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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GENIE3.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GENIE3_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GENIE3.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GENIE3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GENIE3’ version ‘1.28.0’
* checking package namespace information ... NOTE
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘GENIE3’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    VERSION 0.99.4
        Removed argument "seed", use set.seed instead
        Minor improvemtents
* 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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GENIE3.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GENIE3
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘GENIE3’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c GENIE3.c -o GENIE3.o
GENIE3.c: In function ‘find_the_best_threshold_multiregr’:
GENIE3.c:1370:27: warning: ‘best_info’ may be used uninitialized [-Wmaybe-uninitialized]
 1370 |     current_threshold_info=best_info;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
GENIE3.c:1328:31: note: ‘best_info’ was declared here
 1328 |   SCORE_TYPE best_score=-1.0, best_info, current_score, w;
      |                               ^~~~~~~~~
GENIE3.c:1368:24: warning: ‘best_threshold’ may be used uninitialized [-Wmaybe-uninitialized]
 1368 |     current_threshold.f=best_threshold;
      |     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
GENIE3.c:1329:9: note: ‘best_threshold’ was declared here
 1329 |   float best_threshold;
      |         ^~~~~~~~~~~~~~
GENIE3.c: In function ‘build_one_tree_ensemble’:
GENIE3.c:1052:7: warning: ‘fp’ may be used uninitialized [-Wmaybe-uninitialized]
 1052 |       write_one_tree(current_tree, fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENIE3.c:987:9: note: ‘fp’ was declared here
  987 |   FILE *fp;
      |         ^~
GENIE3.c: In function ‘find_the_best_threshold_symb_multiregr’:
GENIE3.c:1466:27: warning: ‘best_info’ may be used uninitialized [-Wmaybe-uninitialized]
 1466 |     current_threshold_info=best_info;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
GENIE3.c:1412:31: note: ‘best_info’ was declared here
 1412 |   SCORE_TYPE best_score=-1.0, best_info, current_score;
      |                               ^~~~~~~~~
GENIE3.c: In function ‘compute_ltrees_variable_importance_multiregr_separate’:
GENIE3.c:1753:6: warning: ‘flag_continue’ may be used uninitialized [-Wmaybe-uninitialized]
 1753 |   if (flag_continue == 1) {
      |      ^
GENIE3.c:1725:7: note: ‘flag_continue’ was declared here
 1725 |   int flag_continue;
      |       ^~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o GENIE3.so GENIE3.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-GENIE3/00new/GENIE3/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘GENIE3’ with signature ‘"SummarizedExperiment"’: no definition for class “SummarizedExperiment”
in method for ‘GENIE3’ with signature ‘"ExpressionSet"’: no definition for class “ExpressionSet”
** 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 (GENIE3)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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.

> 
> testthat::test_check("GENIE3")
Loading required package: GENIE3
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
  6.202   0.372   6.559