-20231121-1132-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33379/workunit_296368/WU296368-20231121-1132-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296368)))
The current plot is available as workunit 296368
#rows are 57555
output$download 1...
saving 'login and webservicepassword' ...
output$scan.frequency <- renderPlot
Warning: Removed 29 rows containing missing values (`geom_line()`).
#rows are 57555
output$download 2...
ggsave to file /tmp/Rtmp31Ldkj/rawDiag-36ac536f691a1b.pdf
Warning: Removed 29 rows containing missing values (`geom_line()`).
generated pdf
/tmp/Rtmp31Ldkj/rawDiag-36ac536f691a1b.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 296370, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:37:16", createdby = "tobiasko", description = "input files:\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_002_S588449_ExpB_2D_12Y_mIgG_37C_1h_negative_control.raw\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_006_S588451_ExpB_2D_12Y_AK23_37C_1h_Treated.raw \np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_004_S588450_ExpB_2D_12Y_AK23_4C_1h_Untreated.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` = 2396982), list(`_classname` = "resource", `_id` = 2396981), list(`_classname` = "resource", `_id` = 2396980)), modified = "2023-11-21 11:37:16", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2397675, container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:37:17", createdby = "tobiasko", filechecksum = "6f6f20478badbce1c526227c56058fcd", junk = "false", modified = "2023-11-21 11:37:17", modifiedby = "tobiasko", name = "WU296370-20231121-1137-rawDiag.pdf", relativepath = "container_33379/workunit_296370/WU296370-20231121-1137-rawDiag.pdf", size = "82560", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33379/workunit_296370/WU296370-20231121-1137-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33379/workunit_296370/WU296370-20231121-1137-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296370)))
The current plot is available as workunit 296370
#rows are 57555
output$download 1...
`geom_smooth()` using formula = 'y ~ x'
#rows are 57555
output$download 2...
ggsave to file /tmp/Rtmp31Ldkj/rawDiag-36ac53653c6a63.pdf
`geom_smooth()` using formula = 'y ~ x'
generated pdf
/tmp/Rtmp31Ldkj/rawDiag-36ac53653c6a63.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 296371, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:38:04", createdby = "tobiasko", description = "input files:\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_002_S588449_ExpB_2D_12Y_mIgG_37C_1h_negative_control.raw\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_006_S588451_ExpB_2D_12Y_AK23_37C_1h_Treated.raw \np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_004_S588450_ExpB_2D_12Y_AK23_4C_1h_Untreated.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` = 2396982), list(`_classname` = "resource", `_id` = 2396981), list(`_classname` = "resource", `_id` = 2396980)), modified = "2023-11-21 11:38:04", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2397676, container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:38:05", createdby = "tobiasko", filechecksum = "06d47315ffc4b43bd7b051ddebd27f05", junk = "false", modified = "2023-11-21 11:38:05", modifiedby = "tobiasko", name = "WU296371-20231121-1138-rawDiag.pdf", relativepath = "container_33379/workunit_296371/WU296371-20231121-1138-rawDiag.pdf", size = "61009", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33379/workunit_296371/WU296371-20231121-1138-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33379/workunit_296371/WU296371-20231121-1138-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296371)))
The current plot is available as workunit 296371
#rows are 57555
output$download 1...
Warning: Removed 15 rows containing non-finite values (`stat_smooth()`).
#rows are 57555
output$download 2...
ggsave to file /tmp/Rtmp31Ldkj/rawDiag-36ac531d4e946f.pdf
Warning: Removed 15 rows containing non-finite values (`stat_smooth()`).
generated pdf
/tmp/Rtmp31Ldkj/rawDiag-36ac531d4e946f.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 296372, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:38:17", createdby = "tobiasko", description = "input files:\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_002_S588449_ExpB_2D_12Y_mIgG_37C_1h_negative_control.raw\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_006_S588451_ExpB_2D_12Y_AK23_37C_1h_Treated.raw \np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_004_S588450_ExpB_2D_12Y_AK23_4C_1h_Untreated.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` = 2396982), list(`_classname` = "resource", `_id` = 2396981), list(`_classname` = "resource", `_id` = 2396980)), modified = "2023-11-21 11:38:17", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2397677, container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:38:18", createdby = "tobiasko", filechecksum = "84de50ace4417c0db6dad615ca5dfa9e", junk = "false", modified = "2023-11-21 11:38:18", modifiedby = "tobiasko", name = "WU296372-20231121-1138-rawDiag.pdf", relativepath = "container_33379/workunit_296372/WU296372-20231121-1138-rawDiag.pdf", size = "84565", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33379/workunit_296372/WU296372-20231121-1138-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33379/workunit_296372/WU296372-20231121-1138-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296372)))
The current plot is available as workunit 296372
#rows are 57555
output$download 1...
#rows are 57555
output$download 2...
ggsave to file /tmp/Rtmp31Ldkj/rawDiag-36ac5321a8ede0.pdf
generated pdf
/tmp/Rtmp31Ldkj/rawDiag-36ac5321a8ede0.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 296373, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:38:34", createdby = "tobiasko", description = "input files:\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_002_S588449_ExpB_2D_12Y_mIgG_37C_1h_negative_control.raw\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_006_S588451_ExpB_2D_12Y_AK23_37C_1h_Treated.raw \np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_004_S588450_ExpB_2D_12Y_AK23_4C_1h_Untreated.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` = 2396982), list(`_classname` = "resource", `_id` = 2396981), list(`_classname` = "resource", `_id` = 2396980)), modified = "2023-11-21 11:38:34", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2397678, container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:38:36", createdby = "tobiasko", filechecksum = "9a2d76bb53ec0b2926fc952b04c5af36", junk = "false", modified = "2023-11-21 11:38:36", modifiedby = "tobiasko", name = "WU296373-20231121-1138-rawDiag.pdf", relativepath = "container_33379/workunit_296373/WU296373-20231121-1138-rawDiag.pdf", size = "296940", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33379/workunit_296373/WU296373-20231121-1138-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33379/workunit_296373/WU296373-20231121-1138-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296373)))
The current plot is available as workunit 296373
#rows are 57555
output$download 1...
#rows are 57555
output$download 2...
ggsave to file /tmp/Rtmp31Ldkj/rawDiag-36ac533aa98161.pdf
generated pdf
/tmp/Rtmp31Ldkj/rawDiag-36ac533aa98161.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 296374, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:38:50", createdby = "tobiasko", description = "input files:\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_002_S588449_ExpB_2D_12Y_mIgG_37C_1h_negative_control.raw\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_006_S588451_ExpB_2D_12Y_AK23_37C_1h_Treated.raw \np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_004_S588450_ExpB_2D_12Y_AK23_4C_1h_Untreated.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` = 2396982), list(`_classname` = "resource", `_id` = 2396981), list(`_classname` = "resource", `_id` = 2396980)), modified = "2023-11-21 11:38:50", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2397679, container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:38:51", createdby = "tobiasko", filechecksum = "510c9933ed2a65d423842e12d22eaed7", junk = "false", modified = "2023-11-21 11:38:51", modifiedby = "tobiasko", name = "WU296374-20231121-1138-rawDiag.pdf", relativepath = "container_33379/workunit_296374/WU296374-20231121-1138-rawDiag.pdf", size = "92549", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33379/workunit_296374/WU296374-20231121-1138-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33379/workunit_296374/WU296374-20231121-1138-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296374)))
The current plot is available as workunit 296374
#rows are 57555
output$download 1...
#rows are 57555
output$download 2...
ggsave to file /tmp/Rtmp31Ldkj/rawDiag-36ac532f06d827.pdf
generated pdf
/tmp/Rtmp31Ldkj/rawDiag-36ac532f06d827.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 296375, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:39:02", createdby = "tobiasko", description = "input files:\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_002_S588449_ExpB_2D_12Y_mIgG_37C_1h_negative_control.raw\np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_006_S588451_ExpB_2D_12Y_AK23_37C_1h_Treated.raw \np33379/Proteomics/QEXACTIVE_1/analytic_20231120/20231120_C33379_004_S588450_ExpB_2D_12Y_AK23_4C_1h_Untreated.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` = 2396982), list(`_classname` = "resource", `_id` = 2396981), list(`_classname` = "resource", `_id` = 2396980)), modified = "2023-11-21 11:39:02", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2397680, container = list(`_classname` = "order", `_id` = 33379), created = "2023-11-21 11:39:03", createdby = "tobiasko", filechecksum = "e34211a07e0fca0dd241f5bae646b78f", junk = "false", modified = "2023-11-21 11:39:03", modifiedby = "tobiasko", name = "WU296375-20231121-1139-rawDiag.pdf", relativepath = "container_33379/workunit_296375/WU296375-20231121-1139-rawDiag.pdf", size = "8948", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33379/workunit_296375/WU296375-20231121-1139-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33379/workunit_296375/WU296375-20231121-1139-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296375)))
The current plot is available as workunit 296375
#rows are 57555
output$download 1...
DEBUG renderPlot
DEBUG queryMass
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
plotQCs
#rows are 57555
output$download 1...
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 57555
output$download 2...