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CHECK report for ABAEnrichment on celaya2

This page was generated on 2019-10-16 12:56:11 -0400 (Wed, 16 Oct 2019).

Package 7/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABAEnrichment 1.14.1
Steffi Grote
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ABAEnrichment
Branch: RELEASE_3_9
Last Commit: e1ebfb5
Last Changed Date: 2019-07-14 10:14:59 -0400 (Sun, 14 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ABAEnrichment
Version: 1.14.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ABAEnrichment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ABAEnrichment_1.14.1.tar.gz
StartedAt: 2019-10-16 00:23:04 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:25:41 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 156.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ABAEnrichment.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ABAEnrichment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ABAEnrichment_1.14.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ABAEnrichment.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.1’
* 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 ... OK
* 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 or elapsed time > 5s
                      user system elapsed
aba_enrich          17.448  6.101  14.588
get_annotated_genes 13.698  6.147   6.115
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ABAEnrichment.Rcheck/00check.log’
for details.

Installation output

ABAEnrichment.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ABAEnrichment
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ABAEnrichment’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c unlock_environment.cc -o unlock_environment.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ABAEnrichment.so RcppExports.o unlock_environment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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)

Tests output

ABAEnrichment.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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/RtmpNqq1KX/file5dfd4beb85c4_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.
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 146 | SKIPPED: 0 | WARNINGS: 49 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
103.607  50.679  77.903

Example timings

ABAEnrichment.Rcheck/ABAEnrichment-Ex.timings

nameusersystemelapsed
aba_enrich17.448 6.10114.588
get_annotated_genes13.698 6.147 6.115
get_expression0.4480.4300.224
get_id0.0280.0080.035
get_name0.0080.0030.011
get_sampled_substructures0.0030.0000.004
get_superstructures0.0740.0190.092
plot_expression0.2080.0500.256