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CHECK report for survcomp on malbec1

This page was generated on 2020-04-15 12:06:19 -0400 (Wed, 15 Apr 2020).

Package 1687/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.36.1
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/survcomp
Branch: RELEASE_3_10
Last Commit: f69c9f2
Last Changed Date: 2020-01-31 14:56:01 -0400 (Fri, 31 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: survcomp
Version: 1.36.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:survcomp.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings survcomp_1.36.1.tar.gz
StartedAt: 2020-04-15 00:59:18 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:00:18 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 60.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: survcomp.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:survcomp.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings survcomp_1.36.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/survcomp.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.36.1’
* 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 ... 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 ... OK
* checking S3 generic/method consistency ... WARNING
concordance:
  function(object, ...)
concordance.index:
  function(x, surv.time, surv.event, cl, weights, comppairs, strat,
           alpha, outx, method, alternative, na.rm)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  concordance.index
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... NOTE
S3 methods shown with full name in documentation object 'concordance.index':
  ‘concordance.index’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/survcomp.Rcheck/00check.log’
for details.

Installation output

survcomp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL survcomp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c concordance.index.c -o concordance.index.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-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:12:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                         ~^~~~~~
foo_mrmr_ensemble_surv.cpp:22:26: 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:202:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                        ~^~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< (nvar-1); ++j){
                         ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:214:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar-1; ++i){
                        ~^~~~~~~~
foo_mrmr_ensemble_surv.cpp:216:28: 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:393:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0; k< rep_boot; ++k){
                        ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:396:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int i=1;i<= size_boot;++i){
                        ~^~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:400:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int i=0; i< size ; ++i ){
                          ~^~~~~~
foo_mrmr_ensemble_surv.cpp:401:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( unsigned int j=0; j< size ; ++j ){
                           ~^~~~~~
foo_mrmr_ensemble_surv.cpp:412:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< rep_boot;++i){
                       ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:419:24: 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:448:25: 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:593:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=1;i<= nsamples;++i){
                       ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:596:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< n; ++i ){
                         ~^~~
foo_mrmr_ensemble_surv.cpp:597:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int j=0; j< n; ++j ){
                          ~^~~
foo_mrmr_ensemble_surv.cpp:604:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0;k< max_elements ;++k){
                       ~^~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:646:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0;i<=max_depth;++i){
                          ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:654:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k< n;++k){
                         ~^~~
foo_mrmr_ensemble_surv.cpp:657:26: 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:661:26: 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:786:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< *npredn;++i){
                       ~^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:820:26: 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:834:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int k=0;k<length_res;k++){
                        ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:839:7: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(i==(*npredn-1)){
      ~^~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:843:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<length_res;k++){
                         ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:801:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
   int cnt=1,cnt2=0;
             ^~~~
foo_mrmr_ensemble_surv.cpp:804:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
   int rootdepth=res_tree.depth(it_final);
       ^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:817:7: warning: unused variable ‘ind’ [-Wunused-variable]
   int ind=0;
       ^~~
foo_mrmr_ensemble_surv.cpp:733:30: warning: unused variable ‘res_all’ [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                              ^~~~~~~
foo_mrmr_ensemble_surv.cpp:733:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                       ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:734:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
  int vec_tmp;
      ^~~~~~~
foo_mrmr_ensemble_surv.cpp:859:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return Rres;
         ^~~~
foo_mrmr_ensemble_surv.cpp:821:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     res_all[k]=res_old[k];
                ~~~~~~~~~^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-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:12:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                         ~^~~~~~
foo_mrmr_surv.cpp:22:26: 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:49:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                        ~^~~~~~~~~~~~~
foo_mrmr_surv.cpp:50:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< nvar; ++j){
                         ~^~~~~~
foo_mrmr_surv.cpp:56:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar; ++i){
                        ~^~~~~~
foo_mrmr_surv.cpp:58:28: 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:301:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i < *nsample; ++i){
                       ~~^~~~~~~~~~
foo_mrmr_surv.cpp:341:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int l=0; l<n; ++l )
                  ~^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c survcomp_init.cpp -o survcomp_init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-survcomp/00new/survcomp/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (survcomp)

Tests output

Example timings

survcomp.Rcheck/survcomp-Ex.timings

nameusersystemelapsed
D.index0.0360.0000.035
balanced.hazard.ratio0.0120.0000.014
bhr.comp0.0120.0000.013
breastCancerData0.6000.0120.613
censor.time0.0040.0000.001
cindex.comp0.0040.0000.004
cindex.comp.meta0.0040.0000.006
combine.est0.0000.0000.001
combine.test000
concordance.index0.0320.0000.032
cvpl0.2480.0000.249
dindex.comp0.0320.0000.030
dindex.comp.meta0.0360.0000.035
fisherz000
forestplot.surv0.0560.0040.061
getsurv20.0040.0000.004
hazard.ratio0.0160.0000.019
hr.comp0.0160.0000.018
hr.comp.meta0.0280.0040.035
hr.comp20.0080.0000.010
iauc.comp0.3400.0080.349
ibsc.comp0.3640.0040.368
km.coxph.plot0.0600.0000.061
logpl0.0200.0000.018
mainz7g0.320.000.32
metaplot.surv0.0040.0000.004
mrmr.cindex0.0040.0000.004
nki7g0.2400.0000.242
no.at.risk0.0080.0000.010
sbrier.score2proba0.2200.0040.221
score2proba0.0160.0000.018
td.sens.spec0.0000.0000.002
tdrocc0.0800.0080.085
test.hetero.est0.0000.0000.001
test.hetero.test0.0000.0000.001
transbig7g0.2960.0080.305
unt7g0.2560.0080.264
upp7g0.2360.0000.237
vdx7g0.3000.0040.308