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CHECK report for multiHiCcompare on tokay2

This page was generated on 2019-10-16 12:42:07 -0400 (Wed, 16 Oct 2019).

Package 1067/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiHiCcompare 1.2.0
John Stansfield
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/multiHiCcompare
Branch: RELEASE_3_9
Last Commit: 1ac2fa1
Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: multiHiCcompare
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiHiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings multiHiCcompare_1.2.0.tar.gz
StartedAt: 2019-10-16 05:28:40 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:36:43 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 482.6 seconds
RetCode: 0
Status:  OK  
CheckDir: multiHiCcompare.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiHiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings multiHiCcompare_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/multiHiCcompare.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.2.0'
* 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 ... NOTE
Namespace in Imports field not imported from: 'GenomeInfoDbData'
  All declared Imports should be used.
* 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 'tail'
.count_manhattan: no visible global function definition for 'axis'
.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'
exportJuicebox: no visible global function definition for 'write.table'
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 global function definition for 'seqlevelsStyle<-'
perm_test: no visible binding for global variable 'chr'
perm_test: no visible binding for global variable 'start'
perm_test: no visible binding for global variable 'end'
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'
topDirs: no visible binding for global variable 'avgLogCPM'
topDirs: no visible binding for global variable 'avgLogFC'
topDirs: no visible binding for global variable 'avgP.adj'
topDirs: no visible binding for global variable 'avgD'
Undefined global functions or variables:
  IRanges avgD avgLogCPM avgLogFC avgP.adj axis chr end hg19_cyto
  logCPM logFC p.adj region1 region2 seqlevelsStyle<- start tail textxy
  write.table
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "end", "start")
  importFrom("utils", "tail", "write.table")
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 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/multiHiCcompare.Rcheck/00check.log'
for details.



Installation output

multiHiCcompare.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/multiHiCcompare_1.2.0.tar.gz && rm -rf multiHiCcompare.buildbin-libdir && mkdir multiHiCcompare.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multiHiCcompare.buildbin-libdir multiHiCcompare_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL multiHiCcompare_1.2.0.zip && rm multiHiCcompare_1.2.0.tar.gz multiHiCcompare_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2556k  100 2556k    0     0  12.2M      0 --:--:-- --:--:-- --:--:-- 12.6M

install for i386

* installing *source* package 'multiHiCcompare' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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_1.2.0.zip
* DONE (multiHiCcompare)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'multiHiCcompare' successfully unpacked and MD5 sums checked

Tests output

multiHiCcompare.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages



> 
> test_check("multiHiCcompare")
== testthat results  ===========================================================
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  49.26    1.64   50.84 

multiHiCcompare.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages



> 
> test_check("multiHiCcompare")
== testthat results  ===========================================================
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  45.01    0.90   45.62 

Example timings

multiHiCcompare.Rcheck/examples_i386/multiHiCcompare-Ex.timings

nameusersystemelapsed
Hicexp-class0.020.000.02
MD_composite0.780.091.01
MD_hicexp0.960.061.01
cyclic_loess1.570.131.71
exportJuicebox0.070.040.12
fastlo1.180.081.23
hic_exactTest000
hic_filter1.470.131.58
hic_glm000
hic_scale0.160.000.16
hic_table0.030.040.05
make_hicexp1.660.221.87
manhattan_hicexp0.610.030.64
meta0.010.020.03
normalized0.020.000.02
perm_test000
plot_counts0.140.000.26
plot_pvals0.170.010.27
pval_heatmap2.340.082.45
resolution0.040.000.03
results0.000.020.02
topDirs0.060.030.09

multiHiCcompare.Rcheck/examples_x64/multiHiCcompare-Ex.timings

nameusersystemelapsed
Hicexp-class0.020.000.02
MD_composite0.190.020.20
MD_hicexp1.500.121.86
cyclic_loess1.810.081.89
exportJuicebox0.030.050.56
fastlo1.270.061.25
hic_exactTest000
hic_filter0.820.030.86
hic_glm000
hic_scale0.130.020.14
hic_table0.010.000.02
make_hicexp2.070.062.13
manhattan_hicexp0.680.030.87
meta0.020.000.02
normalized0.020.010.03
perm_test000
plot_counts0.120.020.14
plot_pvals0.130.020.14
pval_heatmap2.090.062.23
resolution0.020.000.01
results0.020.010.04
topDirs0.090.000.09