BioC 2.14: CHECK report for survcomp on petty

Package: survcomp

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch survcomp_1.14.0.tar.gz

StartedAt: 2014-10-08 00:21:00 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:22:18 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 77.5 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/survcomp.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.14.0’
* 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 ... [8s/10s] 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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'
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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/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-2.14-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	0.045	0.006	0.064
breastCancerData	2.017	0.058	2.102
censor.time	0.003	0.001	0.003
cindex.comp	0.009	0.001	0.010
cindex.comp.meta	0.014	0.002	0.016
combine.est	0.003	0.000	0.004
combine.test	0.003	0.000	0.003
concordance.index	0.022	0.004	0.025
cvpl	0.471	0.005	0.476
dindex.comp	0.024	0.001	0.024
dindex.comp.meta	0.054	0.001	0.056
fisherz	0.002	0.000	0.003
forestplot.surv	0.179	0.005	0.185
getsurv2	0.013	0.001	0.014
hazard.ratio	0.020	0.002	0.022
hr.comp	0.024	0.000	0.025
hr.comp.meta	0.048	0.000	0.048
hr.comp2	0.019	0.000	0.020
iauc.comp	0.859	0.004	0.865
ibsc.comp	0.522	0.016	0.579
km.coxph.plot	0.065	0.002	0.066
logpl	0.047	0.002	0.048
mainz7g	0.520	0.021	0.541
metaplot.surv	0.041	0.001	0.043
mrmr.cindex	0.008	0.000	0.008
nki7g	0.625	0.016	0.641
no.at.risk	0.036	0.001	0.036
sbrier.score2proba	0.403	0.001	0.405
score2proba	0.047	0.000	0.048
td.sens.spec	0.004	0.000	0.015
tdrocc	0.416	0.020	0.437
test.hetero.est	0.003	0.000	0.003
test.hetero.test	0.002	0.000	0.003
transbig7g	0.497	0.015	0.513
unt7g	0.650	0.017	0.669
upp7g	0.484	0.016	0.509
vdx7g	0.500	0.017	0.543