Package: ABAEnrichment

Version: 1.8.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ABAEnrichment_1.8.0.tar.gz

StartedAt: 2018-04-11 21:18:09 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 21:20:47 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 158.0 seconds

RetCode: 0

Status:  OK

CheckDir: ABAEnrichment.Rcheck

Warnings: 0

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###
### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ABAEnrichment_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ABAEnrichment.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.0’
* 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 ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    2.6Mb
    libs   7.3Mb
* 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
Found the following possibly unsafe calls:
File ‘ABAEnrichment/R/aba_enrich.R’:
  unlockBinding("remember", aba_env)

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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    1.9Mb    1.1Mb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.6-bioc/meat/ABAEnrichment.Rcheck/00check.log’
for details.

* installing *source* package ‘ABAEnrichment’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c binom_categorytest.cc -o binom_categorytest.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c binom_randset.cc -o binom_randset.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c blocks.cpp -o blocks.o
blocks.cpp: In function ‘std::set<int> rannum_blocks(std::vector<bed_str>, std::vector<bed_str>, const std::map<std::__cxx11::basic_string<char>, int>&, std::vector<gen_pos_str>)’:
blocks.cpp:33:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j=0; j < candidate_bed.size(); j++){
                   ^
blocks.cpp:37:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int k=0; k < background.size(); k++){  
                    ^
blocks.cpp:79:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int g=0; g<genes_pos.size(); g++){
                   ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c conti_categorytest.cc -o conti_categorytest.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c conti_randset.cc -o conti_randset.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c gene.cc -o gene.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c gene_binom.cc -o gene_binom.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c gene_conti.cc -o gene_conti.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genes.cc -o genes.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genes_binom.cc -o genes_binom.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genes_conti.cc -o genes_conti.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go.cc -o go.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_graph.cc -o go_graph.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_graph_binom.cc -o go_graph_binom.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_graph_conti.cc -o go_graph_conti.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_graph_hyper.cc -o go_graph_hyper.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_groups.cc -o go_groups.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_groups_binom.cc -o go_groups_binom.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_groups_conti.cc -o go_groups_conti.o
go_groups_conti.cc: In member function ‘int* go_groups_conti::calculate_data(std::__cxx11::string&, std::ostream*)’:
go_groups_conti.cc:72:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for ( int idx=0 ; idx < names.size() ; ++idx ) {
                        ^
go_groups_conti.cc: In member function ‘int* go_groups_conti::calculate_rand(std::__cxx11::string&, std::ostream*)’:
go_groups_conti.cc:185:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for ( int idx=0 ; idx < names.size() ; ++idx ) {
                        ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_groups_hyper.cc -o go_groups_hyper.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_obj.cc -o go_obj.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_obj_binom.cc -o go_obj_binom.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_obj_conti.cc -o go_obj_conti.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c go_obj_hyper.cc -o go_obj_hyper.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c hyper_categorytest.cc -o hyper_categorytest.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c hyper_randset.cc -o hyper_randset.o
hyper_randset.cc: In function ‘void hyper_randset(std::__cxx11::string, int, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, bool)’:
hyper_randset.cc:234:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while (random_numbers.size() < n_candidate) { 
                                 ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c idmap.cc -o idmap.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c overall_sign.cc -o overall_sign.o
overall_sign.cc: In member function ‘void overall_significance::print_cdfs(std::ostream&)’:
overall_sign.cc:58:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int set = 0 ; set < cdfs.size() ; ++set )  
                           ^
overall_sign.cc: In member function ‘double overall_significance::alt_sign(int)’:
overall_sign.cc:73:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for ( int set = 0 ; set < cdfs.size() ; ++set ) {
                            ^
overall_sign.cc:75:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if ( (*cdfs[set])[pval] >= dataset ) 
                              ^
overall_sign.cc: In member function ‘double overall_significance::significance(int, double)’:
overall_sign.cc:101:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for ( int set = 0 ; set < cdfs.size() ; ++set ) { 
                           ^
overall_sign.cc:137:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for ( int i=0 ; i < maxima.size() ; i++ ) {
                    ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ran_genelen.cpp -o ran_genelen.o
ran_genelen.cpp: In function ‘std::set<int> rannum_genelen(int, const std::map<std::__cxx11::basic_string<char>, int>&, std::vector<gen_pos_str>, long int)’:
ran_genelen.cpp:20:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while (random_numbers.size() < n_candidate) { 
                               ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c read_bed.cpp -o read_bed.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c roll.cpp -o roll.o
roll.cpp: In function ‘std::set<int> rannum_roll(std::vector<bed_str>, std::vector<bed_str>, const std::map<std::__cxx11::basic_string<char>, int>&, std::vector<gen_pos_str>)’:
roll.cpp:32:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int j=0; j < candidate_bed.size(); j++){  
                  ^
roll.cpp:38:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < background_bed.size(); i++){
                   ^
roll.cpp:105:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int g=0; g<genes_pos.size(); g++){
                   ^
roll.cpp:120:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if ((k == background_bed.size()) || (background_bed[k].chrom != ran_chrom)){
           ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c transitions.cc -o transitions.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c unlock_environment.cc -o unlock_environment.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c wilcox_categorytest.cc -o wilcox_categorytest.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c wilcox_randset.cc -o wilcox_randset.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o ABAEnrichment.so RcppExports.o binom_categorytest.o binom_randset.o blocks.o conti_categorytest.o conti_randset.o gene.o gene_binom.o gene_conti.o genes.o genes_binom.o genes_conti.o go.o go_graph.o go_graph_binom.o go_graph_conti.o go_graph_hyper.o go_groups.o go_groups_binom.o go_groups_conti.o go_groups_hyper.o go_obj.o go_obj_binom.o go_obj_conti.o go_obj_hyper.o hyper_categorytest.o hyper_randset.o idmap.o overall_sign.o ran_genelen.o read_bed.o roll.o transitions.o unlock_environment.o wilcox_categorytest.o wilcox_randset.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/ABAEnrichment.Rcheck/ABAEnrichment/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ABAEnrichment)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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  3  76500000  90500000
3  7 113600000 124700000
1  1 104000000 114900000
4  8  54500000  65400000
  V1        V2        V3
1  1 104000000 114900000
2  3  76500000  90500000
3  5         0   4700000
4  7 113600000 124700000
5  8  54500000  65400000
Read 1535 terms.
Found 1534 nodes.
Graph created.
Reading nodes_per_gene file... 
Found 188 usable entrys in /tmp/RtmpDqEgRg/file2966cb58356_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: 181 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 34.960   1.688  36.948 

name	user	system	elapsed
aba_enrich	3.516	0.104	3.643
get_annotated_genes	2.924	0.152	3.080
get_expression	0.112	0.000	0.111
get_id	0.028	0.000	0.025
get_name	0.012	0.000	0.014
get_sampled_substructures	0.000	0.000	0.002
get_superstructures	0.040	0.000	0.038
plot_expression	0.240	0.000	0.238