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This page was generated on 2022-01-21 13:06:28 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for HiCcompare on tokay2


To the developers/maintainers of the HiCcompare package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCcompare.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 867/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCcompare 1.16.0  (landing page)
John Stansfield , Mikhail Dozmorov
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/HiCcompare
git_branch: RELEASE_3_14
git_last_commit: dafc05f
git_last_commit_date: 2021-10-26 12:36:44 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: HiCcompare
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings HiCcompare_1.16.0.tar.gz
StartedAt: 2022-01-20 21:15:56 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 21:21:38 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 341.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: HiCcompare.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings HiCcompare_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/HiCcompare.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HiCcompare/DESCRIPTION' ... OK
* this is package 'HiCcompare' version '1.16.0'
* package encoding: UTF-8
* 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 'HiCcompare' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
* 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 ... NOTE
.adjust_pval : <anonymous>: no visible binding for global variable
  'p.adj'
.adjust_pval : <anonymous>: no visible binding for global variable
  'p.value'
.adjust_pval: no visible binding for global variable 'p.value'
.adjust_pval: no visible binding for global variable 'p.adj'
.calc.diff.thresh: no visible global function definition for 'sd'
.calc.pval: no visible binding for global variable 'D'
.calc.pval: no visible binding for global variable 'p.value'
.calc.pval: no visible binding for global variable 'p.adj'
.calc.pval: no visible binding for global variable 'adj.M'
.calc.pval: no visible binding for global variable 'fold.change'
.calc.pval: no visible binding for global variable 'adj.IF2'
.calc.pval: no visible binding for global variable 'adj.IF1'
.calc_z2: no visible global function definition for 'sd'
.calc_z2: no visible binding for global variable 'Z'
.calc_z2: no visible global function definition for 'pnorm'
.calc_z2: no visible binding for global variable 'p.value'
.loess.matrix: no visible binding for global variable 'adj.IF1'
.loess.matrix: no visible binding for global variable 'IF1'
.loess.matrix: no visible binding for global variable 'adj.IF2'
.loess.matrix: no visible binding for global variable 'IF2'
.loess.matrix: no visible binding for global variable 'adj.M'
.loess.matrix: no visible binding for global variable 'A'
.sim.mat: no visible global function definition for 'head'
.split_cent: no visible binding for global variable
  'centromere_locations'
.split_cent: no visible binding for global variable 'start1'
.split_cent: no visible binding for global variable 'start2'
.split_cent: no visible binding for global variable 'chr1'
.split_cent: no visible binding for global variable 'chr2'
MA_norm: no visible binding for global variable 'D'
MA_norm: no visible binding for global variable 'M'
MA_norm: no visible binding for global variable 'adj.IF1'
MA_norm: no visible binding for global variable 'IF1'
MA_norm: no visible binding for global variable 'adj.IF2'
MA_norm: no visible binding for global variable 'IF2'
MA_norm: no visible binding for global variable 'adj.M'
cooler2sparse: no visible binding for global variable 'chr1'
cooler2sparse: no visible binding for global variable 'chr2'
cooler2sparse: no visible binding for global variable 'IF'
create.hic.table: no visible binding for global variable 'D'
create.hic.table: no visible binding for global variable 'region2'
create.hic.table: no visible binding for global variable 'region1'
create.hic.table: no visible binding for global variable 'IF2'
create.hic.table: no visible binding for global variable 'M'
create.hic.table: no visible binding for global variable 'IF1'
create.hic.table: no visible binding for global variable 'i'
create.hic.table: no visible binding for global variable 'j'
filter_params: no visible binding for global variable 'M'
filter_params: no visible binding for global variable 'IF1'
filter_params: no visible binding for global variable 'IF2'
filter_params: no visible global function definition for 'axis'
full2sparse: no visible binding for global variable 'IF'
hic_compare : <anonymous>: no visible binding for global variable
  'p.adj'
hic_simulate: no visible binding for global variable 'bias.slope'
hic_simulate: no visible global function definition for 'na.omit'
hicpro2bedpe: no visible binding for global variable 'chr1'
hicpro2bedpe: no visible binding for global variable 'chr2'
manhattan_plot: no visible binding for global variable 'bp'
manhattan_plot: no visible binding for global variable 'count'
sim.other.methods: no visible binding for global variable 'adj.IF1'
sim.other.methods: no visible binding for global variable 'IF1'
sim.other.methods: no visible binding for global variable 'adj.IF2'
sim.other.methods: no visible binding for global variable 'IF2'
sim.other.methods: no visible binding for global variable 'adj.M'
sim.other.methods: no visible binding for global variable 'M'
sim.other.methods: no visible global function definition for 'na.omit'
sim_matrix: no visible binding for global variable 'bias.slope'
total_sum: no visible binding for global variable 'IF2'
total_sum: no visible binding for global variable 'M'
total_sum: no visible binding for global variable 'IF1'
total_sum: no visible binding for global variable 'chr1'
volcano: no visible binding for global variable 'A'
volcano: no visible binding for global variable 'adj.IF1'
volcano: no visible binding for global variable 'adj.IF2'
volcano: no visible binding for global variable 'p.value'
volcano: no visible binding for global variable 'D'
Undefined global functions or variables:
  A D IF IF1 IF2 M Z adj.IF1 adj.IF2 adj.M axis bias.slope bp
  centromere_locations chr1 chr2 count fold.change head i j na.omit
  p.adj p.value pnorm region1 region2 sd start1 start2
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "D", "na.omit", "pnorm", "sd")
  importFrom("utils", "head")
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 LazyData ... WARNING
  LazyData DB of 5.6 MB without LazyDataCompression set
  See ยง1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/HiCcompare.Rcheck/00check.log'
for details.



Installation output

HiCcompare.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/HiCcompare_1.16.0.tar.gz && rm -rf HiCcompare.buildbin-libdir && mkdir HiCcompare.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HiCcompare.buildbin-libdir HiCcompare_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL HiCcompare_1.16.0.zip && rm HiCcompare_1.16.0.tar.gz HiCcompare_1.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 3211k    0 14875    0     0   126k      0  0:00:25 --:--:--  0:00:25  127k
 73 3211k   73 2358k    0     0  2155k      0  0:00:01  0:00:01 --:--:-- 2155k
100 3211k  100 3211k    0     0  2371k      0  0:00:01  0:00:01 --:--:-- 2371k

install for i386

* installing *source* package 'HiCcompare' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'ceiling' 
** help
*** installing help indices
  converting help for package 'HiCcompare'
    finding HTML links ... done
    HMEC.chr10                              html  
    HMEC.chr22                              html  
    HiCcompare-package                      html  
    KRnorm                                  html  
    MA_norm                                 html  
    MD.plot1                                html  
    MD.plot2                                html  
    NHEK.chr10                              html  
    NHEK.chr22                              html  
    SCN                                     html  
    brain_table                             html  
    centromere_locations                    html  
    cooler                                  html  
    cooler2bedpe                            html  
    cooler2sparse                           html  
    create.hic.table                        html  
    filter_params                           html  
    full2sparse                             html  
    get_CNV                                 html  
    hg19_blacklist                          html  
    hg38_blacklist                          html  
    hic_compare                             html  
    hic_diff                                html  
    hic_loess                               html  
    hic_simulate                            html  
    hicpro2bedpe                            html  
    hmec.IS                                 html  
    make_InteractionSet                     html  
    manhattan_plot                          html  
    nhek.IS                                 html  
    remove_centromere                       html  
    sim.other.methods                       html  
    sim_matrix                              html  
    sparse2full                             html  
    split_centromere                        html  
    total_sum                               html  
    visualize_pvals                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'HiCcompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiCcompare' as HiCcompare_1.16.0.zip
* DONE (HiCcompare)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'HiCcompare' successfully unpacked and MD5 sums checked

Tests output

HiCcompare.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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)
> library(HiCcompare)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("HiCcompare")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 28 ]
> 
> proc.time()
   user  system elapsed 
  12.42    0.79   13.23 

HiCcompare.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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)
> library(HiCcompare)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("HiCcompare")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 28 ]
> 
> proc.time()
   user  system elapsed 
  12.34    0.53   13.12 

Example timings

HiCcompare.Rcheck/examples_i386/HiCcompare-Ex.timings

nameusersystemelapsed
KRnorm000
MA_norm0.090.020.11
MD.plot10.330.040.38
MD.plot20.280.040.31
SCN000
cooler2bedpe000
cooler2sparse0.730.010.75
create.hic.table0.000.020.01
filter_params3.020.173.19
full2sparse000
get_CNV000
hic_compare0.50.00.5
hic_diff4.510.084.59
hic_loess0.300.010.32
hic_simulate1.280.001.28
hicpro2bedpe000
make_InteractionSet0.190.000.19
manhattan_plot0.640.030.67
remove_centromere000
sim.other.methods0.860.020.88
sim_matrix2.060.002.06
sparse2full000
split_centromere0.020.000.01
total_sum0.120.000.13
visualize_pvals0.700.030.73

HiCcompare.Rcheck/examples_x64/HiCcompare-Ex.timings

nameusersystemelapsed
KRnorm000
MA_norm0.100.020.11
MD.plot10.500.010.52
MD.plot20.470.020.58
SCN000
cooler2bedpe000
cooler2sparse1.000.021.01
create.hic.table0.020.000.02
filter_params4.790.074.87
full2sparse000
get_CNV000
hic_compare0.500.020.52
hic_diff3.660.033.69
hic_loess0.30.00.3
hic_simulate1.230.031.26
hicpro2bedpe000
make_InteractionSet0.190.010.21
manhattan_plot0.640.030.67
remove_centromere000
sim.other.methods0.870.020.89
sim_matrix1.220.051.27
sparse2full0.000.010.01
split_centromere0.020.000.02
total_sum0.110.020.12
visualize_pvals0.730.030.77