Package: xmapbridge

Version: 1.40.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:xmapbridge.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings xmapbridge_1.40.0.tar.gz

StartedAt: 2019-04-16 03:43:09 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:43:29 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 20.0 seconds

RetCode: 0

Status:  OK

CheckDir: xmapbridge.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:xmapbridge.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings xmapbridge_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/xmapbridge.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xmapbridge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘xmapbridge’ version ‘1.40.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xmapbridge’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘xmapbridge/R/zzz.R’:
  .onLoad has wrong argument list ‘lib, pkg, where’
  .onLoad calls:
    require(methods, quietly = TRUE)

Package startup functions should have two arguments with names starting
  with ‘lib’ and ‘pkg’, respectively.
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

xmap.col: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
  Running ‘xmapbridge_test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/xmapbridge.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL xmapbridge
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘xmapbridge’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xmapbridge)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if( require( "RUnit", quietly=TRUE ) ) {
+   pkg <- "xmapbridge"
+ 
+   if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+     path <- file.path( getwd(), "..", "inst", "unitTests" )
+   }
+   else {
+     path <- system.file( package=pkg, "unitTests" )
+   }
+ 
+   cat( "\nRunning unit tests\n" )
+   print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+   library( package=pkg, character.only=TRUE )
+  
+   testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), dirs=path )
+   tests <- runTestSuite( testSuite )
+  
+   pathReport <- file.path( path, "report" )
+  
+   cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+   printTextProtocol( tests, showDetails=FALSE )
+   printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+   printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+  
+   printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+  
+   tmp <- getErrors( tests )
+   if( tmp$nFail > 0 | tmp$nErr > 0 ) {
+     stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ",  tmp$nErr, ")\n\n", sep="" ) )
+   }
+ } else {
+   warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "xmapbridge"

$getwd
[1] "/home/biocbuild/bbs-3.8-bioc/meat/xmapbridge.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.8-bioc/R/library/xmapbridge/unitTests"



Executing test function test.get.xmap.cache.dir  ...  done successfully.



Executing test function test.graph  ...  done successfully.



Executing test function test.plots  ...  done successfully.



Executing test function test.projects  ...  done successfully.



Executing test function test.utils  ...  done successfully.



Executing test function test.validate.x.and.y  ...  done successfully.

------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Tue Apr 16 03:43:25 2019 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
xmapbridge unit testing - 6 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  0.824   0.112   0.966 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #                               8             o      8               
> #                               8                    8               
> #  `o  o' ooYoYo. .oPYo. .oPYo. 8oPYo. oPYo. o8 .oPYo8 .oPYo. .oPYo. 
> #   `bd'  8' 8  8 .oooo8 8    8 8    8 8  `'  8 8    8 8    8 8oooo8 
> #   d'`b  8  8  8 8    8 8    8 8    8 8      8 8    8 8    8 8.     
> #  o'  `o 8  8  8 `YooP8 8YooP' `YooP' 8      8 `YooP' `YooP8 `Yooo' 
> #                        8                                  8        
> #                        8                              YooP'
> #
> # Author:  Tim Yates and Crispin J Miller
> # Date:    2008/08/13
> # Licence: LGPL-v3
> #
> # This file tests all of the exported methods from the library to make sure
> # they work as expected (generate the correct files), fail cleanly as required,
> # and clean up after themselves in case of faliure after a particular file has
> # been created
> #
> 
> library( xmapbridge )
> 
> .test.env <- new.env( hash=TRUE, parent=emptyenv() )
> 
> ###############################################################################
> ## Assert methods (to make the code look a bit cleaner)
> ###############################################################################
> 
> assertEqual <- function( a, b, msg="not equal" ) {
+   if( class( a ) == "list" && class( b ) == "list" ) {
+     if( !isTRUE( all.equal( a, b ) ) ) {
+       stop( msg )
+     }
+   }
+   else if( a != b ) {
+     stop( msg )
+   }
+   TRUE
+ }
> 
> assertNotEqual <- function( a, b, msg="equal" ) {
+   if( class( a ) == "list" && class( b ) == "list" ) {
+     if( isTRUE( all.equal( a, b ) ) ) {
+       stop( msg )
+     }
+   }
+   else if( a == b ) {
+     stop( msg )
+   }
+   TRUE
+ }
> 
> assertLength <- function( a, len, msg="invalid length" ) {
+   if( length( a ) != len ) {
+     stop( msg )
+   }
+   TRUE
+ }
> 
> assertNull <- function( a, msg="is null" ) {
+   if( !is.null( a ) ) {
+     stop( msg )
+   }
+   TRUE
+ }
> 
> assertNotNull <- function( a, msg="is not null" ) {
+   if( is.null( a ) ) {
+     stop( msg )
+   }
+   TRUE
+ }
> 
> assertNumeric <- function( a, msg="non-numeric" ) {
+   if( !is.number( a ) ) {
+     stop( msg )
+   }
+   TRUE
+ }
> 
> shouldFail <- function( test, msg=paste( "FAIL:", test ) ) {
+   .ok <- FALSE
+   tryCatch( {
+     test()
+     .ok <- TRUE
+   }, warning=function(e) {
+     print( paste( "caught a warning '", e$message, "'" ) ) 
+   }, error=function(e) {
+     print( paste( "Failed (yay) '", e$message, "'" ) ) 
+   } )
+   if( .ok ) {
+     stop( msg )
+   }
+   TRUE
+ }
> 
> ###############################################################################
> ## Setup and Teardown Methods
> ###############################################################################
> 
> .setup <- function() {
+   .test.env$tmp  <- tempdir()
+   .test.env$old  <- Sys.getenv( "XMAP_BRIDGE_CACHE" )
+   Sys.setenv( XMAP_BRIDGE_CACHE=.test.env$tmp )
+ }
> 
> .teardown <- function() {
+   # Delete the temp folder, and reset our environment
+   Sys.setenv( XMAP_BRIDGE_CACHE=.test.env$old )
+   unlink( .test.env$tmp, recursive=TRUE )
+ }
> 
> ###############################################################################
> ## And call the tests...
> ###############################################################################
> 
> # Set up the environment
> ###############################################################################
> 
> .setup()
> 
> # Project tests
> ###############################################################################
> 
> shouldFail( function() { xmap.project.load( "FAIL!" ) }, "Invalid project parameter shouldn't work!" )
[1] "Failed (yay) ' projectid should be an object of class Project, not character '"
[1] TRUE
> shouldFail( function() { xmap.project.save( "FAIL!", list() ) }, "Invalid project parameter shouldn't work!" )
[1] "Failed (yay) ' projectid should be an object of class Project, not character '"
[1] TRUE
> shouldFail( function() { xmap.project.delete( "FAIL!" ) }, "Invalid project parameter shouldn't work!" )
[1] "Failed (yay) ' projectid should be an object of class Project, not character '"
[1] TRUE
> 
> .project <- xmap.project.new( "Project A" )
> .projects <- xmap.project.list()
> assertLength( .projects, 1, paste( "Got", length( .projects ), "projects.  Should have only 1" ) )
[1] TRUE
> assertEqual( .project, .projects[[1]], "Project not equal to project in list" )
[1] TRUE
> 
> .data <- xmap.project.load( .project )
> assertNotNull( .data, "Load failed for data" )
[1] TRUE
> assertLength( .data, 1, "Data should have 1 element" )
[1] TRUE
> assertEqual( "Project A", .data$NAME )
[1] TRUE
> .data$NAME <- "Project Z"
> xmap.project.save( .project, .data )
> .data2 <- xmap.project.load( .project )
> assertEqual( "Project Z", .data2$NAME, "Did not load altered project name" )
[1] TRUE
> assertEqual( .data, .data2, "Saved and loaded data not identical!" )
[1] TRUE
> 
> .project2 <- xmap.project.new( "Project B" )
> .projects <- xmap.project.list()
> assertLength( .projects, 2, paste( "Got", length( .projects ), "projects.  Should have 2" ) )
[1] TRUE
> 
> shouldFail( function() { assertEqual( .project, .project2 ) }, paste( "Project 1 and 2 should not be equal" ) )
[1] "Failed (yay) ' not equal '"
[1] TRUE
> assertNotEqual( .project, .project2, paste( "Project 1 and 2 should not be equal" ) )
[1] TRUE
> 
> xmap.project.delete( .project2 )
> 
> .projects <- xmap.project.list()
> assertLength( .projects, 1, paste( "Got", length( .projects ), "projects.  Should have only 1" ) )
[1] TRUE
> 
> # Graph tests
> ###############################################################################
> 
> shouldFail( function() {    xmap.graph.new( "NonProjectObject", "A Graph", "desc", -10, 10, "1", 1000000, 2000000, ylab="label", species="homo_sapiens" ) }, "Invalid project parameter" )
[1] "Failed (yay) ' projectid should be an object of class Project, not character '"
[1] TRUE
> shouldFail( function() {   xmap.graph.load( "FAIL!" )         }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' graphid should be an object of class Graph, not character '"
[1] TRUE
> shouldFail( function() {   xmap.graph.list( "FAIL!" )         }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' projectid should be an object of class Project, not character '"
[1] TRUE
> shouldFail( function() {   xmap.graph.save( "FAIL!", list() ) }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' graphid should be an object of class Graph, not character '"
[1] TRUE
> shouldFail( function() { xmap.graph.delete( "FAIL!" )         }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' graphid should be an object of class Graph, not character '"
[1] TRUE
> shouldFail( function() {    xmap.graph.new( .project2, "A Graph", "desc", -10, 10, "1", 1000000, 2000000, ylab="label", species="homo_sapiens" ) }, "Writing to a missing project seeme to work?" )
xmapbridge:Project( /tmp/RtmpNSv7tI/2019.Apr.16.03.43.26_0.284.xmb ) 
[1] "Failed (yay) ' non-string argument to internal 'paste' '"
[1] TRUE
> 
> .graph <- xmap.graph.new( .project, "A Graph", "desc", -10, 10, "1", 1000000, 2000000, ylab="label", species="homo_sapiens" )
> 
> .graphs <- xmap.graph.list( .project )
> assertLength( .graphs, 1, paste( "Got", length( .graphs ), "graphs.  Should have only 1" ) )
[1] TRUE
> assertEqual( .graph, .graphs[[1]], "Graph not equal to first graph in list" )
[1] TRUE
> 
> .data <- xmap.graph.load( .graph )
> assertNotNull( .data, "Load failed for data" )
[1] TRUE
> assertLength( .data, 9, "Graph data should have 9 elements" )
[1] TRUE
> assertEqual( .data$MIN, -10 )
[1] TRUE
> .data$MIN <- 0
> xmap.graph.save( .graph, .data )
> .data2 <- xmap.graph.load( .graph )
> assertEqual( .data2$MIN, 0 )
[1] TRUE
> assertEqual( .data, .data2, "Saved and loaded graph data not identical!" )
[1] TRUE
> 
> .graph2 <- xmap.graph.new( .project, "A Graph", "desc", -10, 10, "1", 1000000, 2000000, ylab="label", species="homo_sapiens" )
> 
> .graphs <- xmap.graph.list( .project )
> assertLength( .graphs, 2, paste( "Got", length( .graphs ), "graphs.  Should have 2" ) )
[1] TRUE
> 
> xmap.graph.delete( .graph2 )
> 
> # Plot tests
> ###############################################################################
> 
> .X <- seq( 1000000, 2000000, by=1000 )
> .Y <- runif( length( .X ), -10, 10 )
> .badY <- runif( ( length( .X ) - 1 ), -10, 10 )
> .alphaY <- rep( letters, ceiling( length( .X ) / length( letters ) ) )[ 1:length( .X ) ]
> 
> print( paste( ".X has", length( .X ), "elements, .Y has", length( .Y ), ", .badY has", length( .badY ), "elements, and .alphaY has", length( .alphaY ), "elements" ) )
[1] ".X has 1001 elements, .Y has 1001 , .badY has 1000 elements, and .alphaY has 1001 elements"
> 
> shouldFail( function() {    xmap.plot.new( "FAIL!", "A Plot", .X, .Y, type="line" ) }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' graphid should be an object of class Graph, not character '"
[1] TRUE
> shouldFail( function() {   xmap.plot.load( "FAIL!" )                 }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' plotid should be an object of class Plot, not character '"
[1] TRUE
> shouldFail( function() {   xmap.plot.list( "FAIL!" )                 }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' graphid should be an object of class Graph, not character '"
[1] TRUE
> shouldFail( function() {   xmap.plot.save( "FAIL!", list(), .X, .Y ) }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' plotid should be an object of class Plot, not character '"
[1] TRUE
> shouldFail( function() { xmap.plot.delete( "FAIL!" )                 }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' plotid should be an object of class Plot, not character '"
[1] TRUE
> shouldFail( function() {    xmap.plot.new( .graph2, "A Plot", .X, .Y, type="line" ) }, "Invalid graph parameter shouldn't work!" )
xmapbridge:Project( /tmp/RtmpNSv7tI/2019.Apr.16.03.43.26_0.268.xmb ) 
[1] "Failed (yay) ' non-string argument to internal 'paste' '"
[1] TRUE
> shouldFail( function() {    xmap.plot.new( .graph, "A Plot", .X, .badY, type="line" ) }, "Invalid y list size shouldn't work!" )
[1] "Failed (yay) ' 'x' and 'y' lengths differ '"
[1] TRUE
> 
> .plot <- xmap.plot.new( .graph, "A Plot", .X, .Y, type="line" )
> 
> .plots <- xmap.plot.list( .graph )
> assertLength( .plots, 1, paste( "Got", length( .plots ), "plots.  Should have only 1" ) )
[1] TRUE
> assertEqual( .plot, .plots[[1]], "Plot does not equal the first plot in the list" )
[1] TRUE
> 
> .data <- xmap.plot.load( .plot )
> assertNotNull( .data, "Load failed for plot data" )
[1] TRUE
> shouldFail( function() { assertLength( .data, 0 ) }, "Plot data should have more than 0 elements" )
[1] "Failed (yay) ' invalid length '"
[1] TRUE
> assertEqual( .data$TYPE, "line", "Plot type should be 'line'" )
[1] TRUE
> .data$TYPE <- "area"
> xmap.plot.save( .plot, .data, .X, .Y )
> .data2 <- xmap.plot.load( .plot )
> assertEqual( .data2$TYPE, "area", "Plot type should now be 'area'" )
[1] TRUE
> assertEqual( .data, .data2, "Saved and loaded plot data not identical!" )
[1] TRUE
> 
> .plot2 <- xmap.plot.new( .graph, "A Plot", .X, .Y, type="line" )
> 
> .plots <- xmap.plot.list( .graph )
> assertLength( .plots, 2, paste( "Got", length( .plots ), "plots.  Should have only 2" ) )
[1] TRUE
> 
> xmap.plot.delete( .plot )
> .plots <- xmap.plot.list( .graph )
> assertLength( .plots, 1, paste( "Got", length( .plots ), "plots.  Should have only 1" ) )
[1] TRUE
> 
> # Util tests
> ###############################################################################
> 
> shouldFail( function() { xmap.plot( .X, .badY, species="homo_sapiens", "1", type="line" ) }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' 'x' and 'y' lengths differ '"
[1] TRUE
> shouldFail( function() { xmap.plot( .X, .alphaY, species="homo_sapiens", "1", type="line" ) }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' y seems to contain non-numerics '"
[1] TRUE
> shouldFail( function() { xmap.plot( .X, .Y, species="homo_sapiens", "1", type="INVALID" ) }, "Invalid graph parameter shouldn't work!" )
[1] "Failed (yay) ' 'arg' should be one of \"scatter\", \"line\", \"bar\", \"step\", \"area\", \"steparea\" [dg] [dp] '"
[1] TRUE
> shouldFail( function() { xmap.plot( .X, .Y, species="MONKEY", "1" ) }, "Invalid species parameter shouldn't work!" )
[1] "Failed (yay) ' 'arg' should be one of \"homo_sapiens\", \"mus_musculus\", \"rattus_norvegicus\" '"
[1] TRUE
> shouldFail( function() { xmap.plot( .X, .Y, species="homo_sapiens" ) }, "Missing chromosome should have failed!" )
[1] "Failed (yay) ' You need to specify a chromosome for this plot '"
[1] TRUE
> .projects <- xmap.project.list()
> assertLength( .projects, 1, paste( "Got", length( .projects ), "projects.  There should still just be 1" ) )
[1] TRUE
> 
> .plot <- xmap.plot( .X, .Y, chr="1" )
> .projects <- xmap.project.list()
> assertLength( .projects, 2, paste( "Got", length( .projects ), "projects.  There should be 2" ) )
[1] TRUE
> 
> .graphs <- xmap.graph.list( .plot )
> assertLength( .graphs, 1, paste( "Got", length( .graphs ), "graphs.  There should be 1" ) )
[1] TRUE
> 
> .graph <- xmap.points( .X, .Y )
> .plots <- xmap.plot.list( .plot )
> assertLength( .plots, 2, paste( "Got", length( .plots ), "plots.  There should be 2" ) )
[1] TRUE
> 
> xmap.project.delete( .project )
> xmap.project.delete( .plot )
> .projects <- xmap.project.list()
> assertLength( .projects, 0, paste( "Got", length( .projects ), "projects.  There shouldn't be any" ) )
[1] TRUE
> 
> # Cleanup
> ###############################################################################
> 
> .teardown()
> 
> proc.time()
   user  system elapsed 
  0.912   0.068   0.976 

name	user	system	elapsed
xmap.col	0.020	0.000	0.018
xmap.files	0.072	0.004	0.076
xmap.plot	0.044	0.000	0.045