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Package 519/553HostnameOS / ArchBUILDCHECKBUILD BIN
survcomp 1.6.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/survcomp
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: survcomp
Version: 1.6.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings survcomp_1.6.0.tar.gz
StartedAt: 2012-09-24 03:59:46 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 04:00:27 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 40.6 seconds
RetCode: 0
Status:  OK 
CheckDir: survcomp.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/survcomp.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-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 ‘1.6.0’
* 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 whether package ‘survcomp’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/survcomp.Rcheck/00check.log’
for details.

survcomp.Rcheck/00install.out:

* installing *source* package ‘survcomp’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-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-2.10-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:12:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:22:28: 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:202:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:214:32: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:216:35: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:191:17: warning: unused variable ‘msurv_x’
foo_mrmr_ensemble_surv.cpp:191:27: warning: unused variable ‘ustrat_x’
foo_mrmr_ensemble_surv.cpp: In function ‘void bootstrap_tree(tree<int>&, tree<double>&, double*, int*, int, int, int, int*, int*, double*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:351:7: warning: unused variable ‘cnt_back’
foo_mrmr_ensemble_surv.cpp:286:7: 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*, double*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:393:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:396:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:400:29: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:401:30: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:412:26: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:419:26: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:387:10: 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:448:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable ‘max_val’
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’
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*, double*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:593:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:596:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:597:29: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:604:26: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:646:29: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:654:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:657:69: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:661:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:578:24: warning: unused variable ‘nsamples_boot’
foo_mrmr_ensemble_surv.cpp:578:48: warning: unused variable ‘tmp_val_max_ind’
foo_mrmr_ensemble_surv.cpp:578:66: warning: unused variable ‘prev_sel_tmp’
foo_mrmr_ensemble_surv.cpp:579:21: 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:785:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:819:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:833:26: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:842:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:800:13: warning: unused variable ‘cnt2’
foo_mrmr_ensemble_surv.cpp:803:7: warning: unused variable ‘rootdepth’
foo_mrmr_ensemble_surv.cpp:816:7: warning: unused variable ‘ind’
foo_mrmr_ensemble_surv.cpp:732:30: warning: unused variable ‘res_all’
foo_mrmr_ensemble_surv.cpp:732:39: warning: unused variable ‘res_all2’
foo_mrmr_ensemble_surv.cpp:733:6: warning: unused variable ‘vec_tmp’
In file included from foo_mrmr_ensemble_surv.h:10:0,
                 from foo_mrmr_ensemble_surv.cpp:1:
tree.h: In static member function ‘static int tree<T, tree_node_allocator>::depth(const tree<T, tree_node_allocator>::iterator_base&) [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
foo_mrmr_ensemble_surv.cpp:250:28:   instantiated from here
tree.h:1635:2: warning: statement has no effect
tree.h: In static member function ‘static iter tree<T, tree_node_allocator>::parent(iter) [with iter = tree<int>::pre_order_iterator, T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
foo_mrmr_ensemble_surv.cpp:258:24:   instantiated from here
tree.h:756:2: warning: statement has no effect
tree.h: In static member function ‘static iter tree<T, tree_node_allocator>::parent(iter) [with iter = tree<double>::pre_order_iterator, T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’:
foo_mrmr_ensemble_surv.cpp:258:61:   instantiated from here
tree.h:756:2: warning: statement has no effect
In file included from foo_mrmr_ensemble_surv.h:10:0,
                 from foo_mrmr_ensemble_surv.cpp:1:
tree.h: In member function ‘iter tree<T, tree_node_allocator>::erase(iter) [with iter = tree<int>::pre_order_iterator, T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
foo_mrmr_ensemble_surv.cpp:267:24:   instantiated from here
tree.h:589:2: warning: statement has no effect
tree.h: In member function ‘iter tree<T, tree_node_allocator>::erase(iter) [with iter = tree<double>::pre_order_iterator, T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’:
foo_mrmr_ensemble_surv.cpp:267:54:   instantiated from here
tree.h:589:2: warning: statement has no effect
In file included from foo_mrmr_ensemble_surv.h:10:0,
                 from foo_mrmr_ensemble_surv.cpp:1:
tree.h: In member function ‘tree<T, tree_node_allocator>::pre_order_iterator& tree<T, tree_node_allocator>::pre_order_iterator::operator++() [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
foo_mrmr_ensemble_surv.cpp:281:6:   instantiated from here
tree.h:2046:2: warning: statement has no effect
tree.h: In member function ‘tree<T, tree_node_allocator>::pre_order_iterator& tree<T, tree_node_allocator>::pre_order_iterator::operator++() [with T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’:
foo_mrmr_ensemble_surv.cpp:281:12:   instantiated from here
tree.h:2046:2: warning: statement has no effect
In file included from foo_mrmr_ensemble_surv.h:10:0,
                 from foo_mrmr_ensemble_surv.cpp:1:
tree.h: In member function ‘iter tree<T, tree_node_allocator>::erase(iter) [with iter = tree<double>::leaf_iterator, T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’:
foo_mrmr_ensemble_surv.cpp:560:27:   instantiated from here
tree.h:589:2: warning: statement has no effect
In file included from foo_mrmr_ensemble_surv.h:10:0,
                 from foo_mrmr_ensemble_surv.cpp:1:
tree.h: In member function ‘iter tree<T, tree_node_allocator>::append_child(iter, const T&) [with iter = tree<int>::pre_order_iterator, T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
foo_mrmr_ensemble_surv.cpp:690:55:   instantiated from here
tree.h:883:2: warning: statement has no effect
tree.h:884:2: warning: statement has no effect
tree.h: In member function ‘iter tree<T, tree_node_allocator>::append_child(iter, const T&) [with iter = tree<double>::pre_order_iterator, T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’:
foo_mrmr_ensemble_surv.cpp:691:62:   instantiated from here
tree.h:883:2: warning: statement has no effect
tree.h:884:2: warning: statement has no effect
tree.h: In member function ‘tree<T, tree_node_allocator>::breadth_first_queued_iterator& tree<T, tree_node_allocator>::breadth_first_queued_iterator::operator++() [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
foo_mrmr_ensemble_surv.cpp:808:6:   instantiated from here
tree.h:2273:2: warning: statement has no effect
tree.h: In member function ‘tree<T, tree_node_allocator>::pre_order_iterator& tree<T, tree_node_allocator>::pre_order_iterator::operator--() [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
tree.h:2091:3:   instantiated from ‘tree<T, tree_node_allocator>::pre_order_iterator tree<T, tree_node_allocator>::pre_order_iterator::operator--(int) [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’
foo_mrmr_ensemble_surv.cpp:355:6:   instantiated from here
tree.h:2065:2: warning: statement has no effect
tree.h: In member function ‘tree<T, tree_node_allocator>::pre_order_iterator& tree<T, tree_node_allocator>::pre_order_iterator::operator--() [with T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’:
tree.h:2091:3:   instantiated from ‘tree<T, tree_node_allocator>::pre_order_iterator tree<T, tree_node_allocator>::pre_order_iterator::operator--(int) [with T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’
foo_mrmr_ensemble_surv.cpp:355:16:   instantiated from here
tree.h:2065:2: warning: statement has no effect
tree.h: In member function ‘tree<T, tree_node_allocator>::leaf_iterator& tree<T, tree_node_allocator>::leaf_iterator::operator++() [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
tree.h:2673:4:   instantiated from ‘tree<T, tree_node_allocator>::leaf_iterator tree<T, tree_node_allocator>::leaf_iterator::operator++(int) [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’
foo_mrmr_ensemble_surv.cpp:502:5:   instantiated from here
tree.h:2636:2: warning: statement has no effect
tree.h: In member function ‘tree<T, tree_node_allocator>::leaf_iterator& tree<T, tree_node_allocator>::leaf_iterator::operator++() [with T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’:
tree.h:2673:4:   instantiated from ‘tree<T, tree_node_allocator>::leaf_iterator tree<T, tree_node_allocator>::leaf_iterator::operator++(int) [with T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’
foo_mrmr_ensemble_surv.cpp:526:22:   instantiated from here
tree.h:2636:2: warning: statement has no effect
tree.h: In member function ‘tree<T, tree_node_allocator>::leaf_iterator& tree<T, tree_node_allocator>::leaf_iterator::operator--() [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
tree.h:2681:4:   instantiated from ‘tree<T, tree_node_allocator>::leaf_iterator tree<T, tree_node_allocator>::leaf_iterator::operator--(int) [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’
foo_mrmr_ensemble_surv.cpp:554:6:   instantiated from here
tree.h:2657:2: warning: statement has no effect
tree.h: In member function ‘tree<T, tree_node_allocator>::leaf_iterator& tree<T, tree_node_allocator>::leaf_iterator::operator--() [with T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’:
tree.h:2681:4:   instantiated from ‘tree<T, tree_node_allocator>::leaf_iterator tree<T, tree_node_allocator>::leaf_iterator::operator--(int) [with T = double, tree_node_allocator = std::allocator<tree_node_<double> >]’
foo_mrmr_ensemble_surv.cpp:554:16:   instantiated from here
tree.h:2657:2: warning: statement has no effect
tree.h: In member function ‘iter tree<T, tree_node_allocator>::replace(iter, const tree<T, tree_node_allocator>::iterator_base&) [with iter = tree<int>::pre_order_iterator, T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’:
tree.h:547:3:   instantiated from ‘void tree<T, tree_node_allocator>::copy_(const tree<T, tree_node_allocator>&) [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’
tree.h:531:2:   instantiated from ‘tree<T, tree_node_allocator>::tree(const tree<T, tree_node_allocator>&) [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’
foo_mrmr_ensemble_surv.cpp:611:24:   instantiated from here
tree.h:1113:2: warning: statement has no effect
tree.h:547:3:   instantiated from ‘void tree<T, tree_node_allocator>::copy_(const tree<T, tree_node_allocator>&) [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’
tree.h:531:2:   instantiated from ‘tree<T, tree_node_allocator>::tree(const tree<T, tree_node_allocator>&) [with T = int, tree_node_allocator = std::allocator<tree_node_<int> >]’
foo_mrmr_ensemble_surv.cpp:611:24:   instantiated from here
tree.h:1153:3: warning: statement has no effect
tree.h:1162:5: warning: statement has no effect
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:790:199: warning: ‘x2’ may be used uninitialized in this function
foo_mrmr_ensemble_surv.cpp:740:7: warning: ‘Rres’ may be used uninitialized in this function
foo_mrmr_ensemble_surv.cpp:815:18: warning: ‘res_old’ may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.10-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:12:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:22:28: 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:49:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:50:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:56:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:58:30: 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:300:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:340:20: warning: comparison between signed and unsigned integer expressions
g++ -shared -L/usr/local/lib64 -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/survcomp.Rcheck/survcomp/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘survcomp.Rnw’ 
** testing if installed package can be loaded

* DONE (survcomp)

survcomp.Rcheck/survcomp-Ex.timings:

nameusersystemelapsed
D.index0.0240.0000.024
breastCancerData1.2560.0401.298
censor.time0.0000.0000.001
cindex.comp0.0080.0000.005
cindex.comp.meta0.0040.0000.007
combine.est0.0000.0000.001
combine.test0.0000.0000.001
concordance.index0.0040.0000.004
cvpl0.4640.0000.465
dindex.comp0.0160.0000.014
dindex.comp.meta0.0320.0000.031
fisherz000
forestplot.surv0.0920.0040.100
getsurv20.0080.0000.006
hazard.ratio0.0120.0000.011
hr.comp0.0160.0000.016
hr.comp.meta0.0360.0000.036
hr.comp20.0120.0000.009
iauc.comp0.7240.0000.723
ibsc.comp0.3000.0120.484
km.coxph.plot0.0480.0000.047
logpl0.0400.0000.037
mainz7g0.4560.0080.470
metaplot.surv0.0040.0040.007
mrmr.cindex0.0040.0000.004
nki7g0.2480.0160.291
no.at.risk0.0280.0000.031
sbrier.score2proba0.2120.0000.218
score2proba0.0360.0000.037
td.sens.spec0.0000.0000.002
tdrocc0.3680.0040.401
test.hetero.est000
test.hetero.test0.0000.0040.000
transbig7g0.2240.0080.288
unt7g0.2200.0280.266
upp7g0.2240.0120.237
vdx7g0.2480.0080.254