Package: predictionet

Version: 1.30.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:predictionet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings predictionet_1.30.0.tar.gz

StartedAt: 2019-10-16 04:03:37 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:04:45 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 67.9 seconds

RetCode: 0

Status:  OK

CheckDir: predictionet.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:predictionet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings predictionet_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/predictionet.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘predictionet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘predictionet’ version ‘1.30.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘predictionet’ 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
Packages in Depends field not imported from:
  ‘catnet’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.build.regression.regrnet: no visible global function definition for
  ‘formula’
.build.regression.regrnet: no visible global function definition for
  ‘lm’
.build2.mim: no visible global function definition for ‘cor’
.exportGML: no visible global function definition for ‘vcount’
.exportGML: no visible global function definition for ‘ecount’
.get.ii4triplets.gaussian: no visible global function definition for
  ‘cor’
.pred.onegene.bayesnet.fs : : no visible global function
  definition for ‘quantile’
.regrnet2matrixtopo: no visible global function definition for
  ‘coefficients’
adj.get.hops: no visible global function definition for ‘as’
netinf: no visible global function definition for ‘quantile’
netinf : : no visible global function definition for
  ‘quantile’
netinf: no visible global function definition for ‘cnMatParents’
netinf.cv : : no visible global function definition for
  ‘quantile’
netinf2gml: no visible global function definition for ‘sessionInfo’
netinf2gml: no visible global function definition for ‘ecount’
netinf2gml: no visible global function definition for ‘vcount’
pred.score : : no visible global function definition for
  ‘quantile’
pred.score : myfoo: no visible global function definition for
  ‘complete.cases’
predictionet.stability.cv : : no visible global function
  definition for ‘quantile’
Undefined global functions or variables:
  as cnMatParents coefficients complete.cases cor ecount formula lm
  quantile sessionInfo vcount
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coefficients", "complete.cases", "cor", "formula",
             "lm", "quantile")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/predictionet/libs/predictionet.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘srand’, possibly from ‘srand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/predictionet.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL predictionet
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘predictionet’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c foo_mrmr.cpp -o foo_mrmr.o
foo_mrmr.cpp: In function ‘double get_correlation(double*, int*, int, int, int)’:
foo_mrmr.cpp:13:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                         ~^~~~~~
foo_mrmr.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                         ~^~~~~~
foo_mrmr.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr.cpp:50:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                        ~^~~~~~~~~~~~~
foo_mrmr.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< nvar; ++j){
                         ~^~~~~~
foo_mrmr.cpp:57:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar; ++i){
                        ~^~~~~~
foo_mrmr.cpp:59:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=i+1; j< nvar; ++j){
                           ~^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c mrnet_adapted.cpp -o mrnet_adapted.o
mrnet_adapted.cpp: In function ‘SEXPREC* mrnet_adapted(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_adapted.cpp:58:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i < *nsample; ++i){
                       ~~^~~~~~~~~~
mrnet_adapted.cpp:103:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int l=0; l&, tree&)’:
mrnet_ensemble_standalone.cpp:24:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int j=0;j< length_vec;++j){
                       ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:42:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int j=0;j< length_vec;++j){
                         ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:47:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned int j=0;j< (res.depth(it_main)-1);++j){
                          ~^~~~~~~~~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:60:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned int j=0;j< length_vec;++j){
                           ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:65:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned int j=0;j< length_vec && equiv;++j){
                           ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘int verify_equivalentset_nparents(tree&, tree::pre_order_iterator, tree::pre_order_iterator, tree&, int)’:
mrnet_ensemble_standalone.cpp:111:7: warning: unused variable ‘found’ [-Wunused-variable]
  bool found=false;
       ^~~~~
mrnet_ensemble_standalone.cpp: In function ‘int verify_equivalentset(tree&, tree::pre_order_iterator, tree::pre_order_iterator, int, int*, int*)’:
mrnet_ensemble_standalone.cpp:223:6: warning: variable ‘to_remove’ set but not used [-Wunused-but-set-variable]
  int to_remove[number_leafs];
      ^~~~~~~~~
mrnet_ensemble_standalone.cpp:283:6: warning: unused variable ‘rootdepth’ [-Wunused-variable]
  int rootdepth=tr.depth(it);
      ^~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void build_tree_int(tree&, tree::pre_order_iterator, tree::pre_order_iterator, int*, int, int)’:
mrnet_ensemble_standalone.cpp:304:6: warning: unused variable ‘rootdepth’ [-Wunused-variable]
  int rootdepth=tr.depth(it);
      ^~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_mrmr_fix(double&, double&, double*, int*, int, int, int, int, int, int, int, int*)’:
mrnet_ensemble_standalone.cpp:384:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=1;i<= nsamples;++i){
                       ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:377:16: warning: unused variable ‘boot_val’ [-Wunused-variable]
  double *mim, *boot_val;
                ^~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_mrmr(double&, double&, double*, int*, int, int, int, int, int, int, int, int*)’:
mrnet_ensemble_standalone.cpp:414:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0; k< rep_boot; ++k){
                        ~^~~~~~~~~~
mrnet_ensemble_standalone.cpp:417:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int i=1;i<= size_boot;++i){
                        ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:426:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< rep_boot;++i){
                       ~^~~~~~~~~~
mrnet_ensemble_standalone.cpp:433:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< rep_boot;++i){
                       ~^~~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_tree(tree&, tree&, double*, int*, int, int, int)’:
mrnet_ensemble_standalone.cpp:507:7: warning: unused variable ‘cnt_back’ [-Wunused-variable]
   int cnt_back=cnt2;
       ^~~~~~~~
mrnet_ensemble_standalone.cpp:442:7: warning: unused variable ‘nsub’ [-Wunused-variable]
  int  nsub, *prev_sel,nsamples_boot=nsamples,*to_remove;
       ^~~~
mrnet_ensemble_standalone.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
mrnet_ensemble_standalone.cpp:569:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0;j< nbvar; j++){
                        ~^~~~~~~
mrnet_ensemble_standalone.cpp:558:15: warning: variable ‘jmax’ set but not used [-Wunused-but-set-variable]
  unsigned int jmax;
               ^~~~
mrnet_ensemble_standalone.cpp:560:9: warning: unused variable ‘max_val’ [-Wunused-variable]
  double max_val=-1000;
         ^~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void mrmr_ensemble_one_gene(tree&, tree::pre_order_iterator, double*, int*, int, int, int, int, int, int, double)’:
mrnet_ensemble_standalone.cpp:600:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0;k< max_elements ;++k){
                       ~^~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:658:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (unsigned int i=0;imax_mrmr){
         ~^~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:689:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned int k=0;k< n;++k){
                           ~^~~
mrnet_ensemble_standalone.cpp:586:48: warning: unused variable ‘nprev_sel’ [-Wunused-variable]
  int  *nsub, *prev_sel,nsamples_boot=nsamples, nprev_sel=0;
                                                ^~~~~~~~~
mrnet_ensemble_standalone.cpp:587:10: warning: variable ‘res_vec’ set but not used [-Wunused-but-set-variable]
  double *res_vec, *vec_mean, *vec_sort, *vec_sd,  *vec_local_max_mean, *vec_local_max_sd;;
          ^~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:760:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< *npredn;++i){
                       ~^~~~~~~~~
mrnet_ensemble_standalone.cpp:799:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k&, tree::pre_order_iterator, double*, int*, int, int, int, int, int, int, double)’:
mrnet_ensemble_standalone.cpp:860:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0;k< max_elements ;++k){
                       ~^~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:904:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0;i<=max_depth;++i){
                          ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:912:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k< n;++k){
                         ~^~~
mrnet_ensemble_standalone.cpp:915:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<=max(res_tmp_new.depth(it_local),max_depth) ;++k){
                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:919:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k< n;++k){
                         ~^~~
mrnet_ensemble_standalone.cpp:848:48: warning: unused variable ‘tmp_val_max_ind’ [-Wunused-variable]
  int  *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete;
                                                ^~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:848:66: warning: unused variable ‘prev_sel_tmp’ [-Wunused-variable]
  int  *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete;
                                                                  ^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:849:21: warning: unused variable ‘vec_sort’ [-Wunused-variable]
  double *vec_mean, *vec_sort, *vec_sd,  *vec_local_max_mean, *vec_local_max_sd,tmp_val_max, *mrmr_vec_sort,*vec_sol_local_mrmr;
                     ^~~~~~~~
mrnet_ensemble_standalone.cpp:849:63: warning: variable ‘vec_local_max_sd’ set but not used [-Wunused-but-set-variable]
  double *vec_mean, *vec_sort, *vec_sd,  *vec_local_max_mean, *vec_local_max_sd,tmp_val_max, *mrmr_vec_sort,*vec_sol_local_mrmr;
                                                               ^~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:1029:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< *npredn;++i){
                       ~^~~~~~~~~
mrnet_ensemble_standalone.cpp:1066:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k

name	user	system	elapsed
adj.get.hops	0.021	0.000	0.031
adj.remove.cycles	0.002	0.000	0.002
data.discretize	0.195	0.004	0.199
expO.colon.ras	0.002	0.000	0.001
jorissen.colon.ras	0.002	0.000	0.001
net2pred	0.067	0.012	0.079
netinf	0.257	0.044	0.300
netinf.cv	0.301	0.016	0.317
netinf.predict	0.076	0.000	0.075
netinf2gml	0.263	0.000	0.263
pred.score	0.000	0.003	0.004
predictionet.press.statistic	0.194	0.001	0.194
predictionet.stability.cv	0.214	0.000	0.214