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This page was generated on 2024-04-17 11:38:17 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2041/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SQLDataFrame 1.16.1  (landing page)
Qian Liu
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/SQLDataFrame
git_branch: RELEASE_3_18
git_last_commit: 4a69da1
git_last_commit_date: 2024-02-09 14:15:00 -0400 (Fri, 09 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for SQLDataFrame on merida1


To the developers/maintainers of the SQLDataFrame package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SQLDataFrame.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SQLDataFrame
Version: 1.16.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SQLDataFrame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SQLDataFrame_1.16.1.tar.gz
StartedAt: 2024-04-16 09:28:55 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 09:32:33 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 218.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SQLDataFrame.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SQLDataFrame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SQLDataFrame_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SQLDataFrame.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SQLDataFrame/DESCRIPTION’ ... OK
* this is package ‘SQLDataFrame’ version ‘1.16.1’
* 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 for sufficient/correct file permissions ... 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
* 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’ ‘DelayedArray:::simplify_NULL_dimnames’
  ‘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’
saveSQLDataFrame: no visible binding for global variable ‘u1’
Undefined global functions or variables:
  SurrogateKey concat concatKeys cons localConn u1
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
SQLDataFrame-methods 16.232  0.583  17.783
joinSQLDataFrame      7.312  0.104   7.899
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/SQLDataFrame.Rcheck/00check.log’
for details.



Installation output

SQLDataFrame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SQLDataFrame
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘SQLDataFrame’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SQLDataFrame)

Tests output

SQLDataFrame.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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

Attaching package: 'BiocGenerics'

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, aperm, 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:utils':

    findMatches

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

    I, expand.grid, unname

> 
> test_check("SQLDataFrame")
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 170 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_SQLDataFrame-methods.R:114:1'

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 170 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 54.709   1.224  58.403 

Example timings

SQLDataFrame.Rcheck/SQLDataFrame-Ex.timings

nameusersystemelapsed
SQLDataFrame-class2.5640.0452.706
SQLDataFrame-methods16.232 0.58317.783
joinSQLDataFrame7.3120.1047.899
makeSQLDataFrame1.7340.0201.827
rbindSQLDataFrame3.0310.0223.187
saveSQLDataFrame1.0300.0171.092
unionSQLDataFrame1.8270.0141.931