Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:20 -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 segmenter on tokay2


To the developers/maintainers of the segmenter package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmenter.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 1754/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmenter 1.0.0  (landing page)
Mahmoud Ahmed
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/segmenter
git_branch: RELEASE_3_14
git_last_commit: 45aa76e
git_last_commit_date: 2021-10-26 13:10:57 -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: segmenter
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmenter.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings segmenter_1.0.0.tar.gz
StartedAt: 2022-04-13 02:40:12 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 02:53:20 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 787.9 seconds
RetCode: 0
Status:   OK  
CheckDir: segmenter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmenter.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings segmenter_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/segmenter.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 'segmenter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmenter' version '1.0.0'
* 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 'segmenter' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   3.8Mb
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
annotate_segments 26.10   1.33   44.31
learn_model        0.27   0.08   15.46
binarize_bam       0.00   0.02    9.93
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
annotate_segments 21.69   0.42   22.11
learn_model        0.27   0.04   16.89
binarize_bam       0.02   0.00    9.17
* 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/segmenter.Rcheck/00check.log'
for details.



Installation output

segmenter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/segmenter_1.0.0.tar.gz && rm -rf segmenter.buildbin-libdir && mkdir segmenter.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=segmenter.buildbin-libdir segmenter_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL segmenter_1.0.0.zip && rm segmenter_1.0.0.tar.gz segmenter_1.0.0.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
  2 3923k    2 99687    0     0   510k      0  0:00:07 --:--:--  0:00:07  509k
 48 3923k   48 1911k    0     0  1622k      0  0:00:02  0:00:01  0:00:01 1622k
100 3923k  100 3923k    0     0  2018k      0  0:00:01  0:00:01 --:--:-- 2018k

install for i386

* installing *source* package 'segmenter' ...
** 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 'segmenter'
    finding HTML links ... done
    accessors                               html  
    annotate_segments                       html  
    binarize_bam                            html  
    binarize_bed                            html  
    compare_models                          html  
    count_reads_ranges                      html  
    dot-Binarize                            html  
    dot-LearnModel                          html  
    emissions_file                          html  
    enrichment_files                        html  
    get_frequency                           html  
    get_width                               html  
    learn_model                             html  
    merge_segments_bins                     html  
    methods                                 html  
    model_file                              html  
    overlap_files                           html  
    plot_heatmap                            html  
    range_bins                              html  
    range_counts                            html  
    read_bam_file                           html  
    read_bins_file                          html  
    read_cellmark_file                      html  
    read_chromsize_file                     html  
    read_emissions_file                     html  
    read_enrichment_file                    html  
    read_model_file                         html  
    read_overlap_file                       html  
    read_segements_file                     html  
    read_transitions_file                   html  
    segmentation                            html  
    segments_files                          html  
    test_obj                                html  
    test_objs                               html  
    tidy_ranges                             html  
    transitions_file                        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 'segmenter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmenter' as segmenter_1.0.0.zip
* DONE (segmenter)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'segmenter' successfully unpacked and MD5 sums checked

Tests output

segmenter.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(segmenter)

> 
> test_check("segmenter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 123 ]
> 
> proc.time()
   user  system elapsed 
  60.46    5.15  146.46 

segmenter.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(segmenter)

> 
> test_check("segmenter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 123 ]
> 
> proc.time()
   user  system elapsed 
  58.78    3.93  149.57 

Example timings

segmenter.Rcheck/examples_i386/segmenter-Ex.timings

nameusersystemelapsed
accessors0.080.000.08
annotate_segments26.10 1.3344.31
binarize_bam0.000.029.93
compare_models0.020.000.01
emissions_file000
enrichment_files000
get_frequency0.030.010.05
get_width0.450.240.69
learn_model 0.27 0.0815.46
methods000
model_file000
overlap_files000
plot_heatmap0.640.030.68
read_bam_file0.060.010.07
read_bins_file2.000.172.18
read_cellmark_file000
read_chromsize_file000
read_emissions_file000
read_enrichment_file0.020.000.01
read_model_file000
read_overlap_file000
read_segements_file0.030.000.03
read_transitions_file000
segments_files000
tidy_ranges0.030.000.03
transitions_file000

segmenter.Rcheck/examples_x64/segmenter-Ex.timings

nameusersystemelapsed
accessors0.100.000.09
annotate_segments21.69 0.4222.11
binarize_bam0.020.009.17
compare_models000
emissions_file000
enrichment_files000
get_frequency0.030.000.03
get_width0.500.180.68
learn_model 0.27 0.0416.89
methods000
model_file000
overlap_files000
plot_heatmap0.790.010.81
read_bam_file0.020.020.03
read_bins_file2.730.252.99
read_cellmark_file000
read_chromsize_file000
read_emissions_file000
read_enrichment_file0.020.000.01
read_model_file000
read_overlap_file000
read_segements_file0.040.000.05
read_transitions_file000
segments_files000
tidy_ranges0.070.000.06
transitions_file000