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BioC 3.4: CHECK report for HilbertCurve on malbec1

This page was generated on 2017-04-15 16:13:08 -0400 (Sat, 15 Apr 2017).

Package 592/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HilbertCurve 1.4.0
Zuguang Gu
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/HilbertCurve
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HilbertCurve
Version: 1.4.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings HilbertCurve_1.4.0.tar.gz
StartedAt: 2017-04-14 23:12:23 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:14:08 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 105.2 seconds
RetCode: 0
Status:  OK 
CheckDir: HilbertCurve.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings HilbertCurve_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/HilbertCurve.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HilbertCurve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HilbertCurve’ version ‘1.4.0’
* 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 ‘HilbertCurve’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GenomicHilbertCurve: no visible global function definition for ‘new’
GenomicHilbertCurve: no visible global function definition for
  ‘slotNames’
GenomicHilbertCurve: no visible global function definition for ‘slot<-’
GenomicHilbertCurve: no visible global function definition for ‘slot’
HilbertCurve: no visible global function definition for ‘new’
hc_centered_text,HilbertCurve : <anonymous>: no visible global function
  definition for ‘hist’
hc_layer,GenomicHilbertCurve: no visible global function definition for
  ‘callNextMethod’
hc_points,GenomicHilbertCurve: no visible global function definition
  for ‘callNextMethod’
hc_polygon,GenomicHilbertCurve: no visible global function definition
  for ‘callNextMethod’
hc_rect,GenomicHilbertCurve: no visible global function definition for
  ‘callNextMethod’
hc_segmented_points,HilbertCurve: no visible global function definition
  for ‘rgb’
hc_segments,GenomicHilbertCurve: no visible global function definition
  for ‘callNextMethod’
hc_text,GenomicHilbertCurve: no visible global function definition for
  ‘callNextMethod’
Undefined global functions or variables:
  callNextMethod hist new rgb slot slot<- slotNames
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "hist")
  importFrom("methods", "callNextMethod", "new", "slot", "slot<-",
             "slotNames")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
hc_layer-HilbertCurve-method        12.744  0.080  12.834
hc_layer-GenomicHilbertCurve-method  5.624  0.048   5.678
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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-3.4-bioc/meat/HilbertCurve.Rcheck/00check.log’
for details.


HilbertCurve.Rcheck/00install.out:

* installing *source* package ‘HilbertCurve’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HilbertCurve)

HilbertCurve.Rcheck/HilbertCurve-Ex.timings:

nameusersystemelapsed
GenomicHilbertCurve-class0.0000.0040.001
GenomicHilbertCurve3.0160.0123.196
HilbertCurve-class0.0000.0000.001
HilbertCurve1.6760.0121.688
default_overlay0.0000.0000.001
hc_centered_text-HilbertCurve-method0.0520.0000.056
hc_layer-GenomicHilbertCurve-method5.6240.0485.678
hc_layer-HilbertCurve-method12.744 0.08012.834
hc_layer-dispatch0.0040.0000.000
hc_level-HilbertCurve-method0.0280.0000.027
hc_map-GenomicHilbertCurve-method2.2960.0002.297
hc_normal_points-HilbertCurve-method000
hc_offset-HilbertCurve-method0.0160.0040.020
hc_png-HilbertCurve-method4.0680.0204.088
hc_points-GenomicHilbertCurve-method0.2120.0000.214
hc_points-HilbertCurve-method0.4360.0000.439
hc_points-dispatch000
hc_polygon-GenomicHilbertCurve-method0.4280.0000.428
hc_polygon-HilbertCurve-method0.0480.0000.047
hc_polygon-dispatch000
hc_rect-GenomicHilbertCurve-method0.1280.0000.125
hc_rect-HilbertCurve-method0.0320.0000.030
hc_rect-dispatch000
hc_segmented_points-HilbertCurve-method0.0000.0000.001
hc_segments-GenomicHilbertCurve-method0.5160.0000.515
hc_segments-HilbertCurve-method0.0560.0000.057
hc_segments-dispatch000
hc_text-GenomicHilbertCurve-method0.10.00.1
hc_text-HilbertCurve-method0.0200.0000.021
hc_text-dispatch000
show-HilbertCurve-method0.0080.0000.008
unzoom-HilbertCurve-method0.0080.0000.007
zoom-HilbertCurve-method0.0080.0000.007