Package: GENIE3

Version: 1.5.4

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GENIE3.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GENIE3_1.5.4.tar.gz

StartedAt: 2019-04-09 02:59:35 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:00:17 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 41.7 seconds

RetCode: 0

Status:  OK

CheckDir: GENIE3.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GENIE3.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GENIE3_1.5.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GENIE3.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GENIE3/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GENIE3' version '1.5.4'
* 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 whether package 'GENIE3' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GENIE3/libs/i386/GENIE3.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GENIE3/libs/x64/GENIE3.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GENIE3.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GENIE3_1.5.4.tar.gz && rm -rf GENIE3.buildbin-libdir && mkdir GENIE3.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GENIE3.buildbin-libdir GENIE3_1.5.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GENIE3_1.5.4.zip && rm GENIE3_1.5.4.tar.gz GENIE3_1.5.4.zip
###
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100 24107  100 24107    0     0   382k      0 --:--:-- --:--:-- --:--:--  435k

install for i386

* installing *source* package 'GENIE3' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c GENIE3.c -o GENIE3.o
GENIE3.c: In function 'find_the_best_threshold_multiregr':
GENIE3.c:1368:24: warning: 'best_threshold' may be used uninitialized in this function [-Wmaybe-uninitialized]
     current_threshold.f=best_threshold;
                        ^
GENIE3.c:1370:27: warning: 'best_info' may be used uninitialized in this function [-Wmaybe-uninitialized]
     current_threshold_info=best_info;
                           ^
GENIE3.c: In function 'build_one_tree_ensemble':
GENIE3.c:1052:7: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
       write_one_tree(current_tree, fp);
       ^
GENIE3.c: In function 'find_the_best_threshold_symb_multiregr':
GENIE3.c:1466:27: warning: 'best_info' may be used uninitialized in this function [-Wmaybe-uninitialized]
     current_threshold_info=best_info;
                           ^
GENIE3.c: In function 'BuildTreeEns':
GENIE3.c:1753:6: warning: 'flag_continue' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (flag_continue == 1) {
      ^
GENIE3.c:1725:7: note: 'flag_continue' was declared here
   int flag_continue;
       ^
GENIE3.c: In function 'compute_ltrees_variable_importance_multiregr_separate':
GENIE3.c:1762:3: warning: 'flag_continue' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return flag_continue; 
   ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GENIE3.dll tmp.def GENIE3.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GENIE3.buildbin-libdir/00LOCK-GENIE3/00new/GENIE3/libs/i386
** 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
  converting help for package 'GENIE3'
    finding HTML links ... done
    GENIE3                                  html  
    getLinkList                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GENIE3' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c GENIE3.c -o GENIE3.o
GENIE3.c: In function 'find_the_best_threshold_multiregr':
GENIE3.c:1368:24: warning: 'best_threshold' may be used uninitialized in this function [-Wmaybe-uninitialized]
     current_threshold.f=best_threshold;
                        ^
GENIE3.c:1370:27: warning: 'best_info' may be used uninitialized in this function [-Wmaybe-uninitialized]
     current_threshold_info=best_info;
                           ^
GENIE3.c: In function 'build_one_tree_ensemble':
GENIE3.c:1052:7: warning: 'fp' may be used uninitialized in this function [-Wmaybe-uninitialized]
       write_one_tree(current_tree, fp);
       ^
GENIE3.c: In function 'find_the_best_threshold_symb_multiregr':
GENIE3.c:1466:27: warning: 'best_info' may be used uninitialized in this function [-Wmaybe-uninitialized]
     current_threshold_info=best_info;
                           ^
GENIE3.c: In function 'compute_ltrees_variable_importance_multiregr_separate':
GENIE3.c:1762:3: warning: 'flag_continue' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return flag_continue; 
   ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GENIE3.dll tmp.def GENIE3.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GENIE3.buildbin-libdir/GENIE3/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GENIE3' as GENIE3_1.5.4.zip
* DONE (GENIE3)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GENIE3' successfully unpacked and MD5 sums checked

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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
== testthat results  ===========================================================
OK: 48 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.79    0.45    6.23 

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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
== testthat results  ===========================================================
OK: 48 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.87    0.32    7.18