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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:eiR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings eiR_1.39.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/eiR.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘eiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eiR’ version ‘1.39.0’
* 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 ‘eiR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘ChemmineR’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘RCurl’ ‘RUnit’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
insertEmbeddedDescriptors: no visible global function definition for
  ‘postgresqlWriteTable’
insertEmbeddedDescriptorsByCompoundId: no visible global function
  definition for ‘postgresqlWriteTable’
insertGroupMembers: no visible global function definition for
  ‘postgresqlWriteTable’
Undefined global functions or variables:
  postgresqlWriteTable
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘eiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eiAdd
> ### Title: Add new compounds
> ### Aliases: eiAdd
> 
> ### ** Examples
> 
> 
>    library(snow)
>    r<- 50
>    d<- 40
> 
>    #initialize
>    data(sdfsample)
>    dir=file.path(tempdir(),"add")
>    dir.create(dir)
>    eiInit(sdfsample[1:99],dir=dir,skipPriorities=TRUE)
Loading required package: RSQLite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘RSQLite’
Error: Couldn't find driver SQLite. Looked in:
* global namespace
* in package called SQLite
* in package called RSQLite
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  eiR RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in /tmp/RtmpklTclE/RLIBS_ef2e978c18caf/eiR/unitTests/test_main.R: Error while sourcing  /tmp/RtmpklTclE/RLIBS_ef2e978c18caf/eiR/unitTests/test_main.R : Error : Couldn't find driver SQLite. Looked in:
  * global namespace
  * in package called SQLite
  * in package called RSQLite
  
  Test files with failing tests
  
     test_main.R 
       /tmp/RtmpklTclE/RLIBS_ef2e978c18caf/eiR/unitTests/test_main.R 
  
  
  Error in BiocGenerics:::testPackage("eiR") : 
    unit tests failed for package eiR
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘eiR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘eiR.Rmd’ using rmarkdown
Quitting from lines 109-112 (eiR.Rmd) 
Error: processing vignette 'eiR.Rmd' failed with diagnostics:
Couldn't find driver SQLite. Looked in:
* global namespace
* in package called SQLite
* in package called RSQLite
--- failed re-building ‘eiR.Rmd’

SUMMARY: processing the following file failed:
  ‘eiR.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/eiR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL eiR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘eiR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c optimFunctions.cc -o optimFunctions.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o eiR.so optimFunctions.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-eiR/00new/eiR/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 (eiR)

R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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.

> BiocGenerics:::testPackage("eiR")
test_main start
Loading required package: RSQLite
Loading required package: RSQLite
Error : Couldn't find driver SQLite. Looked in:
* global namespace
* in package called SQLite
* in package called RSQLite
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'RSQLite'
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'RSQLite'


RUNIT TEST PROTOCOL -- Wed Apr 12 06:04:49 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
eiR RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /tmp/RtmpklTclE/RLIBS_ef2e978c18caf/eiR/unitTests/test_main.R: Error while sourcing  /tmp/RtmpklTclE/RLIBS_ef2e978c18caf/eiR/unitTests/test_main.R : Error : Couldn't find driver SQLite. Looked in:
* global namespace
* in package called SQLite
* in package called RSQLite

Test files with failing tests

   test_main.R 
     /tmp/RtmpklTclE/RLIBS_ef2e978c18caf/eiR/unitTests/test_main.R 


Error in BiocGenerics:::testPackage("eiR") : 
  unit tests failed for package eiR
Execution halted