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CHECK report for survcomp on celaya2

This page was generated on 2020-01-16 13:33:26 -0500 (Thu, 16 Jan 2020).

Package 1682/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.37.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/survcomp
Branch: master
Last Commit: 570d28f
Last Changed Date: 2019-10-29 13:35:26 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  NA 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: survcomp
Version: 1.37.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:survcomp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings survcomp_1.37.0.tar.gz
StartedAt: 2020-01-16 09:19:16 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 09:20:58 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 102.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: survcomp.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:survcomp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings survcomp_1.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/survcomp.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.37.0’
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/survcomp.Rcheck/00check.log’
for details.



Installation output

survcomp.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL survcomp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c concordance.index.c -o concordance.index.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o
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: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:387:10: warning: unused variable 'mim' [-Wunused-variable]
        double *mim, *boot_val, *mat_info;
                ^
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable 'max_val' [-Wunused-variable]
        double max_val=-1000;
               ^
foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable 'found' [-Wunused-variable]
        bool found=false;
             ^
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: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:801:13: warning: unused variable 'cnt2' [-Wunused-variable]
                int cnt=1,cnt2=0;
                          ^
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:733:30: warning: unused variable 'res_all' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                    ^
foo_mrmr_ensemble_surv.cpp:821:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
                                res_all[k]=res_old[k];
                                           ^~~~~~~
foo_mrmr_ensemble_surv.cpp:816:25: note: initialize the variable 'res_old' to silence this warning
                int *res_all, *res_old;
                                      ^
                                       = nullptr
18 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c survcomp_init.cpp -o survcomp_init.o
clang++ -std=gnu++11 -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 -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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.index0.0500.0080.058
balanced.hazard.ratio0.0260.0050.032
bhr.comp0.0230.0020.025
breastCancerData0.9820.0791.063
censor.time0.0010.0010.002
cindex.comp0.0050.0010.007
cindex.comp.meta0.0080.0020.009
combine.est0.0020.0010.003
combine.test0.0010.0010.001
concordance.index0.0070.0050.012
cvpl0.3780.0100.388
dindex.comp0.0270.0010.029
dindex.comp.meta0.0730.0110.085
fisherz0.0010.0000.001
forestplot.surv0.0870.0030.090
getsurv20.0050.0000.006
hazard.ratio0.0220.0040.026
hr.comp0.0200.0010.021
hr.comp.meta0.0530.0020.055
hr.comp20.0200.0010.022
iauc.comp0.5520.0530.610
ibsc.comp0.4670.0190.494
km.coxph.plot0.0840.0030.088
logpl0.0200.0020.022
mainz7g0.3030.0140.317
metaplot.surv0.0060.0010.010
mrmr.cindex0.0040.0010.006
nki7g0.3360.0120.348
no.at.risk0.0220.0010.024
sbrier.score2proba0.3810.0050.386
score2proba0.0290.0010.031
td.sens.spec0.0040.0010.006
tdrocc0.2340.0710.305
test.hetero.est0.0020.0000.002
test.hetero.test0.0000.0000.001
transbig7g0.2790.0140.292
unt7g0.2740.0150.290
upp7g0.3070.0160.322
vdx7g0.3290.0170.345