Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:06:41 -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 ODER on tokay2


To the developers/maintainers of the ODER package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ODER.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 1315/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ODER 1.0.0  (landing page)
David Zhang
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/ODER
git_branch: RELEASE_3_14
git_last_commit: 53a24c4
git_last_commit_date: 2021-10-26 13:13:04 -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: ODER
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ODER.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ODER_1.0.0.tar.gz
StartedAt: 2022-01-23 23:28:57 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 23:54:13 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 1515.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ODER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ODER.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ODER_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ODER.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 'ODER/DESCRIPTION' ... OK
* this is package 'ODER' 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 'ODER' 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
annotatERs          115.89   6.20  122.61
add_expressed_genes 100.83   3.96  106.10
get_opt_ers          76.56   1.00   77.58
ODER                 12.67   1.34   14.01
get_ers               5.41   0.36    6.61
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
annotatERs          102.64   1.42  104.28
add_expressed_genes  80.61   1.51   82.76
get_opt_ers          73.06   1.11   74.18
ODER                 13.91   0.47   14.38
get_ers               5.44   0.62    6.82
* 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

ODER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ODER_1.0.0.tar.gz && rm -rf ODER.buildbin-libdir && mkdir ODER.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ODER.buildbin-libdir ODER_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ODER_1.0.0.zip && rm ODER_1.0.0.tar.gz ODER_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 2139k    2 45685    0     0   292k      0  0:00:07 --:--:--  0:00:07  291k
100 2139k  100 2139k    0     0  5134k      0 --:--:-- --:--:-- --:--:-- 5130k

install for i386

* installing *source* package 'ODER' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ODER'
    finding HTML links ... done
    ODER                                    html  
    add_expressed_genes                     html  
    annotatERs                              html  
    file_cache                              html  
    get_chr_info                            html  
    get_count_matrix                        html  
    get_coverage                            html  
    get_ers                                 html  
    get_opt_ers                             html  
    gtex_SRP012682_SRX222703_lung_auc_1     html  
    gtex_SRP012682_SRX222703_lung_coverage_1
                                            html  
    gtex_SRP012682_SRX222703_lung_erdelta_1
                                            html  
    gtex_SRP012682_SRX222703_lung_ers_1     html  
    lung_junc_21_22                         html  
    plot_ers                                html  
    pseudogene                              html  
    refine_ERs                              html  
    tissue_options                          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 'ODER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ODER' as ODER_1.0.0.zip
* DONE (ODER)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ODER' successfully unpacked and MD5 sums checked

Tests output

ODER.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.

> library(testthat)
> library(ODER)
> 
> test_check("ODER")
Starting 2 test processes
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
   3.92    0.32  393.03 

ODER.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.

> library(testthat)
> library(ODER)
> 
> test_check("ODER")
Starting 2 test processes
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
   5.81    0.45  371.82 

Example timings

ODER.Rcheck/examples_i386/ODER-Ex.timings

nameusersystemelapsed
ODER12.67 1.3414.01
add_expressed_genes100.83 3.96106.10
annotatERs115.89 6.20122.61
file_cache0.310.000.31
get_chr_info0.060.000.06
get_count_matrix2.450.253.95
get_coverage0.530.000.53
get_ers5.410.366.61
get_opt_ers76.56 1.0077.58
plot_ers0.940.040.98
refine_ERs1.50.01.5

ODER.Rcheck/examples_x64/ODER-Ex.timings

nameusersystemelapsed
ODER13.91 0.4714.38
add_expressed_genes80.61 1.5182.76
annotatERs102.64 1.42104.28
file_cache0.380.020.39
get_chr_info0.060.010.08
get_count_matrix2.360.273.99
get_coverage0.510.020.53
get_ers5.440.626.82
get_opt_ers73.06 1.1174.18
plot_ers1.000.061.06
refine_ERs1.710.001.70