su: ignoring --preserve-environment, it's mutually exclusive with --login
Loading required package: MASS
Attaching package: ‘shinyjs’
The following object is masked from ‘package:shiny’:
runExample
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removeClass, show
Attaching package: ‘shinyWidgets’
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alert
Loading required package: ggplot2
Loading required package: ggpubr
Attaching package: ‘ggpubr’
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mutate
Attaching package: ‘survminer’
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myeloma
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select
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filter
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layout
Attaching package: ‘DT’
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Listening on http://127.0.0.1:33801
Warning: Navigation containers expect a collection of `bslib::nav()`/`shiny::tabPanel()`s and/or `bslib::nav_menu()`/`shiny::navbarMenu()`s. Consider using `header` or `footer` if you wish to place content above (or below) every panel's contents.
Warning in file(file, "rt") :
cannot open file '/data/scissor_20201218/[Loading...]/data/[Loading...]/[Loading...]/cancercell.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Warning in file(file, "rt") :
cannot open file '/data/scissor_20201218/LAML/data/Van et al.(GSE116256)/[Loading...]/cancercell.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Warning in if (input$Deconvolution %in% c("MuSiC", "CIBERSORTx") & (input$cancertype %in% :
the condition has length > 1 and only the first element will be used
Warning in if (input$Deconvolution %in% c("MuSiC", "CIBERSORTx") & (input$cancertype %in% :
the condition has length > 1 and only the first element will be used
Warning: Outer names are only allowed for unnamed scalar atomic inputs
Warning: The select input "gene" contains a large number of options; consider using server-side selectize for massively improved performance. See the Details section of the ?selectizeInput help topic.
Warning: Error in [.data.frame: undefined columns selected
105: stop
104: [.data.frame
101: clean [global.R#341]
100: renderPrint [/media/volume/sdb/scissor/server.R#984]
99: func
83: renderFunc
82: output$printcoxres
1: runApp
Warning in if (is.na(data.pool$genelist)) { :
the condition has length > 1 and only the first element will be used
Warning in file(file, "rt") :
cannot open file '/data/scissor_20201218/HNSC/expression/I/miRNA_match/IL12A.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Warning in file(file, "rt") :
cannot open file '/data/scissor_20201218/HNSC/expression/I/protein_match/IL12A.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
at -0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
radius 4.0027e-07
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
all data on boundary of neighborhood. make span bigger
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at -0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
zero-width neighborhood. make span bigger
Warning: Computation failed in `stat_smooth()`:
NA/NaN/Inf in foreign function call (arg 5)
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
at -0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
radius 3.4971e-06
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
all data on boundary of neighborhood. make span bigger
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at -0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
zero-width neighborhood. make span bigger
Warning: Computation failed in `stat_smooth()`:
NA/NaN/Inf in foreign function call (arg 5)
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
at -0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
radius 4.0027e-07
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
all data on boundary of neighborhood. make span bigger
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at -0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
zero-width neighborhood. make span bigger
Warning: Computation failed in `stat_smooth()`:
NA/NaN/Inf in foreign function call (arg 5)
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
at -0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
radius 3.4971e-06
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
all data on boundary of neighborhood. make span bigger
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at -0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
zero-width neighborhood. make span bigger
Warning: Computation failed in `stat_smooth()`:
NA/NaN/Inf in foreign function call (arg 5)
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
at -0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
radius 4.0027e-07
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
all data on boundary of neighborhood. make span bigger
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at -0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
zero-width neighborhood. make span bigger
Warning: Computation failed in `stat_smooth()`:
NA/NaN/Inf in foreign function call (arg 5)
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
at -0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
radius 3.4971e-06
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
all data on boundary of neighborhood. make span bigger
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at -0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
zero-width neighborhood. make span bigger
Warning: Computation failed in `stat_smooth()`:
NA/NaN/Inf in foreign function call (arg 5)
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
at -0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
radius 4.0027e-07
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
all data on boundary of neighborhood. make span bigger
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at -0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 0.00063267
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
zero-width neighborhood. make span bigger
Warning: Computation failed in `stat_smooth()`:
NA/NaN/Inf in foreign function call (arg 5)
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
at -0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
radius 3.4971e-06
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
all data on boundary of neighborhood. make span bigger
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at -0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 0.00187
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
zero-width neighborhood. make span bigger
Warning: Computation failed in `stat_smooth()`:
NA/NaN/Inf in foreign function call (arg 5)
Warning: Error in lm.fit: 0 (non-NA) cases
172: stop
171: lm.fit
170: lm
168: renderPlot [/media/volume/sdb/scissor/server.R#513]
166: func
126: drawPlot
112:
96: drawReactive
83: renderFunc
82: output$doubleplotResult
1: runApp
Warning in if (input$Deconvolution %in% c("MuSiC", "CIBERSORTx") & (input$cancertype %in% :
the condition has length > 1 and only the first element will be used
Warning: Outer names are only allowed for unnamed scalar atomic inputs
Warning in if (is.na(data.pool$genelist) & input$load) { :
the condition has length > 1 and only the first element will be used
Warning in file(file, "rt") :
cannot open file '/data/scissor_20201218/BRCA/miRNA/e/.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Warning in file(file, "rt") :
cannot open file '/data/scissor_20201218/BRCA/protein/N/No matched protein.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Execution halted