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BioC 3.4: CHECK report for ABAEnrichment on malbec1

This page was generated on 2017-04-15 16:13:10 -0400 (Sat, 15 Apr 2017).

Package 7/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABAEnrichment 1.4.0
Steffi Grote
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ABAEnrichment
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ABAEnrichment
Version: 1.4.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ABAEnrichment_1.4.0.tar.gz
StartedAt: 2017-04-14 20:49:48 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 20:52:14 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 146.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ABAEnrichment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ABAEnrichment_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ABAEnrichment.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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  7.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.8Mb
    libs   4.3Mb
* 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 loading without being on the library search path ... 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 global function definition for ‘write.table’
aba_enrich : <anonymous>: no visible global function definition for
  ‘quantile’
aba_enrich: no visible global function definition for ‘quantile’
aba_enrich: no visible global function definition for ‘aggregate’
aba_enrich: no visible global function definition for ‘read.table’
get_expression: no visible global function definition for ‘aggregate’
load_by_name: no visible global function definition for ‘data’
plot_expression: no visible global function definition for
  ‘heat.colors’
plot_expression: no visible global function definition for ‘rainbow’
rearrange_output: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate data heat.colors quantile rainbow read.table write.table
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "data", "read.table", "write.table")
to your NAMESPACE file.
* 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    1.7Mb    1.0Mb       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
Examples with CPU or elapsed time > 5s
             user system elapsed
aba_enrich 43.084  0.392  43.536
* 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-3.4-bioc/meat/ABAEnrichment.Rcheck/00check.log’
for details.


ABAEnrichment.Rcheck/00install.out:

* installing *source* package ‘ABAEnrichment’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c gene.cc -o gene.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c genes.cc -o genes.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c go.cc -o go.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c go_graph.cc -o go_graph.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c go_graph_hyper.cc -o go_graph_hyper.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c go_groups.cc -o go_groups.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c go_groups_hyper.cc -o go_groups_hyper.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c go_obj.cc -o go_obj.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c go_obj_hyper.cc -o go_obj_hyper.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c hyper_categorytest.cc -o hyper_categorytest.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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)’:
hyper_randset.cc:227:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while (random_numbers.size() < n_candidate) { 
                                 ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c idmap.cc -o idmap.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c read_bed.cpp -o read_bed.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c transitions.cc -o transitions.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c unlock_environment.cc -o unlock_environment.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c wilcox_categorytest.cc -o wilcox_categorytest.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c wilcox_randset.cc -o wilcox_randset.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o ABAEnrichment.so RcppExports.o blocks.o gene.o genes.o go.o go_graph.o go_graph_hyper.o go_groups.o go_groups_hyper.o go_obj.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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)

ABAEnrichment.Rcheck/ABAEnrichment-Ex.timings:

nameusersystemelapsed
aba_enrich43.084 0.39243.536
get_expression0.5040.0320.536
get_name0.0080.0000.005
get_sampled_substructures0.0000.0000.001
get_superstructures0.0240.0000.022
plot_expression0.5880.0160.606