Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:06:18 -0400 (Sat, 23 Oct 2021).

CHECK results for AnVIL on riesling1

To the developers/maintainers of the AnVIL package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnVIL.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 70/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnVIL 1.5.7  (landing page)
Martin Morgan
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/AnVIL
git_branch: master
git_last_commit: 97595d8
git_last_commit_date: 2021-10-19 18:06:24 -0400 (Tue, 19 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AnVIL
Version: 1.5.7
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnVIL.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AnVIL_1.5.7.tar.gz
StartedAt: 2021-10-23 04:54:26 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 04:59:58 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 331.6 seconds
RetCode: 0
Status:   OK  
CheckDir: AnVIL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnVIL.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AnVIL_1.5.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/AnVIL.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnVIL/DESCRIPTION' ... OK
* this is package 'AnVIL' version '1.5.7'
* 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 'AnVIL' 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 ... NOTE
Unexported objects imported by ':::' calls:
  'rapiclient:::build_op_url' 'rapiclient:::get_parameters'
  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 ... 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 R/sysdata.rda ... 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 NOTE
See
  'D:/biocbuild/bbs-3.14-bioc/meat/AnVIL.Rcheck/00check.log'
for details.



Installation output

AnVIL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/AnVIL_1.5.7.tar.gz && rm -rf AnVIL.buildbin-libdir && mkdir AnVIL.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnVIL.buildbin-libdir AnVIL_1.5.7.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL AnVIL_1.5.7.zip && rm AnVIL_1.5.7.tar.gz AnVIL_1.5.7.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  405k  100  405k    0     0  1549k      0 --:--:-- --:--:-- --:--:-- 1555k

install for i386

* installing *source* package 'AnVIL' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AnVIL'
    finding HTML links ... done
    Response                                html  
    Service                                 html  
    Services                                html  
    av                                      html  
    avnotebooks                             html  
    avworkflow                              html  
    avworkspace                             html  
    drs                                     html  
    gcloud                                  html  
    gsutil                                  html  
    install                                 html  
    localize                                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 'AnVIL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnVIL' as AnVIL_1.5.7.zip
* DONE (AnVIL)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'AnVIL' successfully unpacked and MD5 sums checked

Tests output

AnVIL.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(AnVIL)
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

> 
> test_check("AnVIL")
== Skipped tests ===============================================================
* !gcloud_exists() is TRUE (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
   2.10    0.79    3.34 

AnVIL.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(AnVIL)
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

> 
> test_check("AnVIL")
== Skipped tests ===============================================================
* !gcloud_exists() is TRUE (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
   1.92    0.81    3.12 

Example timings

AnVIL.Rcheck/examples_i386/AnVIL-Ex.timings

nameusersystemelapsed
Response0.010.000.02
Service000
Services0.250.030.99
av000
avnotebooks000
avworkflow000
avworkspace0.010.000.02
drs000
gcloud000
gsutil0.000.020.01
install0.030.000.16

AnVIL.Rcheck/examples_x64/AnVIL-Ex.timings

nameusersystemelapsed
Response000
Service0.010.000.02
Services0.190.060.78
av0.000.020.01
avnotebooks000
avworkflow0.000.010.02
avworkspace000
drs000
gcloud000
gsutil0.000.020.01
install0.020.000.41