Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:05:59 -0500 (Mon, 24 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" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 cageminer on tokay2


To the developers/maintainers of the cageminer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cageminer.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 236/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cageminer 1.0.0  (landing page)
Fabrício Almeida-Silva
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/cageminer
git_branch: RELEASE_3_14
git_last_commit: 32c8304
git_last_commit_date: 2021-10-26 13:11:20 -0500 (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: cageminer
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cageminer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cageminer_1.0.0.tar.gz
StartedAt: 2022-01-23 16:25:49 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 16:36:42 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 653.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cageminer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cageminer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cageminer_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cageminer.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 'cageminer/DESCRIPTION' ... OK
* this is package 'cageminer' 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 'cageminer' 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 ... 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 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
plot_snp_circos 7.17   2.11    9.28
mine_step2      2.83   0.11   23.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plot_snp_circos 6.44   0.08    6.51
mine_step2      2.50   0.08   26.00
* 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: OK


Installation output

cageminer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cageminer_1.0.0.tar.gz && rm -rf cageminer.buildbin-libdir && mkdir cageminer.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cageminer.buildbin-libdir cageminer_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cageminer_1.0.0.zip && rm cageminer_1.0.0.tar.gz cageminer_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
100  408k  100  408k    0     0  1181k      0 --:--:-- --:--:-- --:--:-- 1183k

install for i386

* installing *source* package 'cageminer' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cageminer'
    finding HTML links ... done
    chr_length                              html  
    gcn                                     html  
    gene_ranges                             html  
    guides                                  html  
    hubs                                    html  
    mine2                                   html  
    mine_candidates                         html  
    mine_step1                              html  
    mine_step2                              html  
    mine_step3                              html  
    mined_candidates                        html  
    pepper_se                               html  
    plot_snp_circos                         html  
    plot_snp_distribution                   html  
    score_genes                             html  
    simulate_windows                        html  
    snp_pos                                 html  
    tfs                                     html  
*** copying figures
** 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 'cageminer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cageminer' as cageminer_1.0.0.zip
* DONE (cageminer)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cageminer' successfully unpacked and MD5 sums checked

Tests output

cageminer.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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(cageminer)

> 
> test_check("cageminer")
Enrichment analysis for module cyan...


Number of genes < 'pick_top'. Picking all genes.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  32.23    4.10   73.09 

cageminer.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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(cageminer)

> 
> test_check("cageminer")
Enrichment analysis for module cyan...


Number of genes < 'pick_top'. Picking all genes.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  31.82    1.25   66.73 

Example timings

cageminer.Rcheck/examples_i386/cageminer-Ex.timings

nameusersystemelapsed
chr_length000
gcn000
gene_ranges0.070.000.06
guides0.040.000.05
hubs000
mine20.000.010.01
mine_candidates000
mine_step10.140.050.19
mine_step2 2.83 0.1123.70
mine_step30.420.110.54
mined_candidates000
pepper_se0.020.010.03
plot_snp_circos7.172.119.28
plot_snp_distribution0.050.010.11
score_genes0.010.020.14
simulate_windows1.770.082.28
snp_pos0.000.010.02
tfs000

cageminer.Rcheck/examples_x64/cageminer-Ex.timings

nameusersystemelapsed
chr_length000
gcn0.010.000.02
gene_ranges0.080.010.09
guides0.060.000.06
hubs0.000.020.02
mine20.020.000.01
mine_candidates000
mine_step10.330.000.33
mine_step2 2.50 0.0826.00
mine_step30.490.030.51
mined_candidates000
pepper_se0.040.010.07
plot_snp_circos6.440.086.51
plot_snp_distribution0.020.000.02
score_genes0.000.020.01
simulate_windows1.070.001.08
snp_pos0.000.010.02
tfs000