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CHECK report for SQLDataFrame on tokay1

This page was generated on 2021-05-06 12:33:46 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SQLDataFrame package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1781/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SQLDataFrame 1.4.2  (landing page)
Qian Liu
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SQLDataFrame
Branch: RELEASE_3_12
Last Commit: 5849521
Last Changed Date: 2020-11-23 17:18:29 -0400 (Mon, 23 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SQLDataFrame
Version: 1.4.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SQLDataFrame.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SQLDataFrame_1.4.2.tar.gz
StartedAt: 2021-05-06 07:14:55 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:17:23 -0400 (Thu, 06 May 2021)
EllapsedTime: 147.9 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: SQLDataFrame.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SQLDataFrame.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SQLDataFrame_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SQLDataFrame.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SQLDataFrame/DESCRIPTION' ... OK
* this is package 'SQLDataFrame' version '1.4.2'
* package encoding: UTF-8
* 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 'SQLDataFrame' 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 ... WARNING
'::' or ':::' import not declared from: 'tidyselect'
Missing object imported by a ':::' call: 'dbplyr:::db_create_indexes.DBIConnection'
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'dbplyr:::anti_join.tbl_lazy'
  'dbplyr:::db_create_index.DBIConnection'
  'dbplyr:::inner_join.tbl_lazy' 'dbplyr:::left_join.tbl_lazy'
  'dbplyr:::semi_join.tbl_lazy' 'dbplyr:::sqlite_version'
  'dbplyr:::union.tbl_lazy' 'dplyr:::random_table_name'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.doCompatibleFunction: no visible binding for global variable 'cons'
.extract_tbl_rows_by_key: no visible binding for global variable
  'SurrogateKey'
.extract_tbl_rows_by_key: no visible binding for global variable
  'concatKeys'
.union_SQLDataFrame_sqlite: no visible binding for global variable
  'localConn'
SQLDataFrame: no visible binding for global variable 'cons'
filter.SQLDataFrame: no visible binding for global variable
  'SurrogateKey'
filter.SQLDataFrame: no visible binding for global variable 'concat'
Undefined global functions or variables:
  SurrogateKey concat concatKeys cons localConn
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
SQLDataFrame-methods 5.05      0    5.04
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/SQLDataFrame.Rcheck/00check.log'
for details.



Installation output

SQLDataFrame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SQLDataFrame_1.4.2.tar.gz && rm -rf SQLDataFrame.buildbin-libdir && mkdir SQLDataFrame.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SQLDataFrame.buildbin-libdir SQLDataFrame_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SQLDataFrame_1.4.2.zip && rm SQLDataFrame_1.4.2.tar.gz SQLDataFrame_1.4.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 51228  100 51228    0     0  2915k      0 --:--:-- --:--:-- --:--:-- 3126k

install for i386

* installing *source* package 'SQLDataFrame' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SQLDataFrame'
    finding HTML links ... done
    SQLDataFrame-class                      html  
    SQLDataFrame-methods                    html  
    joinSQLDataFrame                        html  
    makeSQLDataFrame                        html  
    rbindSQLDataFrame                       html  
    saveSQLDataFrame                        html  
    unionSQLDataFrame                       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 'SQLDataFrame' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SQLDataFrame' as SQLDataFrame_1.4.2.zip
* DONE (SQLDataFrame)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SQLDataFrame' successfully unpacked and MD5 sums checked

Tests output

SQLDataFrame.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> library(testthat)
> library(SQLDataFrame)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: dbplyr

Attaching package: 'dbplyr'

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

    ident, sql

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    combine, intersect, setdiff, union

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    first, rename

The following object is masked from 'package:base':

    expand.grid

> 
> test_check("SQLDataFrame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 174 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  18.71    0.42   19.15 

SQLDataFrame.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> library(testthat)
> library(SQLDataFrame)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: dbplyr

Attaching package: 'dbplyr'

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

    ident, sql

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    combine, intersect, setdiff, union

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    first, rename

The following object is masked from 'package:base':

    expand.grid

> 
> test_check("SQLDataFrame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 174 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  18.09    0.20   18.29 

Example timings

SQLDataFrame.Rcheck/examples_i386/SQLDataFrame-Ex.timings

nameusersystemelapsed
SQLDataFrame-class1.390.051.44
SQLDataFrame-methods4.590.004.59
joinSQLDataFrame2.740.012.75
makeSQLDataFrame0.670.020.69
rbindSQLDataFrame1.030.001.03
saveSQLDataFrame0.250.000.25
unionSQLDataFrame0.610.030.64

SQLDataFrame.Rcheck/examples_x64/SQLDataFrame-Ex.timings

nameusersystemelapsed
SQLDataFrame-class1.280.011.30
SQLDataFrame-methods5.050.005.04
joinSQLDataFrame2.840.032.87
makeSQLDataFrame1.110.001.11
rbindSQLDataFrame1.660.001.66
saveSQLDataFrame0.340.020.36
unionSQLDataFrame0.750.010.76