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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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###
### Running command:
###
### rm -rf ABAEnrichment.buildbin-libdir ABAEnrichment.Rcheck && mkdir ABAEnrichment.buildbin-libdir ABAEnrichment.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ABAEnrichment.buildbin-libdir ABAEnrichment_1.4.0.tar.gz >ABAEnrichment.Rcheck\00install.out 2>&1 && cp ABAEnrichment.Rcheck\00install.out ABAEnrichment-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ABAEnrichment.buildbin-libdir --install="check:ABAEnrichment-install.out" --force-multiarch --no-vignettes --timings ABAEnrichment_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/ABAEnrichment.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.4.0'
* 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 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
** checking loading without being on the library search path ... 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 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 ... 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-3.4-bioc/meat/ABAEnrichment.buildbin-libdir/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)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
aba_enrich 108.39 22.89 131.29
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
aba_enrich 80.87 22.44 104.78
* 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-3.4-bioc/meat/ABAEnrichment.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ABAEnrichment' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -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::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++){
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c gene.cc -o gene.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c genes.cc -o genes.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go.cc -o go.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_graph.cc -o go_graph.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_graph_hyper.cc -o go_graph_hyper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_groups.cc -o go_groups.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_groups_hyper.cc -o go_groups_hyper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_obj.cc -o go_obj.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_obj_hyper.cc -o go_obj_hyper.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c hyper_categorytest.cc -o hyper_categorytest.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c hyper_randset.cc -o hyper_randset.o
hyper_randset.cc: In function 'void hyper_randset(std::string, int, std::string, std::string, std::string)':
hyper_randset.cc:227:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (random_numbers.size() < n_candidate) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c idmap.cc -o idmap.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -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++ ) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c ran_genelen.cpp -o ran_genelen.o
ran_genelen.cpp: In function 'std::set<int> rannum_genelen(int, const std::map<std::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) {
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c read_bed.cpp -o read_bed.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -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::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)){
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c transitions.cc -o transitions.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c unlock_environment.cc -o unlock_environment.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c wilcox_categorytest.cc -o wilcox_categorytest.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c wilcox_randset.cc -o wilcox_randset.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ABAEnrichment.dll tmp.def 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 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/ABAEnrichment.buildbin-libdir/ABAEnrichment/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'ABAEnrichment' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -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::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++){
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c gene.cc -o gene.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c genes.cc -o genes.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go.cc -o go.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_graph.cc -o go_graph.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_graph_hyper.cc -o go_graph_hyper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_groups.cc -o go_groups.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_groups_hyper.cc -o go_groups_hyper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_obj.cc -o go_obj.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c go_obj_hyper.cc -o go_obj_hyper.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c hyper_categorytest.cc -o hyper_categorytest.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c hyper_randset.cc -o hyper_randset.o
hyper_randset.cc: In function 'void hyper_randset(std::string, int, std::string, std::string, std::string)':
hyper_randset.cc:227:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (random_numbers.size() < n_candidate) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c idmap.cc -o idmap.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -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++ ) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c ran_genelen.cpp -o ran_genelen.o
ran_genelen.cpp: In function 'std::set<int> rannum_genelen(int, const std::map<std::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) {
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c read_bed.cpp -o read_bed.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -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::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)){
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c transitions.cc -o transitions.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c unlock_environment.cc -o unlock_environment.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c wilcox_categorytest.cc -o wilcox_categorytest.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c wilcox_randset.cc -o wilcox_randset.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ABAEnrichment.dll tmp.def 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 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/ABAEnrichment.buildbin-libdir/ABAEnrichment/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ABAEnrichment' as ABAEnrichment_1.4.0.zip
* DONE (ABAEnrichment)