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BioC 3.2: CHECK report for survcomp on oaxaca

This page was generated on 2015-10-27 17:39:31 -0400 (Tue, 27 Oct 2015).

Package 1032/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.20.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/survcomp
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  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: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings survcomp_1.20.0.tar.gz
StartedAt: 2015-10-27 08:20:45 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 08:21:29 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 44.5 seconds
RetCode: 0
Status:  OK 
CheckDir: survcomp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings survcomp_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/survcomp.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.20.0’
* 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 ... [5s/5s] 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 ... [5s/5s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/survcomp.Rcheck/00check.log’
for details.


survcomp.Rcheck/00install.out:

* installing *source* package ‘survcomp’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c concordance.index.c -o concordance.index.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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: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: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: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:578:24: 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: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:820:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
                                res_all[k]=res_old[k];
                                           ^˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:815:25: note: initialize the variable 'res_old' to silence this warning
                int *res_all, *res_old;
                                      ^
                                       = NULL
18 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
clang++ -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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.index0.0240.0030.052
breastCancerData0.8200.0270.849
censor.time0.0010.0000.001
cindex.comp0.0050.0010.005
cindex.comp.meta0.0060.0000.007
combine.est0.0020.0000.002
combine.test0.0010.0000.001
concordance.index0.0030.0010.004
cvpl0.2140.0010.216
dindex.comp0.0130.0000.013
dindex.comp.meta0.0280.0010.028
fisherz0.0020.0000.001
forestplot.surv0.0680.0010.069
getsurv20.0120.0000.013
hazard.ratio0.0100.0010.012
hr.comp0.0130.0000.013
hr.comp.meta0.0920.0000.093
hr.comp20.0060.0000.007
iauc.comp0.3570.0040.361
ibsc.comp0.3260.0120.358
km.coxph.plot0.0390.0010.039
logpl0.0170.0010.017
mainz7g0.2320.0060.239
metaplot.surv0.0350.0010.036
mrmr.cindex0.0030.0000.004
nki7g0.2470.0050.253
no.at.risk0.0930.0000.093
sbrier.score2proba0.2140.0090.224
score2proba0.0190.0000.020
td.sens.spec0.0030.0000.020
tdrocc0.1880.0150.206
test.hetero.est0.0000.0000.001
test.hetero.test0.0010.0000.001
transbig7g0.2880.0080.296
unt7g0.2550.0070.261
upp7g0.2520.0070.259
vdx7g0.2460.0070.254