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CHECK report for Organism.dplyr on tokay2

This page was generated on 2020-10-17 11:57:20 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Organism.dplyr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1247/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Organism.dplyr 1.16.0
Martin Morgan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Organism.dplyr
Branch: RELEASE_3_11
Last Commit: 38abeff
Last Changed Date: 2020-04-27 15:05:41 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Organism.dplyr
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Organism.dplyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Organism.dplyr_1.16.0.tar.gz
StartedAt: 2020-10-17 06:41:18 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:54:49 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 811.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Organism.dplyr.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Organism.dplyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Organism.dplyr_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Organism.dplyr.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Organism.dplyr/DESCRIPTION' ... OK
* this is package 'Organism.dplyr' version '1.16.0'
* 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 'Organism.dplyr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/filter.Rd:152: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/filter.Rd:155: file link 'select,src_organism-method' in package 'Organism.dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/select.Rd:137: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/src.Rd:130: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/src.Rd:133: file link 'select,src_organism-method' in package 'Organism.dplyr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Organism.dplyr.Rcheck/00install.out' for details.
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  'AnnotationDbi:::smartKeys' 'GenomicFeatures:::.exons_with_3utr'
  'GenomicFeatures:::.exons_with_5utr'
  'GenomicFeatures:::get_TxDb_seqinfo0'
  'S4Vectors:::extract_data_frame_rows'
  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
.toGRanges: no visible binding for global variable '.'
intronsByTranscript,src_organism: no visible binding for global
  variable '.'
orgPackageName,src_organism: no visible binding for global variable
  'name'
orgPackageName,src_organism: no visible binding for global variable
  'organism'
orgPackageName,src_organism: no visible binding for global variable
  'OrgDb'
Undefined global functions or variables:
  . OrgDb name organism
* 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
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/Organism.dplyr.Rcheck/00check.log'
for details.

Installation output

Organism.dplyr.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Organism.dplyr_1.16.0.tar.gz && rm -rf Organism.dplyr.buildbin-libdir && mkdir Organism.dplyr.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Organism.dplyr.buildbin-libdir Organism.dplyr_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Organism.dplyr_1.16.0.zip && rm Organism.dplyr_1.16.0.tar.gz Organism.dplyr_1.16.0.zip
###
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  % 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  201k  100  201k    0     0  3332k      0 --:--:-- --:--:-- --:--:-- 3737k

install for i386

* installing *source* package 'Organism.dplyr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Organism.dplyr'
    finding HTML links ... done
    Genomic-Extractors                      html  
    finding level-2 HTML links ... done

    filter                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/filter.Rd:152: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/filter.Rd:155: file link 'select,src_organism-method' in package 'Organism.dplyr' does not exist and so has been treated as a topic
    select                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/select.Rd:137: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
    src                                     html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/src.Rd:130: file link 'transcripts_tbl' in package 'Organism.dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpCIoeCH/R.INSTALL2e106e76760b/Organism.dplyr/man/src.Rd:133: file link 'select,src_organism-method' in package 'Organism.dplyr' does not exist and so has been treated as a topic
    utils                                   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 'Organism.dplyr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Organism.dplyr' as Organism.dplyr_1.16.0.zip
* DONE (Organism.dplyr)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Organism.dplyr' successfully unpacked and MD5 sums checked

Tests output

Organism.dplyr.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(Organism.dplyr)
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: AnnotationFilter

Attaching package: 'AnnotationFilter'

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

    not

> 
> test_check("Organism.dplyr")
== testthat results  ===========================================================
[ OK: 190 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 127.04    6.73  173.17

Organism.dplyr.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(Organism.dplyr)
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: AnnotationFilter

Attaching package: 'AnnotationFilter'

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

    not

> 
> test_check("Organism.dplyr")
== testthat results  ===========================================================
[ OK: 190 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 120.89    5.15  129.34

Example timings

Organism.dplyr.Rcheck/examples_i386/Organism.dplyr-Ex.timings

nameusersystemelapsed
Genomic-Extractors3.580.624.27
filter0.270.000.27
select2.010.022.04
src0.320.010.33
utils000

Organism.dplyr.Rcheck/examples_x64/Organism.dplyr-Ex.timings

nameusersystemelapsed
Genomic-Extractors3.180.113.28
filter0.260.000.26
select1.950.052.00
src0.230.000.23
utils000