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CHECK report for GENIE3 on malbec1

This page was generated on 2019-04-16 11:52:55 -0400 (Tue, 16 Apr 2019).

Package 615/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GENIE3 1.4.3
Van Anh Huynh-Thu
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GENIE3
Branch: RELEASE_3_8
Last Commit: ae719c7
Last Changed Date: 2019-01-31 18:54:03 -0400 (Thu, 31 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GENIE3
Version: 1.4.3
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GENIE3.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GENIE3_1.4.3.tar.gz
StartedAt: 2019-04-16 00:10:35 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:10:55 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 19.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GENIE3.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GENIE3.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GENIE3_1.4.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/GENIE3.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GENIE3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GENIE3’ version ‘1.4.3’
* 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 ‘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
* 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 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 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/GENIE3.Rcheck/00check.log’
for details.



Installation output

GENIE3.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL GENIE3
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘GENIE3’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-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: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:1762:10: warning: ‘flag_continue’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   return flag_continue; 
          ^
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o GENIE3.so GENIE3.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (GENIE3)

Tests output

GENIE3.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  6.376   0.284   6.673 

Example timings

GENIE3.Rcheck/GENIE3-Ex.timings

nameusersystemelapsed
GENIE30.2680.0000.271
getLinkList0.0640.0000.065