Package: HilbertCurve

Version: 1.10.1

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HilbertCurve.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings HilbertCurve_1.10.1.tar.gz

StartedAt: 2018-10-17 02:41:18 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:44:51 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 212.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: HilbertCurve.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HilbertCurve.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings HilbertCurve_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/HilbertCurve.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HilbertCurve/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HilbertCurve' version '1.10.1'
* 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 whether package 'HilbertCurve' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/GenomicHilbertCurve-class.rd:30: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/GenomicHilbertCurve.rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/HilbertCurve.rd:33: file link 'grob' in package 'grid' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_centered_text-HilbertCurve-method.rd:16: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_layer-GenomicHilbertCurve-method.rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_layer-HilbertCurve-method.rd:17: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_normal_points-HilbertCurve-method.rd:17: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_points-GenomicHilbertCurve-method.rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_points-HilbertCurve-method.rd:18: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_polygon-GenomicHilbertCurve-method.rd:16: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_polygon-HilbertCurve-method.rd:17: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_rect-GenomicHilbertCurve-method.rd:16: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_rect-HilbertCurve-method.rd:17: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_segmented_points-HilbertCurve-method.rd:19: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_segments-GenomicHilbertCurve-method.rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_segments-HilbertCurve-method.rd:16: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_text-GenomicHilbertCurve-method.rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_text-HilbertCurve-method.rd:15: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/HilbertCurve.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
hc_layer-HilbertCurve-method        14.24   0.45   15.97
hc_layer-GenomicHilbertCurve-method  7.96   0.22    8.17
GenomicHilbertCurve                  6.55   0.17    6.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
hc_layer-HilbertCurve-method        16.31   0.45   16.78
hc_layer-GenomicHilbertCurve-method 10.00   0.13   10.13
GenomicHilbertCurve                  9.27   0.13    9.97
hc_png-HilbertCurve-method           5.96   0.18    6.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/HilbertCurve.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/HilbertCurve_1.10.1.tar.gz && rm -rf HilbertCurve.buildbin-libdir && mkdir HilbertCurve.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HilbertCurve.buildbin-libdir HilbertCurve_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL HilbertCurve_1.10.1.zip && rm HilbertCurve_1.10.1.tar.gz HilbertCurve_1.10.1.zip
###
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100 5184k  100 5184k    0     0  50.2M      0 --:--:-- --:--:-- --:--:-- 53.8M

install for i386

* installing *source* package 'HilbertCurve' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HilbertCurve'
    finding HTML links ... done
    GenomicHilbertCurve-class               html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/GenomicHilbertCurve-class.rd:30: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    GenomicHilbertCurve                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/GenomicHilbertCurve.rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    HilbertCurve-class                      html  
    HilbertCurve                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/HilbertCurve.rd:33: file link 'grob' in package 'grid' does not exist and so has been treated as a topic
    default_overlay                         html  
    hc_centered_text-HilbertCurve-method    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_centered_text-HilbertCurve-method.rd:16: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    hc_layer-GenomicHilbertCurve-method     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_layer-GenomicHilbertCurve-method.rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    hc_layer-HilbertCurve-method            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_layer-HilbertCurve-method.rd:17: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    hc_layer-dispatch                       html  
    hc_level-HilbertCurve-method            html  
    hc_map-GenomicHilbertCurve-method       html  
    hc_normal_points-HilbertCurve-method    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_normal_points-HilbertCurve-method.rd:17: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    hc_offset-HilbertCurve-method           html  
    hc_png-HilbertCurve-method              html  
    hc_points-GenomicHilbertCurve-method    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_points-GenomicHilbertCurve-method.rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    hc_points-HilbertCurve-method           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_points-HilbertCurve-method.rd:18: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    hc_points-dispatch                      html  
    hc_polygon-GenomicHilbertCurve-method   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_polygon-GenomicHilbertCurve-method.rd:16: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    hc_polygon-HilbertCurve-method          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_polygon-HilbertCurve-method.rd:17: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    hc_polygon-dispatch                     html  
    hc_rect-GenomicHilbertCurve-method      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_rect-GenomicHilbertCurve-method.rd:16: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    hc_rect-HilbertCurve-method             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_rect-HilbertCurve-method.rd:17: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    hc_rect-dispatch                        html  
    hc_segmented_points-HilbertCurve-method
                                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_segmented_points-HilbertCurve-method.rd:19: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    hc_segments-GenomicHilbertCurve-method
                                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_segments-GenomicHilbertCurve-method.rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    hc_segments-HilbertCurve-method         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_segments-HilbertCurve-method.rd:16: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    hc_segments-dispatch                    html  
    hc_text-GenomicHilbertCurve-method      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_text-GenomicHilbertCurve-method.rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    hc_text-HilbertCurve-method             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp44Nmsd/R.INSTALL18843c5fe8b/HilbertCurve/man/hc_text-HilbertCurve-method.rd:15: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    hc_text-dispatch                        html  
    show-HilbertCurve-method                html  
    unzoom-HilbertCurve-method              html  
    zoom-HilbertCurve-method                html  
** building package indices
** installing vignettes
   'HilbertCurve.Rmd' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'HilbertCurve' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HilbertCurve' as HilbertCurve_1.10.1.zip
* DONE (HilbertCurve)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'HilbertCurve' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(HilbertCurve)))
> 
> test_check("HilbertCurve")
== testthat results  ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.31    0.28    3.56 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(HilbertCurve)))
> 
> test_check("HilbertCurve")
== testthat results  ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.14    0.20    4.34