survcomp 1.26.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/survcomp | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings survcomp_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/survcomp.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.26.0’
* 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 ... 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 ‘complete.cases’
D.index: no visible global function definition for ‘coxph’
D.index: no visible global function definition for ‘pchisq’
D.index: no visible global function definition for ‘qnorm’
censor.time: no visible global function definition for ‘complete.cases’
cindex.comp: no visible global function definition for ‘cor’
cindex.comp: no visible global function definition for ‘pt’
cindex.comp.meta: no visible global function definition for ‘cor’
cindex.comp.meta: no visible global function definition for ‘pt’
combine.est: no visible global function definition for ‘complete.cases’
combine.test: no visible global function definition for ‘pchisq’
combine.test: no visible global function definition for ‘qnorm’
combine.test: no visible global function definition for ‘pnorm’
combine.test: no visible global function definition for ‘pt’
concordance.index: no visible global function definition for
‘complete.cases’
concordance.index: no visible global function definition for ‘qnorm’
concordance.index: no visible global function definition for ‘pnorm’
cvpl: no visible global function definition for ‘complete.cases’
cvpl: no visible global function definition for ‘coxph’
cvpl: no visible global function definition for ‘formula’
cvpl: no visible global function definition for ‘predict’
dindex.comp: no visible global function definition for ‘cor’
dindex.comp: no visible global function definition for ‘pt’
dindex.comp.meta: no visible global function definition for ‘cor’
dindex.comp.meta: no visible global function definition for ‘pt’
forestplot.surv: no visible global function definition for ‘plot.new’
hazard.ratio: no visible global function definition for
‘complete.cases’
hazard.ratio: no visible global function definition for ‘coxph’
hazard.ratio: no visible global function definition for ‘pchisq’
hazard.ratio: no visible global function definition for ‘qnorm’
hr.comp: no visible global function definition for ‘cor’
hr.comp: no visible global function definition for ‘pt’
hr.comp.meta: no visible global function definition for ‘cor’
hr.comp.meta: no visible global function definition for ‘pt’
hr.comp2: no visible global function definition for ‘cor’
hr.comp2: no visible global function definition for ‘pt’
iauc.comp: no visible global function definition for ‘complete.cases’
iauc.comp: no visible global function definition for ‘wilcox.test’
ibsc.comp: no visible global function definition for ‘complete.cases’
ibsc.comp: no visible global function definition for ‘wilcox.test’
km.coxph.plot: no visible global function definition for ‘par’
km.coxph.plot: no visible global function definition for ‘plot’
km.coxph.plot: no visible global function definition for ‘survfit’
km.coxph.plot: no visible global function definition for ‘title’
km.coxph.plot: no visible global function definition for ‘abline’
km.coxph.plot: no visible global function definition for ‘legend’
km.coxph.plot: no visible global function definition for ‘mtext’
km.coxph.plot: no visible global function definition for ‘text’
km.coxph.plot: no visible global function definition for ‘axis’
logpl: no visible global function definition for ‘complete.cases’
metaplot.surv: no visible global function definition for ‘qnorm’
metaplot.surv: no visible global function definition for ‘par’
metaplot.surv: no visible global function definition for ‘plot’
metaplot.surv: no visible global function definition for ‘axis’
metaplot.surv: no visible global function definition for ‘abline’
metaplot.surv: no visible global function definition for ‘lines’
metaplot.surv: no visible global function definition for ‘text’
metaplot.surv: no visible global function definition for ‘rect’
metaplot.surv: no visible global function definition for ‘polygon’
mrmr.cindex: no visible global function definition for ‘complete.cases’
no.at.risk: no visible global function definition for ‘survfit’
sbrier.score2proba: no visible global function definition for
‘complete.cases’
sbrier.score2proba: no visible global function definition for ‘survfit’
sbrier.score2proba: no visible global function definition for ‘Surv’
sbrier.score2proba: no visible global function definition for ‘predict’
score2proba: no visible global function definition for ‘complete.cases’
score2proba: no visible global function definition for ‘coxph’
score2proba: no visible global function definition for ‘survfit’
score2proba: no visible global function definition for ‘predict’
td.sens.spec: no visible global function definition for
‘complete.cases’
tdrocc: no visible global function definition for ‘complete.cases’
test.hetero.est: no visible global function definition for
‘complete.cases’
test.hetero.est: no visible global function definition for ‘pchisq’
test.hetero.test: no visible global function definition for ‘qnorm’
test.hetero.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
Surv abline axis complete.cases cor coxph formula legend lines mtext
par pchisq plot plot.new pnorm polygon predict pt qnorm rect survfit
text title wilcox.test
Consider adding
importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
"par", "plot", "plot.new", "polygon", "rect", "text",
"title")
importFrom("stats", "complete.cases", "cor", "formula", "pchisq",
"pnorm", "predict", "pt", "qnorm", "wilcox.test")
to your NAMESPACE file.
* 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 ... 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-3.5-bioc/meat/survcomp.Rcheck/00check.log’
for details.
* installing *source* package ‘survcomp’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c concordance.index.c -o concordance.index.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -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: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:732:39: warning: unused variable 'res_all2' [-Wunused-variable]
int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
^
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: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 -fPIC -Wall -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-3.5-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)