BioC 3.0: CHECK report for survcomp on perceval

Package: survcomp

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch survcomp_1.16.0.tar.gz

StartedAt: 2015-04-10 06:52:28 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 06:53:17 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 49.5 seconds

RetCode: 0

Status:  OK

CheckDir: survcomp.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch survcomp_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/survcomp.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘survcomp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘survcomp’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘survcomp’ can be installed ... [6s/7s] 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
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘survival’
  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
.extract.all.parents: warning in matrix(0, nc = nsol, nr = (maxparents
  + 1)): partial argument match of 'nr' to 'nrow'
.extract.all.parents: warning in matrix(0, nc = nsol, nr = (maxparents
  + 1)): partial argument match of 'nc' to 'ncol'
cvpl: no visible global function definition for ‘coxph’
D.index: no visible global function definition for ‘coxph’
hazard.ratio: no visible global function definition for ‘coxph’
km.coxph.plot: no visible global function definition for ‘survfit’
no.at.risk: no visible global function definition for ‘survfit’
sbrier.score2proba: no visible global function definition for ‘survfit’
sbrier.score2proba: no visible global function definition for ‘Surv’
score2proba: no visible global function definition for ‘coxph’
score2proba: no visible global function definition for ‘survfit’
* 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 ‘survcomp/libs/survcomp.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘foo_mrmr_ensemble_surv.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘foo_mrmr_ensemble_surv.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 ... [7s/7s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘xtable’
* 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/survcomp.Rcheck/00check.log’
for details.

* installing *source* package ‘survcomp’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c concordance.index.c -o concordance.index.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o
foo_mrmr_ensemble_surv.cpp: In function ‘double get_correlation_ensemble(double*, int*, int, int, int)’:
foo_mrmr_ensemble_surv.cpp:12: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:22: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp: In function ‘void build_mim_cIndex_subset(double*, double*, int*, int, int, int*, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int*)’:
foo_mrmr_ensemble_surv.cpp:202: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:203: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:214: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:216: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:191: warning: unused variable ‘msurv_x’
foo_mrmr_ensemble_surv.cpp:191: warning: unused variable ‘ustrat_x’
foo_mrmr_ensemble_surv.cpp: In function ‘void bootstrap_tree(tree<int, std::allocator<tree_node_<int> > >&, tree<double, std::allocator<tree_node_<double> > >&, double*, int*, int, int, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:351: warning: unused variable ‘cnt_back’
foo_mrmr_ensemble_surv.cpp:286: warning: unused variable ‘nsub’
foo_mrmr_ensemble_surv.cpp: In function ‘void bootstrap_mrmr(double&, double&, double*, int*, int, int, int, int, int, int, int, int*, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:393: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:396: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:400: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:401: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:412: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:419: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:387: warning: unused variable ‘mim’
foo_mrmr_ensemble_surv.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
foo_mrmr_ensemble_surv.cpp:448: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:439: warning: unused variable ‘max_val’
foo_mrmr_ensemble_surv.cpp: In function ‘int verify_equivalentset_nparents(tree<int, std::allocator<tree_node_<int> > >&, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, tree<double, std::allocator<tree_node_<double> > >&, int)’:
foo_mrmr_ensemble_surv.cpp:467: warning: unused variable ‘found’
foo_mrmr_ensemble_surv.cpp: In function ‘void mrmr_ensemble_one_gene_remove(tree<int, std::allocator<tree_node_<int> > >&, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, double*, int*, int, int, int, int, int, int, double, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:593: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:596: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:597: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:604: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:646: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:654: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:657: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:661: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:578: warning: unused variable ‘nsamples_boot’
foo_mrmr_ensemble_surv.cpp:578: warning: unused variable ‘tmp_val_max_ind’
foo_mrmr_ensemble_surv.cpp:578: warning: unused variable ‘prev_sel_tmp’
foo_mrmr_ensemble_surv.cpp:579: warning: unused variable ‘vec_sort’
foo_mrmr_ensemble_surv.cpp: In function ‘SEXPREC* mrmr_cIndex_ensemble_remove(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
foo_mrmr_ensemble_surv.cpp:785: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:819: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:833: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:838: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:842: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:800: warning: unused variable ‘cnt2’
foo_mrmr_ensemble_surv.cpp:803: warning: unused variable ‘rootdepth’
foo_mrmr_ensemble_surv.cpp:816: warning: unused variable ‘ind’
foo_mrmr_ensemble_surv.cpp:732: warning: unused variable ‘res_all’
foo_mrmr_ensemble_surv.cpp:732: warning: unused variable ‘res_all2’
foo_mrmr_ensemble_surv.cpp:733: warning: unused variable ‘vec_tmp’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
foo_mrmr_surv.cpp: In function ‘double get_correlation(double*, int*, int, int, int)’:
foo_mrmr_surv.cpp:12: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:22: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr_surv.cpp:49: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:50: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:56: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:58: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp: In function ‘SEXPREC* mrmr_cIndex(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
foo_mrmr_surv.cpp:300: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:340: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/survcomp.Rcheck/survcomp/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survcomp)

name	user	system	elapsed
D.index	0.031	0.006	0.038
breastCancerData	1.446	0.057	1.505
censor.time	0.002	0.000	0.002
cindex.comp	0.005	0.001	0.006
cindex.comp.meta	0.008	0.001	0.008
combine.est	0.003	0.001	0.003
combine.test	0.002	0.001	0.001
concordance.index	0.024	0.003	0.026
cvpl	0.359	0.002	0.361
dindex.comp	0.016	0.000	0.016
dindex.comp.meta	0.030	0.000	0.031
fisherz	0.001	0.000	0.001
forestplot.surv	0.108	0.003	0.111
getsurv2	0.009	0.001	0.009
hazard.ratio	0.011	0.002	0.013
hr.comp	0.016	0.000	0.016
hr.comp.meta	0.032	0.000	0.032
hr.comp2	0.01	0.00	0.01
iauc.comp	0.533	0.008	0.541
ibsc.comp	0.358	0.012	0.372
km.coxph.plot	0.047	0.002	0.053
logpl	0.029	0.001	0.030
mainz7g	0.337	0.017	0.355
metaplot.surv	0.005	0.002	0.014
mrmr.cindex	0.005	0.000	0.005
nki7g	0.477	0.015	0.491
no.at.risk	0.026	0.001	0.027
sbrier.score2proba	0.344	0.003	0.346
score2proba	0.037	0.001	0.037
td.sens.spec	0.003	0.000	0.003
tdrocc	0.344	0.022	0.371
test.hetero.est	0.002	0.000	0.002
test.hetero.test	0.002	0.000	0.002
transbig7g	0.306	0.012	0.318
unt7g	0.431	0.012	0.443
upp7g	0.295	0.012	0.308
vdx7g	0.330	0.013	0.344