Multiple platform build/check report for BioC 3.14 - CHECK results for ODER on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

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: 2022-04-12 23:52:36 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-13 00:12:55 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 1218.5 seconds

RetCode: 1

Status: ERROR

CheckDir: ODER.Rcheck

Warnings: NA

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### 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
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ODER.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 '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          133.31   2.56  136.12
add_expressed_genes 122.39   4.45  135.67
get_opt_ers          84.30   0.65   85.10
ODER                 15.11   1.23   16.36
get_ers               7.20   0.50    8.65
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
annotatERs          106.03   1.36  107.59
add_expressed_genes  87.61   1.57   89.89
get_opt_ers          80.87   1.30   82.17
ODER                 14.58   0.67   15.25
get_ers               4.00   0.35    5.23
* 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'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    2.   \-testthat::test_dir(...)
    3.     \-testthat:::test_files(...)
    4.       \-testthat:::test_files(...)
    5.         +-testthat::with_reporter(...)
    6.         | \-base::tryCatch(...)
    7.         |   \-base tryCatchList(expr, classes, parentenv, handlers)
    8.         |     \-base tryCatchOne(expr, names, parentenv, handlers[[1L]])
    9.         |       \-base doTryCatch(return(expr), name, parentenv, handler)
   10.         \-testthat:::parallel_event_loop_chunky(queue, reporters)
   11.           \-queue$poll(Inf)
   12.             \-base::lapply(...)
   13.               \-testthat FUN(X[[i]], ...)
   14.                 \-private$handle_error(msg, i)
   15.                   \-rlang::abort(...)
  Execution halted
* 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 ERROR
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ODER.Rcheck/00check.log'
for details.

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###
### 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
###
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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
 17 2139k   17  371k    0     0   933k      0  0:00:02 --:--:--  0:00:02  933k
100 2139k  100 2139k    0     0  1636k      0  0:00:01  0:00:01 --:--:-- 1636k

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


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(ODER)
> 
> test_check("ODER")
Starting 2 test processes
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
   4.09    0.29  388.64


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(ODER)
> 
> test_check("ODER")
Starting 2 test processes


Error:
! testthat subprocess failed to start, stderr:
Error in data$sofile[[paste0("arch-", .Platform$r_arch)]] : 

  subscript out of bounds

Calls: callr_startup_hook -> <Anonymous>

Caused by error:
! R session crashed with exit code 1
Backtrace:
     x
  1. \-testthat::test_check("ODER")
  2.   \-testthat::test_dir(...)
  3.     \-testthat:::test_files(...)
  4.       \-testthat:::test_files(...)
  5.         +-testthat::with_reporter(...)
  6.         | \-base::tryCatch(...)
  7.         |   \-base tryCatchList(expr, classes, parentenv, handlers)
  8.         |     \-base tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.         |       \-base doTryCatch(return(expr), name, parentenv, handler)
 10.         \-testthat:::parallel_event_loop_chunky(queue, reporters)
 11.           \-queue$poll(Inf)
 12.             \-base::lapply(...)
 13.               \-testthat FUN(X[[i]], ...)
 14.                 \-private$handle_error(msg, i)
 15.                   \-rlang::abort(...)
Execution halted

name	user	system	elapsed
ODER	15.11	1.23	16.36
add_expressed_genes	122.39	4.45	135.67
annotatERs	133.31	2.56	136.12
file_cache	0.56	0.00	0.57
get_chr_info	0.08	0.03	0.11
get_count_matrix	2.64	0.11	4.05
get_coverage	0.54	0.03	0.56
get_ers	7.20	0.50	8.65
get_opt_ers	84.30	0.65	85.10
plot_ers	0.88	0.03	0.90
refine_ERs	1.59	0.00	1.60

name	user	system	elapsed
ODER	14.58	0.67	15.25
add_expressed_genes	87.61	1.57	89.89
annotatERs	106.03	1.36	107.59
file_cache	0.42	0.01	0.44
get_chr_info	0.08	0.02	0.09
get_count_matrix	2.28	0.23	3.86
get_coverage	0.71	0.03	0.74
get_ers	4.00	0.35	5.23
get_opt_ers	80.87	1.30	82.17
plot_ers	0.91	0.05	0.95
refine_ERs	1.45	0.00	1.45

CHECK results for ODER on tokay2

Summary

Command output

Installation output

Tests output

Example timings