BioC 3.2: CHECK report for survcomp on perceval

Package: survcomp

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings survcomp_1.20.0.tar.gz

StartedAt: 2015-11-10 09:59:45 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 10:00:31 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 46.2 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 survcomp_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/survcomp.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.20.0’
* 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 ... [5s/6s] 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 ... [6s/6s] 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

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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-3.2-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	0.025	0.005	0.046
breastCancerData	0.905	0.036	0.941
censor.time	0.002	0.001	0.002
cindex.comp	0.005	0.001	0.006
cindex.comp.meta	0.008	0.001	0.009
combine.est	0.002	0.000	0.002
combine.test	0.002	0.000	0.001
concordance.index	0.005	0.002	0.007
cvpl	0.228	0.002	0.229
dindex.comp	0.014	0.000	0.014
dindex.comp.meta	0.033	0.000	0.033
fisherz	0.001	0.000	0.002
forestplot.surv	0.099	0.001	0.101
getsurv2	0.007	0.001	0.007
hazard.ratio	0.011	0.001	0.012
hr.comp	0.020	0.001	0.020
hr.comp.meta	0.029	0.000	0.030
hr.comp2	0.009	0.000	0.009
iauc.comp	0.500	0.009	0.509
ibsc.comp	0.290	0.011	0.314
km.coxph.plot	0.041	0.002	0.043
logpl	0.024	0.002	0.024
mainz7g	0.322	0.013	0.335
metaplot.surv	0.106	0.001	0.108
mrmr.cindex	0.004	0.000	0.005
nki7g	0.306	0.011	0.316
no.at.risk	0.020	0.001	0.021
sbrier.score2proba	0.239	0.009	0.249
score2proba	0.021	0.001	0.022
td.sens.spec	0.003	0.000	0.004
tdrocc	0.198	0.016	0.215
test.hetero.est	0.002	0.000	0.002
test.hetero.test	0.001	0.001	0.002
transbig7g	0.337	0.014	0.352
unt7g	0.316	0.014	0.330
upp7g	0.315	0.011	0.327
vdx7g	0.317	0.011	0.328