| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:28 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the survcomp package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/survcomp.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1997/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| survcomp 1.48.0 (landing page) Benjamin Haibe-Kains
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: survcomp |
| Version: 1.48.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:survcomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings survcomp_1.48.0.tar.gz |
| StartedAt: 2023-04-10 22:59:55 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:00:55 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 60.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: survcomp.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:survcomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings survcomp_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/survcomp.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.48.0’
* 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-3.16-bioc/meat/survcomp.Rcheck/00check.log’
for details.
survcomp.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL survcomp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -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++ -mmacosx-version-min=10.13 -std=gnu++14 -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: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:467:7: warning: unused variable 'found' [-Wunused-variable]
bool found=false;
^
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: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:817:7: warning: unused variable 'ind' [-Wunused-variable]
int ind=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:801:13: warning: unused variable 'cnt2' [-Wunused-variable]
int cnt=1,cnt2=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: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
20 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c survcomp_init.cpp -o survcomp_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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/4.2/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)
survcomp.Rcheck/survcomp-Ex.timings
| name | user | system | elapsed | |
| D.index | 0.024 | 0.006 | 0.031 | |
| balanced.hazard.ratio | 0.009 | 0.002 | 0.012 | |
| bhr.comp | 0.010 | 0.001 | 0.011 | |
| breastCancerData | 0.394 | 0.016 | 0.411 | |
| censor.time | 0.000 | 0.001 | 0.001 | |
| cindex.comp | 0.002 | 0.000 | 0.003 | |
| cindex.comp.meta | 0.003 | 0.000 | 0.004 | |
| combine.est | 0.001 | 0.000 | 0.001 | |
| combine.test | 0 | 0 | 0 | |
| concordance.index | 0.001 | 0.003 | 0.004 | |
| cvpl | 0.085 | 0.002 | 0.088 | |
| dindex.comp | 0.022 | 0.002 | 0.024 | |
| dindex.comp.meta | 0.014 | 0.001 | 0.014 | |
| fisherz | 0.000 | 0.000 | 0.001 | |
| forestplot.surv | 0.024 | 0.001 | 0.026 | |
| getsurv2 | 0.003 | 0.000 | 0.003 | |
| hazard.ratio | 0.006 | 0.002 | 0.008 | |
| hr.comp | 0.007 | 0.000 | 0.007 | |
| hr.comp.meta | 0.014 | 0.001 | 0.014 | |
| hr.comp2 | 0.005 | 0.000 | 0.005 | |
| iauc.comp | 0.182 | 0.011 | 0.194 | |
| ibsc.comp | 0.185 | 0.009 | 0.196 | |
| km.coxph.plot | 0.029 | 0.001 | 0.031 | |
| logpl | 0.007 | 0.001 | 0.008 | |
| mainz7g | 0.152 | 0.005 | 0.163 | |
| metaplot.surv | 0.003 | 0.001 | 0.004 | |
| mrmr.cindex | 0.002 | 0.000 | 0.002 | |
| nki7g | 0.170 | 0.005 | 0.174 | |
| no.at.risk | 0.008 | 0.000 | 0.009 | |
| sbrier.score2proba | 0.133 | 0.002 | 0.136 | |
| score2proba | 0.010 | 0.000 | 0.011 | |
| td.sens.spec | 0.001 | 0.001 | 0.001 | |
| tdrocc | 0.076 | 0.022 | 0.098 | |
| test.hetero.est | 0.001 | 0.000 | 0.001 | |
| test.hetero.test | 0 | 0 | 0 | |
| transbig7g | 0.162 | 0.005 | 0.168 | |
| unt7g | 0.157 | 0.005 | 0.162 | |
| upp7g | 0.184 | 0.006 | 0.191 | |
| vdx7g | 0.180 | 0.007 | 0.188 | |