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CHECK report for predictionet on veracruz1

This page was generated on 2018-04-12 13:35:02 -0400 (Thu, 12 Apr 2018).

Package 1062/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
predictionet 1.24.0
Benjamin Haibe-Kains
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/predictionet
Branch: RELEASE_3_6
Last Commit: 098f5b6
Last Changed Date: 2017-10-30 12:39:36 -0400 (Mon, 30 Oct 2017)
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 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: predictionet
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings predictionet_1.24.0.tar.gz
StartedAt: 2018-04-12 07:50:18 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 07:51:35 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 77.3 seconds
RetCode: 0
Status:  OK 
CheckDir: predictionet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings predictionet_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/predictionet.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.24.0’
* 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 loading without being on the library search path ... 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 : <anonymous>: 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 : <anonymous>: no visible global function definition for
  ‘quantile’
netinf: no visible global function definition for ‘cnMatParents’
netinf.cv : <anonymous>: 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 : <anonymous>: no visible global function definition for
  ‘quantile’
pred.score : myfoo: no visible global function definition for
  ‘complete.cases’
predictionet.stability.cv : <anonymous>: 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
File ‘predictionet/libs/predictionet.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mrnet_ensemble_standalone.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mrnet_ensemble_standalone.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/predictionet.Rcheck/00check.log’
for details.

Installation output

predictionet.Rcheck/00install.out

* installing *source* package ‘predictionet’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c foo_mrmr.cpp -o foo_mrmr.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mrnet_adapted.cpp -o mrnet_adapted.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mrnet_adapted2.cpp -o mrnet_adapted2.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mrnet_ensemble_standalone.cpp -o mrnet_ensemble_standalone.o
mrnet_ensemble_standalone.cpp:111:7: warning: unused variable 'found' [-Wunused-variable]
        bool found=false;
             ^
mrnet_ensemble_standalone.cpp:283:6: warning: unused variable 'rootdepth' [-Wunused-variable]
        int rootdepth=tr.depth(it);
            ^
mrnet_ensemble_standalone.cpp:304:6: warning: unused variable 'rootdepth' [-Wunused-variable]
        int rootdepth=tr.depth(it);
            ^
mrnet_ensemble_standalone.cpp:377:16: warning: unused variable 'boot_val' [-Wunused-variable]
        double *mim, *boot_val;
                      ^
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:560:9: warning: unused variable 'max_val' [-Wunused-variable]
        double max_val=-1000;
               ^
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:777:13: warning: unused variable 'cnt2' [-Wunused-variable]
                int cnt=1,cnt2=0;
                          ^
mrnet_ensemble_standalone.cpp:780:7: warning: unused variable 'rootdepth' [-Wunused-variable]
                int rootdepth=res_tree.depth(it_final);
                    ^
mrnet_ensemble_standalone.cpp:794:7: warning: unused variable 'ind' [-Wunused-variable]
                int ind=0;
                    ^
mrnet_ensemble_standalone.cpp:722:30: warning: unused variable 'res_all' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
                                    ^
mrnet_ensemble_standalone.cpp:723:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
        int vec_tmp;
            ^
mrnet_ensemble_standalone.cpp:722:39: warning: unused variable 'res_all2' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
                                             ^
mrnet_ensemble_standalone.cpp:800:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
                                res_all[k]=res_old[k];
                                           ^˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:793:25: note: initialize the variable 'res_old' to silence this warning
                int *res_all, *res_old;
                                      ^
                                       = NULL
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:1046:13: warning: unused variable 'cnt2' [-Wunused-variable]
                int cnt=1,cnt2=0;
                          ^
mrnet_ensemble_standalone.cpp:1049:7: warning: unused variable 'rootdepth' [-Wunused-variable]
                int rootdepth=res_tree.depth(it_final);
                    ^
mrnet_ensemble_standalone.cpp:1063:7: warning: unused variable 'ind' [-Wunused-variable]
                int ind=0;
                    ^
mrnet_ensemble_standalone.cpp:992:30: warning: unused variable 'res_all' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                    ^
mrnet_ensemble_standalone.cpp:992:39: warning: unused variable 'res_all2' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                             ^
mrnet_ensemble_standalone.cpp:993:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
        int vec_tmp;
            ^
mrnet_ensemble_standalone.cpp:1067:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
                                res_all[k]=res_old[k];
                                           ^˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1062:25: note: initialize the variable 'res_old' to silence this warning
                int *res_all, *res_old;
                                      ^
                                       = NULL
25 warnings generated.
clang++ -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 predictionet.so foo_mrmr.o mrnet_adapted.o mrnet_adapted2.o mrnet_ensemble_standalone.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/predictionet.Rcheck/predictionet/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (predictionet)

Tests output

Example timings

predictionet.Rcheck/predictionet-Ex.timings

nameusersystemelapsed
adj.get.hops0.0460.0010.047
adj.remove.cycles0.0020.0010.003
data.discretize0.2940.0120.307
expO.colon.ras0.0010.0000.001
jorissen.colon.ras0.0010.0010.003
net2pred0.1250.0110.139
netinf1.0310.0291.086
netinf.cv0.5910.0060.607
netinf.predict0.0650.0030.072
netinf2gml0.4170.0030.431
pred.score0.0060.0010.006
predictionet.press.statistic0.2540.0030.257
predictionet.stability.cv0.3900.0060.402