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This page was generated on 2021-08-02 12:05:21 -0400 (Mon, 02 Aug 2021).

CHECK results for predictionet on merida1

To the developers/maintainers of the predictionet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/predictionet.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1408/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
predictionet 1.39.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-08-01 14:50:04 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/predictionet
Branch: master
Last Commit: ffdf209
Last Changed Date: 2021-05-19 11:50:21 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64... NOT SUPPORTED ...
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: predictionet
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:predictionet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings predictionet_1.39.0.tar.gz
StartedAt: 2021-08-02 05:31:31 -0400 (Mon, 02 Aug 2021)
EndedAt: 2021-08-02 05:32:56 -0400 (Mon, 02 Aug 2021)
EllapsedTime: 85.6 seconds
RetCode: 0
Status:   OK  
CheckDir: predictionet.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:predictionet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings predictionet_1.39.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/predictionet.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.39.0’
* 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 : <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 LazyData ... 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 ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 sizes of PDF files under ‘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-3.14-bioc/meat/predictionet.Rcheck/00check.log’
for details.



Installation output

predictionet.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL predictionet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘predictionet’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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++ -mmacosx-version-min=10.13 -std=gnu++14 -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++ -mmacosx-version-min=10.13 -std=gnu++14 -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++ -mmacosx-version-min=10.13 -std=gnu++14 -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:723:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
        int vec_tmp;
            ^
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: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;
                                      ^
                                       = nullptr
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: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: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: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:992:39: warning: unused variable 'res_all2' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                             ^
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: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;
                                      ^
                                       = nullptr
25 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-predictionet/00new/predictionet/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (predictionet)

Tests output


Example timings

predictionet.Rcheck/predictionet-Ex.timings

nameusersystemelapsed
adj.get.hops0.0160.0020.017
adj.remove.cycles0.0020.0030.004
data.discretize0.2250.0170.242
expO.colon.ras0.0010.0010.002
jorissen.colon.ras0.0010.0020.003
net2pred0.0740.0080.082
netinf0.4150.0250.440
netinf.cv0.3080.0080.316
netinf.predict0.0860.0040.091
netinf2gml0.3290.0050.335
pred.score0.0090.0010.010
predictionet.press.statistic0.3090.0070.316
predictionet.stability.cv0.3140.0060.320