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BioC 3.2: CHECK report for survcomp on zin1

This page was generated on 2015-08-24 10:47:58 -0700 (Mon, 24 Aug 2015).

Package 1000/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.19.1
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/survcomp
Last Changed Rev: 106601 / Revision: 107696
Last Changed Date: 2015-07-21 02:11:41 -0700 (Tue, 21 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: survcomp
Version: 1.19.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings survcomp_1.19.1.tar.gz
StartedAt: 2015-08-24 04:10:40 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 04:11:08 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 28.0 seconds
RetCode: 0
Status:  OK 
CheckDir: survcomp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings survcomp_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/survcomp.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.19.1’
* 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 ... [4s/4s] 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'
D.index: no visible global function definition for ‘coxph’
cvpl: 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 ... [4s/4s] 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/survcomp.Rcheck/00check.log’
for details.

survcomp.Rcheck/00install.out:

* installing *source* package ‘survcomp’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c concordance.index.c -o concordance.index.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -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:12:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                            ^
foo_mrmr_ensemble_surv.cpp:22:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {  
                            ^
foo_mrmr_ensemble_surv.cpp: In function ‘double returnConcordanceIndexC(int*, int*, double*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:106:10: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable]
   double uhs[Ns];
          ^
foo_mrmr_ensemble_surv.cpp:107:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
   double rphs[Ns];
          ^
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:202:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                           ^
foo_mrmr_ensemble_surv.cpp:203:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< (nvar-1); ++j){
                                   ^
foo_mrmr_ensemble_surv.cpp:214:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar-1; ++i){
                                ^
foo_mrmr_ensemble_surv.cpp:216:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=i+1; j< nvar-1; ++j){
                                   ^
foo_mrmr_ensemble_surv.cpp:191:17: warning: unused variable ‘msurv_x’ [-Wunused-variable]
  int *namat_x, *msurv_x, *ustrat_x, *cl2_x, *se_x, *strat_x;
                 ^
foo_mrmr_ensemble_surv.cpp:191:27: warning: unused variable ‘ustrat_x’ [-Wunused-variable]
  int *namat_x, *msurv_x, *ustrat_x, *cl2_x, *se_x, *strat_x;
                           ^
foo_mrmr_ensemble_surv.cpp: In function ‘void bootstrap_tree(tree<int>&, tree<double>&, double*, int*, int, int, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:351:7: warning: unused variable ‘cnt_back’ [-Wunused-variable]
   int cnt_back=cnt2;
       ^
foo_mrmr_ensemble_surv.cpp:286:7: warning: unused variable ‘nsub’ [-Wunused-variable]
  int  nsub, *prev_sel,nsamples_boot=nsamples,*to_remove;
       ^
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:393:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0; k< rep_boot; ++k){
                           ^
foo_mrmr_ensemble_surv.cpp:396:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int i=1;i<= size_boot;++i){
                            ^
foo_mrmr_ensemble_surv.cpp:400:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int i=0; i< size ; ++i ){
                             ^
foo_mrmr_ensemble_surv.cpp:401:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( unsigned int j=0; j< size ; ++j ){
                              ^
foo_mrmr_ensemble_surv.cpp:412:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< rep_boot;++i){
                          ^
foo_mrmr_ensemble_surv.cpp:419:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< rep_boot;++i){
                          ^
foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable ‘mim’ [-Wunused-variable]
  double *mim, *boot_val, *mat_info;
          ^
foo_mrmr_ensemble_surv.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
foo_mrmr_ensemble_surv.cpp:448:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0;j< nbvar; j++){
                           ^
foo_mrmr_ensemble_surv.cpp:437:15: warning: variable ‘jmax’ set but not used [-Wunused-but-set-variable]
  unsigned int jmax;
               ^
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable ‘max_val’ [-Wunused-variable]
  double max_val=-1000;
         ^
foo_mrmr_ensemble_surv.cpp: In function ‘int verify_equivalentset_nparents(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, tree<double>&, int)’:
foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable ‘found’ [-Wunused-variable]
  bool found=false;
       ^
foo_mrmr_ensemble_surv.cpp: In function ‘void mrmr_ensemble_one_gene_remove(tree<int>&, tree<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:593:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=1;i<= nsamples;++i){
                           ^
foo_mrmr_ensemble_surv.cpp:596:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< n; ++i ){
                            ^
foo_mrmr_ensemble_surv.cpp:597:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int j=0; j< n; ++j ){
                             ^
foo_mrmr_ensemble_surv.cpp:604:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0;k< max_elements ;++k){
                          ^
foo_mrmr_ensemble_surv.cpp:646:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0;i<=max_depth;++i){ 
                             ^
foo_mrmr_ensemble_surv.cpp:654:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k< n;++k){
                            ^
foo_mrmr_ensemble_surv.cpp:657:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<=max(res_tmp_new.depth(it_local),max_depth) ;++k){
                                                                     ^
foo_mrmr_ensemble_surv.cpp:661:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k< n;++k){
                            ^
foo_mrmr_ensemble_surv.cpp:578:24: warning: unused variable ‘nsamples_boot’ [-Wunused-variable]
  int  *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete; 
                        ^
foo_mrmr_ensemble_surv.cpp:578:48: 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; 
                                                ^
foo_mrmr_ensemble_surv.cpp:578:66: 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; 
                                                                  ^
foo_mrmr_ensemble_surv.cpp:579:21: 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;
                     ^
foo_mrmr_ensemble_surv.cpp:579:63: warning: variable ‘vec_local_max_sd’ set but not used [-Wunused-but-set-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;
                                                               ^
foo_mrmr_ensemble_surv.cpp: In function ‘SEXPREC* mrmr_cIndex_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
foo_mrmr_ensemble_surv.cpp:785:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< *npredn;++i){
                           ^
foo_mrmr_ensemble_surv.cpp:819:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<length_res_old;k++){
                           ^
foo_mrmr_ensemble_surv.cpp:833:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int k=0;k<length_res;k++){
                          ^
foo_mrmr_ensemble_surv.cpp:838:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(i==(*npredn-1)){
                   ^
foo_mrmr_ensemble_surv.cpp:842:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<length_res;k++){
                           ^
foo_mrmr_ensemble_surv.cpp:800:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
   int cnt=1,cnt2=0;
             ^
foo_mrmr_ensemble_surv.cpp:803:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
   int rootdepth=res_tree.depth(it_final);
       ^
foo_mrmr_ensemble_surv.cpp:816:7: warning: unused variable ‘ind’ [-Wunused-variable]
   int ind=0;
       ^
foo_mrmr_ensemble_surv.cpp:732:30: warning: unused variable ‘res_all’ [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                              ^
foo_mrmr_ensemble_surv.cpp:732:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                       ^
foo_mrmr_ensemble_surv.cpp:733:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
  int vec_tmp;
      ^
foo_mrmr_ensemble_surv.cpp:858:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return Rres;
         ^
foo_mrmr_ensemble_surv.cpp:820:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     res_all[k]=res_old[k];
                         ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -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:12:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                            ^
foo_mrmr_surv.cpp:22:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {  
                            ^
foo_mrmr_surv.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr_surv.cpp:49:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                           ^
foo_mrmr_surv.cpp:50:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< nvar; ++j){
                            ^
foo_mrmr_surv.cpp:56:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar; ++i){
                           ^
foo_mrmr_surv.cpp:58:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=i+1; j< nvar; ++j){
                              ^
foo_mrmr_surv.cpp: In function ‘double returnConcordanceIndexC(int*, int*, double*, int*, double*, int*, double*, int*, int*, int*, int*, int*)’:
foo_mrmr_surv.cpp:146:10: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable]
   double uhs[Ns];
          ^
foo_mrmr_surv.cpp:147:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
   double rphs[Ns];
          ^
foo_mrmr_surv.cpp: In function ‘SEXPREC* mrmr_cIndex(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
foo_mrmr_surv.cpp:300:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i < *nsample; ++i){
                            ^
foo_mrmr_surv.cpp:340:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int l=0; l<n; ++l )  
                    ^
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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)

survcomp.Rcheck/survcomp-Ex.timings:

nameusersystemelapsed
D.index0.0240.0000.025
breastCancerData0.7330.0040.737
censor.time0.0010.0000.002
cindex.comp0.0050.0000.004
cindex.comp.meta0.0070.0000.007
combine.est0.0020.0000.002
combine.test0.0010.0000.001
concordance.index0.0000.0040.005
cvpl0.1820.0010.189
dindex.comp0.0130.0000.019
dindex.comp.meta0.0330.0000.041
fisherz0.0010.0000.002
forestplot.surv0.0550.0000.059
getsurv20.0050.0000.005
hazard.ratio0.0090.0000.010
hr.comp0.0120.0000.011
hr.comp.meta0.0220.0000.023
hr.comp20.010.000.01
iauc.comp0.3980.0030.402
ibsc.comp0.3230.0000.324
km.coxph.plot0.0260.0040.031
logpl0.0170.0000.017
mainz7g0.2080.0040.212
metaplot.surv0.0030.0000.004
mrmr.cindex0.0030.0000.003
nki7g0.2210.0000.220
no.at.risk0.0220.0000.022
sbrier.score2proba0.1870.0000.187
score2proba0.0220.0000.022
td.sens.spec0.0020.0000.002
tdrocc0.230.000.23
test.hetero.est0.0000.0040.001
test.hetero.test0.0000.0000.001
transbig7g0.2190.0080.227
unt7g0.2090.0040.213
upp7g0.2000.0000.201
vdx7g0.1920.0040.197