##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:iCARE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings iCARE_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/iCARE.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘iCARE/DESCRIPTION’ ... OK
* this is package ‘iCARE’ version ‘1.35.0’
* 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 ‘iCARE’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  bc_data.rda    1.2Mb    658Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
compute.absolute.risk.split.interval 6.775  1.895   8.670
compute.absolute.risk                4.207  1.280   5.527
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/iCARE.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL iCARE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘iCARE’ ...
** this is package ‘iCARE’ version ‘1.35.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c source.c -o source.o
source.c: In function ‘dVec_alloc’:
source.c:45:10: warning: old-style function definition [-Wold-style-definition]
   45 | double * dVec_alloc(n, initFlag, initVal)
      |          ^~~~~~~~~~
source.c: In function ‘iVec_alloc’:
source.c:64:7: warning: old-style function definition [-Wold-style-definition]
   64 | int * iVec_alloc(n, initFlag, initVal)
      |       ^~~~~~~~~~
source.c: In function ‘dMat_alloc’:
source.c:81:11: warning: old-style function definition [-Wold-style-definition]
   81 | double ** dMat_alloc(nrow, ncol, initFlag, initVal)
      |           ^~~~~~~~~~
source.c: In function ‘matrix_free’:
source.c:98:6: warning: old-style function definition [-Wold-style-definition]
   98 | void matrix_free(x, n)
      |      ^~~~~~~~~~~
source.c: In function ‘get_non_miss’:
source.c:114:12: warning: old-style function definition [-Wold-style-definition]
  114 | static int get_non_miss(vec, n, ovec)
      |            ^~~~~~~~~~~~
source.c: In function ‘X_y’:
source.c:135:13: warning: old-style function definition [-Wold-style-definition]
  135 | static void X_y(X, nr, nc, y, index, ni, ret)
      |             ^~~
source.c: In function ‘X_y2’:
source.c:155:13: warning: old-style function definition [-Wold-style-definition]
  155 | static void X_y2(X, nc, y, z, index, ni, ret)
      |             ^~~~
source.c: In function ‘vec_mult’:
source.c:185:15: warning: old-style function definition [-Wold-style-definition]
  185 | static double vec_mult(x, y, index, ni)
      |               ^~~~~~~~
source.c: In function ‘vec_lteq_c’:
source.c:203:12: warning: old-style function definition [-Wold-style-definition]
  203 | static int vec_lteq_c(vec, n, c)
      |            ^~~~~~~~~~
source.c: In function ‘mean_2val’:
source.c:224:15: warning: old-style function definition [-Wold-style-definition]
  224 | static double mean_2val(vec, subvec, nsub, weights)
      |               ^~~~~~~~~
source.c: In function ‘mat_from_vec’:
source.c:241:13: warning: old-style function definition [-Wold-style-definition]
  241 | static void mat_from_vec(vec, nr, nc, mat)
      |             ^~~~~~~~~~~~
source.c: In function ‘quant_vecs’:
source.c:256:12: warning: old-style function definition [-Wold-style-definition]
  256 | static int quant_vecs(probs, nprobs, n, ivec, lo, hi, h)
      |            ^~~~~~~~~~
source.c: In function ‘quantile’:
source.c:284:13: warning: old-style function definition [-Wold-style-definition]
  284 | static void quantile(x, n, probs, nprobs, lo, hi, h, ivec, ni, qs)
      |             ^~~~~~~~
source.c: In function ‘var_dvec’:
source.c:338:15: warning: old-style function definition [-Wold-style-definition]
  338 | static double var_dvec(vec, n)
      |               ^~~~~~~~
source.c: In function ‘get_cutpoints’:
source.c:358:12: warning: old-style function definition [-Wold-style-definition]
  358 | static int get_cutpoints(quantiles, nq, ref_LP, nref)
      |            ^~~~~~~~~~~~~
source.c: In function ‘get_miss_perc’:
source.c:406:12: warning: old-style function definition [-Wold-style-definition]
  406 | static int get_miss_perc(cutpoints, ncuts, miss_LP)
      |            ^~~~~~~~~~~~~
source.c: In function ‘vec_ab’:
source.c:427:12: warning: old-style function definition [-Wold-style-definition]
  427 | static int vec_ab(x, n, a, b)
      |            ^~~~~~
source.c: In function ‘get_newEndpoints’:
source.c:444:13: warning: old-style function definition [-Wold-style-definition]
  444 | static void get_newEndpoints(cutpoints, ncuts, miss_LP, miss_perc, ref_LP, nref, rcut1, rcut2)
      |             ^~~~~~~~~~~~~~~~
source.c: In function ‘get_subs_2cut’:
source.c:471:12: warning: old-style function definition [-Wold-style-definition]
  471 | static int get_subs_2cut(x, n, a, b, ret)
      |            ^~~~~~~~~~~~~
source.c: In function ‘get_wgts’:
source.c:493:13: warning: old-style function definition [-Wold-style-definition]
  493 | static void get_wgts(weights, subvec, nsub, retvec)
      |             ^~~~~~~~
source.c: In function ‘ref_risk1’:
source.c:511:6: warning: old-style function definition [-Wold-style-definition]
  511 | void ref_risk1(ref_risks, betavec, zmat, refmat, n_beta, nr_z, nc_z, nr_ref, nc_ref,
      |      ^~~~~~~~~
source.c: In function ‘get_int’:
source.c:619:13: warning: old-style function definition [-Wold-style-definition]
  619 | static void get_int(nsub, age_new, t, aexp_rr, lambda, comp, zbeta, holder)
      |             ^~~~~~~
source.c: In function ‘finalVal’:
source.c:645:15: warning: old-style function definition [-Wold-style-definition]
  645 | static double finalVal(nsub, zbeta, expzbeta, age_new, age_int, lambda, loglambda, compRates, holder, tempv, weights)
      |               ^~~~~~~~
source.c: In function ‘ref_risk2’:
source.c:684:6: warning: old-style function definition [-Wold-style-definition]
  684 | void ref_risk2(betavec, zmat, refmat, n_beta, nr_z, nc_z, nr_ref, nc_ref,
      |      ^~~~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o iCARE.so source.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-iCARE/00new/iCARE/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (iCARE)

R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("iCARE")

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

   user  system elapsed 
  1.287   0.368   1.655 
   user  system elapsed 
  1.389   0.205   1.594 
   user  system elapsed 
  1.316   0.199   1.516 


RUNIT TEST PROTOCOL -- Mon Mar 24 23:05:59 2025 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
iCARE RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 13.687   3.103  16.783