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CHECK report for ABAEnrichment on tokay1

This page was generated on 2021-01-24 11:53:31 -0500 (Sun, 24 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE ABAEnrichment PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 7/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABAEnrichment 1.20.0
Steffi Grote
Snapshot Date: 2021-01-23 14:40:16 -0500 (Sat, 23 Jan 2021)
URL: https://git.bioconductor.org/packages/ABAEnrichment
Branch: RELEASE_3_12
Last Commit: 608433a
Last Changed Date: 2020-10-27 11:07:16 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ABAEnrichment
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ABAEnrichment.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ABAEnrichment_1.20.0.tar.gz
StartedAt: 2021-01-24 00:15:17 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 00:20:49 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 332.3 seconds
RetCode: 0
Status:  OK  
CheckDir: ABAEnrichment.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ABAEnrichment.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ABAEnrichment_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ABAEnrichment.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ABAEnrichment/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ABAEnrichment' version '1.20.0'
* 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 'ABAEnrichment' 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 ... NOTE
Unexported objects imported by ':::' calls:
  'GOfuncR:::binom_category_test' 'GOfuncR:::binom_randset'
  'GOfuncR:::conti_category_test' 'GOfuncR:::conti_randset'
  'GOfuncR:::hyper_category_test' 'GOfuncR:::hyper_randset'
  'GOfuncR:::wilcox_category_test' 'GOfuncR:::wilcox_randset'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aba_enrich: no visible binding for global variable 'signal'
aba_enrich: no visible binding for global variable 'gene_id'
get_annotated_genes: no visible binding for global variable 'signal'
get_annotated_genes: no visible binding for global variable 'gene_id'
get_annotated_genes: no visible binding for global variable
  'structure_id'
Undefined global functions or variables:
  gene_id signal structure_id
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/ABAEnrichment/libs/i386/ABAEnrichment.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/ABAEnrichment/libs/x64/ABAEnrichment.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
aba_enrich          10.92   0.71   15.74
get_annotated_genes  6.10   0.43    6.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
aba_enrich 9.78   0.61   13.83
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ABAEnrichment.Rcheck/00check.log'
for details.

Installation output

ABAEnrichment.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ABAEnrichment_1.20.0.tar.gz && rm -rf ABAEnrichment.buildbin-libdir && mkdir ABAEnrichment.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ABAEnrichment.buildbin-libdir ABAEnrichment_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ABAEnrichment_1.20.0.zip && rm ABAEnrichment_1.20.0.tar.gz ABAEnrichment_1.20.0.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
100 2605k  100 2605k    0     0  4503k      0 --:--:-- --:--:-- --:--:-- 4530k

install for i386

* installing *source* package 'ABAEnrichment' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c unlock_environment.cc -o unlock_environment.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ABAEnrichment.dll tmp.def RcppExports.o unlock_environment.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ABAEnrichment.buildbin-libdir/00LOCK-ABAEnrichment/00new/ABAEnrichment/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ABAEnrichment'
    finding HTML links ... done
    aba_enrich                              html  
    get_annotated_genes                     html  
    get_expression                          html  
    get_id                                  html  
    get_name                                html  
    get_sampled_substructures               html  
    get_superstructures                     html  
    plot_expression                         html  
    finding level-2 HTML links ... done

** 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 'ABAEnrichment' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c unlock_environment.cc -o unlock_environment.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ABAEnrichment.dll tmp.def RcppExports.o unlock_environment.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ABAEnrichment.buildbin-libdir/ABAEnrichment/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ABAEnrichment' as ABAEnrichment_1.20.0.zip
* DONE (ABAEnrichment)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ABAEnrichment' successfully unpacked and MD5 sums checked

Tests output

ABAEnrichment.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(ABAEnrichment)
> 
> test_check("ABAEnrichment")
    V1        V2        V3
2 chr3  76500000  90500000
3 chr7 113600000 124700000
1 chr1 104000000 114900000
4 chr8  54500000  65400000
    V1        V2        V3
1 chr1 104000000 114900000
2 chr3  76500000  90500000
3 chr5         0   4700000
4 chr7 113600000 124700000
5 chr8  54500000  65400000
Read 1535 terms.
Found 1534 nodes.
Graph created.
Reading nodes_per_gene file... 
Found 188 usable entrys in C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmp8k3qI2\file2fe4508f5798_Allen:4005 with 678 GOs
Creating 1000 random gene sets from 4 random regions...
The candidate does not fit - try again...
This was trial 1
The candidate does not fit - try again...
This was trial 2
The candidate does not fit - try again...
This was trial 3
The candidate does not fit - try again...
This was trial 4
The candidate does not fit - try again...
This was trial 5
The candidate does not fit - try again...
This was trial 6
The candidate does not fit - try again...
This was trial 7
The candidate does not fit - try again...
This was trial 8
The candidate does not fit - try again...
This was trial 9
The candidate does not fit - try again...
This was trial 10
Error: 10 times in a row the candidate regions could not be placed randomly without forcing them to overlap. Consider using larger background regions.
== Warnings ====================================================================
-- Warning (test_0load_by_name.R:6:2): Load data on first request --------------
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_0load_by_name.R:6:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:17:1): (code run outside of `test_that()`) -------
No expression data for genes: abc, 0.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:17:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No expression data for genes: abc, 0.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:37:1): (code run outside of `test_that()`) -------
No expression data for genes: abc, 0.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:37:0
-- Warning (test_aba_enrich.R:44:2): genes that are not in data are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("abc" %in% res3$genes[, 1], is_false()) test_aba_enrich.R:44:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:45:2): genes that are not in data are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("8312" %in% res3$genes[, 1], is_true()) test_aba_enrich.R:45:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:56:1): (code run outside of `test_that()`) -------
No expression data for genes: SOX8, FOXG1.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:56:0
-- Warning (test_aba_enrich.R:74:1): (code run outside of `test_that()`) -------
No expression data for genes: SOX8, FOXG1.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:74:0
-- Warning (test_aba_enrich.R:96:5): One candidate or background gene without expression data stops. --
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:96:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:97:5): One candidate or background gene without expression data stops. --
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:97:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:108:5): One candidate or background gene without coordinates stops. --
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:108:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:108:5): One candidate or background gene without coordinates stops. --
No coordinates available for genes: LINC00239, MIRLET7BHG.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:108:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:109:5): One candidate or background gene without coordinates stops. --
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:109:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:109:5): One candidate or background gene without coordinates stops. --
No coordinates available for genes: LINC00239, MIRLET7BHG.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:109:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:113:1): (code run outside of `test_that()`) ------
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:113:0
-- Warning (test_aba_enrich.R:113:1): (code run outside of `test_that()`) ------
No coordinates available for genes: LINC00239, MIRLET7BHG.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:113:0
-- Warning (test_aba_enrich.R:116:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("NGFR" %in% res4$genes[, 1], is_true()) test_aba_enrich.R:116:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:117:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("HSPB2" %in% res4$genes[, 1], is_true()) test_aba_enrich.R:117:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:118:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("TESTI" %in% res4$genes[, 1], is_false()) test_aba_enrich.R:118:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:119:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("MUELL" %in% res4$genes[, 1], is_false()) test_aba_enrich.R:119:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:120:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("LINC00239" %in% res4$genes[, 1], is_false()) test_aba_enrich.R:120:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:121:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("MIRLET7BHG" %in% res4$genes[, 1], is_false()) test_aba_enrich.R:121:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:127:1): (code run outside of `test_that()`) ------
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:127:0
-- Warning (test_aba_enrich.R:130:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("NGFR" %in% res4b$genes[, 1], is_true()) test_aba_enrich.R:130:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:131:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("HSPB2" %in% res4b$genes[, 1], is_true()) test_aba_enrich.R:131:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:132:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("TESTI" %in% res4b$genes[, 1], is_false()) test_aba_enrich.R:132:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:133:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("MUELL" %in% res4b$genes[, 1], is_false()) test_aba_enrich.R:133:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:134:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("LINC00239" %in% res4b$genes[, 1], is_true()) test_aba_enrich.R:134:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:135:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("MIRLET7BHG" %in% res4b$genes[, 1], is_true()) test_aba_enrich.R:135:8
 2. testthat:::condition(object)
-- Warning (test_detect_identifier.R:17:4): ENSEMBL is not recognized ----------
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that(...) test_detect_identifier.R:17:8
 2. testthat:::condition(object)
-- Warning (test_detect_identifier.R:18:4): ENSEMBL is not recognized ----------
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that(...) test_detect_identifier.R:18:8
 2. testthat:::condition(object)
-- Warning (test_detect_identifier.R:19:4): ENSEMBL is not recognized ----------
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that(...) test_detect_identifier.R:19:8
 2. testthat:::condition(object)
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No expression data for genes: MIRLET7BHG.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:20:5): warning and return(NULL) when no node below fwer-threshold --
No significantly enriched brain regions at FWER-threshold 0.05
Backtrace:
 1. testthat::expect_that(get_annotated_genes(res_dev), equals(NULL)) test_get_annotated_genes.R:20:4
 6. ABAEnrichment::get_annotated_genes(res_dev)
 7. ABAEnrichment:::get_signi_combis(res, fwer_threshold)
-- Warning (test_get_annotated_genes.R:20:5): warning and return(NULL) when no node below fwer-threshold --
No expression data found for the input.
Backtrace:
 1. testthat::expect_that(get_annotated_genes(res_dev), equals(NULL)) test_get_annotated_genes.R:20:4
 6. ABAEnrichment::get_annotated_genes(res_dev)
-- Warning (test_get_superstructures.R:16:2): superstructures include structure itself --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_get_superstructures.R:16:8
 2. testthat:::condition(object)
-- Warning (test_get_superstructures.R:17:2): superstructures include structure itself --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_get_superstructures.R:17:8
 2. testthat:::condition(object)
-- Warning (test_get_superstructures.R:42:2): superstructures include structure itself --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_get_superstructures.R:42:8
 2. testthat:::condition(object)
-- Warning (test_get_superstructures.R:43:2): superstructures include structure itself --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_get_superstructures.R:43:8
 2. testthat:::condition(object)

[ FAIL 0 | WARN 49 | SKIP 0 | PASS 146 ]
> 
> proc.time()
   user  system elapsed 
  79.59   13.34   92.20

ABAEnrichment.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(ABAEnrichment)
> 
> test_check("ABAEnrichment")
    V1        V2        V3
2 chr3  76500000  90500000
3 chr7 113600000 124700000
1 chr1 104000000 114900000
4 chr8  54500000  65400000
    V1        V2        V3
1 chr1 104000000 114900000
2 chr3  76500000  90500000
3 chr5         0   4700000
4 chr7 113600000 124700000
5 chr8  54500000  65400000
Read 1535 terms.
Found 1534 nodes.
Graph created.
Reading nodes_per_gene file... 
Found 188 usable entrys in C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpkjrtx8\file23941e543bdd_Allen:4005 with 678 GOs
Creating 1000 random gene sets from 4 random regions...
The candidate does not fit - try again...
This was trial 1
The candidate does not fit - try again...
This was trial 2
The candidate does not fit - try again...
This was trial 3
The candidate does not fit - try again...
This was trial 4
The candidate does not fit - try again...
This was trial 5
The candidate does not fit - try again...
This was trial 6
The candidate does not fit - try again...
This was trial 7
The candidate does not fit - try again...
This was trial 8
The candidate does not fit - try again...
This was trial 9
The candidate does not fit - try again...
This was trial 10
Error: 10 times in a row the candidate regions could not be placed randomly without forcing them to overlap. Consider using larger background regions.
== Warnings ====================================================================
-- Warning (test_0load_by_name.R:6:2): Load data on first request --------------
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_0load_by_name.R:6:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:17:1): (code run outside of `test_that()`) -------
No expression data for genes: abc, 0.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:17:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No expression data for genes: abc, 0.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:25:1): (code run outside of `test_that()`) -------
No statistics for cutoff >= 0.999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:25:0
-- Warning (test_aba_enrich.R:37:1): (code run outside of `test_that()`) -------
No expression data for genes: abc, 0.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:37:0
-- Warning (test_aba_enrich.R:44:2): genes that are not in data are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("abc" %in% res3$genes[, 1], is_false()) test_aba_enrich.R:44:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:45:2): genes that are not in data are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("8312" %in% res3$genes[, 1], is_true()) test_aba_enrich.R:45:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:56:1): (code run outside of `test_that()`) -------
No expression data for genes: SOX8, FOXG1.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:56:0
-- Warning (test_aba_enrich.R:74:1): (code run outside of `test_that()`) -------
No expression data for genes: SOX8, FOXG1.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:74:0
-- Warning (test_aba_enrich.R:96:5): One candidate or background gene without expression data stops. --
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:96:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:97:5): One candidate or background gene without expression data stops. --
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:97:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:108:5): One candidate or background gene without coordinates stops. --
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:108:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:108:5): One candidate or background gene without coordinates stops. --
No coordinates available for genes: LINC00239, MIRLET7BHG.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:108:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:109:5): One candidate or background gene without coordinates stops. --
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:109:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:109:5): One candidate or background gene without coordinates stops. --
No coordinates available for genes: LINC00239, MIRLET7BHG.
  These genes were not included in the analysis.
Backtrace:
 1. testthat::expect_that(...) test_aba_enrich.R:109:4
 8. ABAEnrichment::aba_enrich(...)
-- Warning (test_aba_enrich.R:113:1): (code run outside of `test_that()`) ------
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:113:0
-- Warning (test_aba_enrich.R:113:1): (code run outside of `test_that()`) ------
No coordinates available for genes: LINC00239, MIRLET7BHG.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:113:0
-- Warning (test_aba_enrich.R:116:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("NGFR" %in% res4$genes[, 1], is_true()) test_aba_enrich.R:116:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:117:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("HSPB2" %in% res4$genes[, 1], is_true()) test_aba_enrich.R:117:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:118:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("TESTI" %in% res4$genes[, 1], is_false()) test_aba_enrich.R:118:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:119:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("MUELL" %in% res4$genes[, 1], is_false()) test_aba_enrich.R:119:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:120:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("LINC00239" %in% res4$genes[, 1], is_false()) test_aba_enrich.R:120:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:121:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("MIRLET7BHG" %in% res4$genes[, 1], is_false()) test_aba_enrich.R:121:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:127:1): (code run outside of `test_that()`) ------
No expression data for genes: TESTI, MUELL.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_aba_enrich.R:127:0
-- Warning (test_aba_enrich.R:130:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("NGFR" %in% res4b$genes[, 1], is_true()) test_aba_enrich.R:130:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:131:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("HSPB2" %in% res4b$genes[, 1], is_true()) test_aba_enrich.R:131:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:132:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("TESTI" %in% res4b$genes[, 1], is_false()) test_aba_enrich.R:132:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:133:2): genes that are not in data or coordinates are not returned in the genes object --
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that("MUELL" %in% res4b$genes[, 1], is_false()) test_aba_enrich.R:133:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:134:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("LINC00239" %in% res4b$genes[, 1], is_true()) test_aba_enrich.R:134:8
 2. testthat:::condition(object)
-- Warning (test_aba_enrich.R:135:2): genes that are not in data or coordinates are not returned in the genes object --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that("MIRLET7BHG" %in% res4b$genes[, 1], is_true()) test_aba_enrich.R:135:8
 2. testthat:::condition(object)
-- Warning (test_detect_identifier.R:17:4): ENSEMBL is not recognized ----------
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that(...) test_detect_identifier.R:17:8
 2. testthat:::condition(object)
-- Warning (test_detect_identifier.R:18:4): ENSEMBL is not recognized ----------
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that(...) test_detect_identifier.R:18:8
 2. testthat:::condition(object)
-- Warning (test_detect_identifier.R:19:4): ENSEMBL is not recognized ----------
`is_false()` is deprecated. Please use `expect_false()` instead.
Backtrace:
 1. testthat::expect_that(...) test_detect_identifier.R:19:8
 2. testthat:::condition(object)
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No expression data for genes: MIRLET7BHG.
  These genes were not included in the analysis.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:16:1): (code run outside of `test_that()`) --
No statistics for cutoff >= 0.9999. No candidate gene expression above cutoff.
Backtrace:
 1. ABAEnrichment::aba_enrich(...) test_get_annotated_genes.R:16:0
-- Warning (test_get_annotated_genes.R:20:5): warning and return(NULL) when no node below fwer-threshold --
No significantly enriched brain regions at FWER-threshold 0.05
Backtrace:
 1. testthat::expect_that(get_annotated_genes(res_dev), equals(NULL)) test_get_annotated_genes.R:20:4
 6. ABAEnrichment::get_annotated_genes(res_dev)
 7. ABAEnrichment:::get_signi_combis(res, fwer_threshold)
-- Warning (test_get_annotated_genes.R:20:5): warning and return(NULL) when no node below fwer-threshold --
No expression data found for the input.
Backtrace:
 1. testthat::expect_that(get_annotated_genes(res_dev), equals(NULL)) test_get_annotated_genes.R:20:4
 6. ABAEnrichment::get_annotated_genes(res_dev)
-- Warning (test_get_superstructures.R:16:2): superstructures include structure itself --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_get_superstructures.R:16:8
 2. testthat:::condition(object)
-- Warning (test_get_superstructures.R:17:2): superstructures include structure itself --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_get_superstructures.R:17:8
 2. testthat:::condition(object)
-- Warning (test_get_superstructures.R:42:2): superstructures include structure itself --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_get_superstructures.R:42:8
 2. testthat:::condition(object)
-- Warning (test_get_superstructures.R:43:2): superstructures include structure itself --
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_get_superstructures.R:43:8
 2. testthat:::condition(object)

[ FAIL 0 | WARN 49 | SKIP 0 | PASS 146 ]
> 
> proc.time()
   user  system elapsed 
  67.60   15.64   79.26

Example timings

ABAEnrichment.Rcheck/examples_i386/ABAEnrichment-Ex.timings

nameusersystemelapsed
aba_enrich10.92 0.7115.74
get_annotated_genes6.100.436.50
get_expression0.110.020.13
get_id0.020.000.02
get_name000
get_sampled_substructures000
get_superstructures0.060.000.07
plot_expression0.250.000.42

ABAEnrichment.Rcheck/examples_x64/ABAEnrichment-Ex.timings

nameusersystemelapsed
aba_enrich 9.78 0.6113.83
get_annotated_genes4.360.364.25
get_expression0.060.050.11
get_id0.020.000.01
get_name000
get_sampled_substructures000
get_superstructures0.030.020.05
plot_expression0.200.030.23