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This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 78/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnVIL 1.12.4  (landing page)
Martin Morgan
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/AnVIL
git_branch: RELEASE_3_17
git_last_commit: 648ec2d
git_last_commit_date: 2023-08-16 14:44:09 -0400 (Wed, 16 Aug 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for AnVIL on kjohnson2


To the developers/maintainers of the AnVIL package:
- 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: AnVIL
Version: 1.12.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnVIL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnVIL_1.12.4.tar.gz
StartedAt: 2023-10-17 02:38:21 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 02:39:59 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 98.5 seconds
RetCode: 0
Status:   OK  
CheckDir: AnVIL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnVIL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnVIL_1.12.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/AnVIL.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnVIL/DESCRIPTION’ ... OK
* this is package ‘AnVIL’ version ‘1.12.4’
* 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 ‘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
* 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 startup messages can be suppressed ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
Services 0.368  0.059   7.675
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/AnVIL.Rcheck/00check.log’
for details.



Installation output

AnVIL.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘AnVIL’ ...
** 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 (AnVIL)

Tests output

AnVIL.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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(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")
[ FAIL 0 | WARN 0 | SKIP 4 | PASS 46 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• !gcloud_exists() is TRUE (4): 'test_Services.R:2:5', 'test_api.R:2:5',
  'test_api.R:38:5', 'test_gcloud_sdk.R:17:5'

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 46 ]
> 
> proc.time()
   user  system elapsed 
  3.510   0.911   8.549 

Example timings

AnVIL.Rcheck/AnVIL-Ex.timings

nameusersystemelapsed
Response0.0110.0200.107
Service0.0150.0010.024
Services0.3680.0597.675
av0.0160.0340.199
avnotebooks0.0100.0190.109
avworkflow0.0130.0270.135
avworkflow_configuration0.0200.0160.083
avworkspace0.0010.0010.001
drs0.0040.0070.044
gadgets000
gadgets_developer000
gcloud0.0100.0190.098
gsutil0.0160.0330.174
install0.1210.0131.264