Back to Multiple platform build/check report for BioC 3.16:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:59 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for BaseSpaceR on lconway


To the developers/maintainers of the BaseSpaceR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BaseSpaceR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 116/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BaseSpaceR 1.42.0  (landing page)
Jared O'Connell
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/BaseSpaceR
git_branch: RELEASE_3_16
git_last_commit: 17f4ade
git_last_commit_date: 2022-11-01 11:08:02 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BaseSpaceR
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BaseSpaceR_1.42.0.tar.gz
StartedAt: 2023-04-10 18:53:56 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 18:54:48 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 52.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BaseSpaceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BaseSpaceR_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/BaseSpaceR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK
* this is package ‘BaseSpaceR’ version ‘1.42.0’
* 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 ‘BaseSpaceR’ 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 ... NOTE
'library' or 'require' call to ‘Rsamtools’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
asBamFile: no visible global function definition for ‘BamFile’
GET,ServiceURI: no visible global function definition for
  ‘basicHeaderGatherer’
GET,ServiceURI: no visible global function definition for
  ‘basicTextGatherer’
GET,ServiceURI: no visible global function definition for ‘getForm’
GET,ServiceURI: no visible global function definition for ‘curlOptions’
POST,ServiceURI: no visible global function definition for
  ‘basicHeaderGatherer’
POST,ServiceURI: no visible global function definition for
  ‘basicTextGatherer’
POST,ServiceURI: no visible global function definition for
  ‘curlPerform’
POSTForm,ServiceURI: no visible global function definition for
  ‘basicHeaderGatherer’
POSTForm,ServiceURI: no visible global function definition for
  ‘basicTextGatherer’
POSTForm,ServiceURI: no visible global function definition for
  ‘postForm’
POSTForm,ServiceURI: no visible global function definition for
  ‘curlOptions’
getBAMs,AppResults: no visible binding for global variable
  ‘BamFileList’
getFiles,AppAuth : .toDisk: no visible global function definition for
  ‘CFILE’
getFiles,AppAuth : .toDisk: no visible global function definition for
  ‘curlPerform’
getFiles,AppAuth : .toMem: no visible global function definition for
  ‘getURLContent’
getFiles,AppAuth : .toMem: no visible binding for global variable
  ‘dsize’
Undefined global functions or variables:
  BamFile BamFileList CFILE basicHeaderGatherer basicTextGatherer
  curlOptions curlPerform dsize getForm getURLContent postForm
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
Runs-class 0.139  0.009   6.272
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/BaseSpaceR.Rcheck/00check.log’
for details.



Installation output

BaseSpaceR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘BaseSpaceR’ ...
** using staged installation
** R
** data
** 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 (BaseSpaceR)

Tests output


Example timings

BaseSpaceR.Rcheck/BaseSpaceR-Ex.timings

nameusersystemelapsed
AppAuth-class0.0940.0160.462
AppResults-class0.0000.0000.001
AppSessionAuth0.0010.0000.001
AppSessions-class0.0000.0000.001
Coverage0.0070.0010.010
Error000
Files-class0.0560.0061.732
FilesExtra0.0640.0061.485
Genomes-class0.0780.0051.175
Projects-class0.1020.0052.364
Response-class0.0020.0010.003
Runs-class0.1390.0096.272
Samples-class0.0990.0062.771
ServiceURI-class0.0000.0000.001
Users-class0.0490.0040.640
Variants0.0530.0051.812
data-aAuth0.0240.0030.182