predictionet 1.17.0
Benjamin Haibe-Kains , Catharina Olsen
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/predictionet | | Last Changed Rev: 109592 / Revision: 116626 | | Last Changed Date: 2015-10-13 12:59:53 -0700 (Tue, 13 Oct 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings predictionet_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/predictionet.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.17.0’
* 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 ... [9s/9s] 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’
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:
cnMatParents coefficients complete.cases cor ecount formula lm
quantile sessionInfo vcount
Consider adding
importFrom("stats", "coefficients", "complete.cases", "cor", "formula",
"lm", "quantile")
importFrom("utils", "sessionInfo")
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 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 the system RNG.
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 ... [4s/4s] 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-3.3-bioc/meat/predictionet.Rcheck/00check.log’
for details.
* installing *source* package ‘predictionet’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c foo_mrmr.cpp -o foo_mrmr.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c mrnet_adapted.cpp -o mrnet_adapted.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c mrnet_adapted2.cpp -o mrnet_adapted2.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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-3.3-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)