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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ABAEnrichment.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ABAEnrichment_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ABAEnrichment.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
aba_enrich          11.562  0.803   7.881
get_annotated_genes  9.743  0.493   3.506
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/ABAEnrichment.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ABAEnrichment
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ABAEnrichment’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c unlock_environment.cc -o unlock_environment.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o ABAEnrichment.so RcppExports.o unlock_environment.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-ABAEnrichment/00new/ABAEnrichment/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ABAEnrichment)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 /tmp/Rtmpf2YWci/file91aef6b2df149_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 
122.427   6.329  46.186