Multiple platform build/check report for BioC 3.13 - CHECK results for multiHiCcompare on tokay2

Package: multiHiCcompare

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiHiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings multiHiCcompare_1.10.0.tar.gz

StartedAt: 2021-10-15 02:28:06 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:34:24 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 378.4 seconds

RetCode: 0

Status: OK

CheckDir: multiHiCcompare.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiHiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings multiHiCcompare_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/multiHiCcompare.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'multiHiCcompare/DESCRIPTION' ... OK
* this is package 'multiHiCcompare' version '1.10.0'
* 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 'multiHiCcompare' 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
* 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
.count_manhattan: no visible global function definition for 'textxy'
cyclic_loess: no visible binding for global variable 'chr'
cyclic_loess: no visible binding for global variable 'region1'
cyclic_loess: no visible binding for global variable 'region2'
exportJuicebox: no visible binding for global variable 'logCPM'
exportJuicebox: no visible binding for global variable 'logFC'
exportJuicebox: no visible binding for global variable 'p.adj'
fastlo: no visible binding for global variable 'chr'
fastlo: no visible binding for global variable 'region1'
fastlo: no visible binding for global variable 'region2'
hic_exactTest: no visible binding for global variable 'chr'
hic_exactTest: no visible binding for global variable 'region1'
hic_exactTest: no visible binding for global variable 'region2'
hic_filter: no visible binding for global variable 'hg19_cyto'
hic_glm: no visible binding for global variable 'chr'
hic_glm: no visible binding for global variable 'region1'
hic_glm: no visible binding for global variable 'region2'
make_hicexp: no visible binding for global variable 'hg19_cyto'
make_hicexp: no visible binding for global variable 'region2'
make_hicexp: no visible binding for global variable 'region1'
make_hicexp: no visible binding for global variable 'chr'
perm_test: no visible binding for global variable 'chr'
perm_test: no visible global function definition for 'IRanges'
topDirs: no visible binding for global variable 'logCPM'
topDirs: no visible binding for global variable 'logFC'
topDirs: no visible binding for global variable 'p.adj'
Undefined global functions or variables:
  IRanges chr hg19_cyto logCPM logFC p.adj region1 region2 textxy
* 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 ... OK
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/multiHiCcompare.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/multiHiCcompare_1.10.0.tar.gz && rm -rf multiHiCcompare.buildbin-libdir && mkdir multiHiCcompare.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multiHiCcompare.buildbin-libdir multiHiCcompare_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL multiHiCcompare_1.10.0.zip && rm multiHiCcompare_1.10.0.tar.gz multiHiCcompare_1.10.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 2557k    0  7887    0     0  91467      0  0:00:28 --:--:--  0:00:28 91709
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100 2557k  100 2557k    0     0  1901k      0  0:00:01  0:00:01 --:--:-- 1901k

install for i386

* installing *source* package 'multiHiCcompare' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'multiHiCcompare'
    finding HTML links ... done
    HCT116_r1                               html  
    HCT116_r2                               html  
    HCT116_r3                               html  
    HCT116_r4                               html  
    HCT116_r5                               html  
    HCT116_r6                               html  
    Hicexp-class                            html  
    MD_composite                            html  
    MD_hicexp                               html  
    cyclic_loess                            html  
    exportJuicebox                          html  
    fastlo                                  html  
    hg19_cyto                               html  
    hg38_cyto                               html  
    hic_exactTest                           html  
    hic_filter                              html  
    hic_glm                                 html  
    hic_scale                               html  
    hic_table                               html  
    hicexp2                                 html  
    hicexp_diff                             html  
    make_hicexp                             html  
    manhattan_hicexp                        html  
    meta                                    html  
    normalized                              html  
    perm_test                               html  
    plot_counts                             html  
    plot_pvals                              html  
    pval_heatmap                            html  
    resolution                              html  
    results                                 html  
    show                                    html  
    smartApply                              html  
    topDirs                                 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 'multiHiCcompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'multiHiCcompare' as multiHiCcompare_1.10.0.zip
* DONE (multiHiCcompare)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'multiHiCcompare' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(multiHiCcompare)
> 
> test_check("multiHiCcompare")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  41.04    1.43   42.42


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(multiHiCcompare)
> 
> test_check("multiHiCcompare")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  42.79    0.64   43.35

name	user	system	elapsed
Hicexp-class	0.01	0.01	0.03
MD_composite	0.25	0.02	0.27
MD_hicexp	1.29	0.13	1.42
cyclic_loess	1.97	0.10	2.08
exportJuicebox	0.06	0.00	0.09
fastlo	1.66	0.04	1.69
hic_exactTest	0	0	0
hic_filter	0.56	0.07	0.64
hic_glm	0	0	0
hic_scale	0.08	0.00	0.08
hic_table	0.02	0.00	0.01
make_hicexp	0.75	0.07	0.81
manhattan_hicexp	0.43	0.00	0.44
meta	0.00	0.01	0.02
normalized	0.02	0.00	0.01
perm_test	0	0	0
plot_counts	0.06	0.02	0.08
plot_pvals	0.06	0.00	0.06
pval_heatmap	1.55	0.03	1.58
resolution	0.00	0.01	0.01
results	0.01	0.00	0.02
topDirs	0.07	0.00	0.06

name	user	system	elapsed
Hicexp-class	0.03	0.02	0.05
MD_composite	0.22	0.01	0.23
MD_hicexp	1.40	0.05	1.45
cyclic_loess	1.54	0.06	1.60
exportJuicebox	0.03	0.00	0.07
fastlo	1.08	0.03	1.11
hic_exactTest	0	0	0
hic_filter	0.56	0.00	0.57
hic_glm	0	0	0
hic_scale	0.11	0.02	0.12
hic_table	0.05	0.00	0.04
make_hicexp	1.33	0.00	1.33
manhattan_hicexp	0.48	0.01	0.50
meta	0.02	0.00	0.02
normalized	0.01	0.00	0.01
perm_test	0	0	0
plot_counts	0.07	0.00	0.07
plot_pvals	0.04	0.02	0.06
pval_heatmap	1.24	0.02	1.25
resolution	0.00	0.01	0.01
results	0.01	0.02	0.04
topDirs	0.05	0.00	0.04

CHECK results for multiHiCcompare on tokay2

Summary

Command output

Installation output

Tests output

Example timings