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This page was generated on 2022-04-13 12:06:52 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 methrix on tokay2


To the developers/maintainers of the methrix package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methrix.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1115/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methrix 1.8.0  (landing page)
Anand Mayakonda
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/methrix
git_branch: RELEASE_3_14
git_last_commit: 19065b7
git_last_commit_date: 2021-10-26 12:55:50 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: methrix
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methrix.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings methrix_1.8.0.tar.gz
StartedAt: 2022-04-12 22:38:53 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 22:46:12 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 438.6 seconds
RetCode: 0
Status:   OK  
CheckDir: methrix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methrix.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings methrix_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/methrix.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methrix/DESCRIPTION' ... OK
* this is package 'methrix' version '1.8.0'
* 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 'methrix' 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
convert_HDF5_methrix: no visible global function definition for
  'metadata'
convert_methrix: no visible global function definition for 'metadata'
extract_CPGs: no visible global function definition for
  'standardChromosomes'
get_region_summary: no visible binding for global variable '..keep'
get_stats: no visible global function definition for 'metadata'
is_h5: no visible global function definition for 'metadata'
methrix_pca: no visible global function definition for 'barplot'
methrix_pca: no visible global function definition for 'points'
methrix_report: no visible global function definition for 'metadata'
remove_snps: no visible global function definition for 'metadata'
remove_snps: no visible global function definition for
  'seqlevelsStyle<-'
write_bigwigs: no visible global function definition for 'metadata'
write_bigwigs: no visible global function definition for 'seqlengths<-'
write_bigwigs: no visible global function definition for 'seqlengths'
show,methrix: no visible global function definition for 'metadata'
Undefined global functions or variables:
  ..keep barplot metadata points seqlengths seqlengths<-
  seqlevelsStyle<- standardChromosomes
Consider adding
  importFrom("graphics", "barplot", "points")
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
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
remove_snps 7.53   0.77    9.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
remove_snps 5.83   0.28     6.9
* 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-3.14-bioc/meat/methrix.Rcheck/00check.log'
for details.



Installation output

methrix.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/methrix_1.8.0.tar.gz && rm -rf methrix.buildbin-libdir && mkdir methrix.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methrix.buildbin-libdir methrix_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL methrix_1.8.0.zip && rm methrix_1.8.0.tar.gz methrix_1.8.0.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 2457k    0 13287    0     0   154k      0  0:00:15 --:--:--  0:00:15  154k
 45 2457k   45 1129k    0     0  1053k      0  0:00:02  0:00:01  0:00:01 1053k
100 2457k  100 2457k    0     0  1411k      0  0:00:01  0:00:01 --:--:-- 1411k

install for i386

* installing *source* package 'methrix' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'methrix'
    finding HTML links ... done
    combine_methrix                         html  
    convert_HDF5_methrix                    html  
    convert_methrix                         html  
    coverage_filter                         html  
    extract_CPGs                            html  
    get_matrix                              html  
    get_region_summary                      html  
    finding level-2 HTML links ... done

    get_stats                               html  
    load_HDF5_methrix                       html  
    mask_methrix                            html  
    methrix-class                           html  
    methrix2bsseq                           html  
    methrix_data                            html  
    methrix_pca                             html  
    methrix_report                          html  
    order_by_sd                             html  
    plot_coverage                           html  
    plot_density                            html  
    plot_pca                                html  
    plot_stats                              html  
    plot_violin                             html  
    read_bedgraphs                          html  
    region_filter                           html  
    remove_snps                             html  
    remove_uncovered                        html  
    save_HDF5_methrix                       html  
    subset_methrix                          html  
    write_bedgraphs                         html  
    write_bigwigs                           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 'methrix' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methrix' as methrix_1.8.0.zip
* DONE (methrix)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'methrix' successfully unpacked and MD5 sums checked

Tests output

methrix.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(methrix)
Loading required package: data.table
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> test_check("methrix")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
  30.50    2.64   33.65 

methrix.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(methrix)
Loading required package: data.table
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> test_check("methrix")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
  33.01    1.00   34.46 

Example timings

methrix.Rcheck/examples_i386/methrix-Ex.timings

nameusersystemelapsed
convert_HDF5_methrix0.460.220.72
convert_methrix0.330.030.39
coverage_filter0.830.000.83
extract_CPGs000
get_matrix0.170.020.18
get_region_summary0.190.010.21
get_stats0.930.020.95
load_HDF5_methrix0.520.060.64
mask_methrix0.190.000.18
methrix2bsseq000
methrix_data0.010.020.04
methrix_pca0.850.020.85
methrix_report000
order_by_sd0.010.010.04
plot_coverage1.030.051.07
plot_density1.860.051.91
plot_pca0.910.000.90
plot_stats1.220.021.24
plot_violin1.080.001.07
read_bedgraphs000
region_filter0.010.010.04
remove_snps7.530.779.67
remove_uncovered0.800.010.81
save_HDF5_methrix0.510.110.67
subset_methrix0.030.000.03
write_bedgraphs0.330.000.33
write_bigwigs0.360.000.36

methrix.Rcheck/examples_x64/methrix-Ex.timings

nameusersystemelapsed
convert_HDF5_methrix0.390.060.48
convert_methrix0.330.060.47
coverage_filter0.860.020.88
extract_CPGs000
get_matrix0.190.000.18
get_region_summary0.190.000.19
get_stats0.980.011.00
load_HDF5_methrix0.490.050.58
mask_methrix0.150.010.17
methrix2bsseq000
methrix_data0.020.020.03
methrix_pca0.920.000.93
methrix_report000
order_by_sd0.020.000.01
plot_coverage1.110.001.11
plot_density1.920.021.94
plot_pca101
plot_stats1.340.001.34
plot_violin1.140.001.14
read_bedgraphs000
region_filter0.030.010.04
remove_snps5.830.286.90
remove_uncovered0.920.000.92
save_HDF5_methrix0.530.130.70
subset_methrix0.030.000.03
write_bedgraphs0.390.030.45
write_bigwigs0.450.030.49