Multiple platform build/check report for BioC 3.20 - CHECK results for BaseSpaceR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4739
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4482
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4510
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4462
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 nebbiolo2

To the developers/maintainers of the BaseSpaceR package:
- 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 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: BaseSpaceR

Version: 1.50.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BaseSpaceR_1.50.0.tar.gz

StartedAt: 2024-11-28 20:18:43 -0500 (Thu, 28 Nov 2024)

EndedAt: 2024-11-28 20:23:09 -0500 (Thu, 28 Nov 2024)

EllapsedTime: 266.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: BaseSpaceR.Rcheck

Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BaseSpaceR_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BaseSpaceR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK
* this is package ‘BaseSpaceR’ version ‘1.50.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    BUG FIXES
  Cannot process chunk/lines:
    Changed Access token and projects ID used in the vignette to reflect changes in
  Cannot process chunk/lines:
    the permission enforcements performed by BaseSpace 
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... WARNING
checkRd: (5) Genomes-class.Rd:49-52: \item in \describe must have non-empty label
checkRd: (5) Genomes-class.Rd:53-58: \item in \describe must have non-empty label
checkRd: (5) Genomes-class.Rd:59-62: \item in \describe must have non-empty label
checkRd: (5) Projects-class.Rd:55-58: \item in \describe must have non-empty label
checkRd: (5) Projects-class.Rd:59-64: \item in \describe must have non-empty label
checkRd: (5) Projects-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) Runs-class.Rd:55-58: \item in \describe must have non-empty label
checkRd: (5) Runs-class.Rd:59-64: \item in \describe must have non-empty label
checkRd: (5) Runs-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) Samples-class.Rd:63-66: \item in \describe must have non-empty label
checkRd: (5) Samples-class.Rd:67-72: \item in \describe must have non-empty label
checkRd: (5) Samples-class.Rd:73-76: \item in \describe must have non-empty label
checkRd: (5) Users-class.Rd:33-36: \item in \describe must have non-empty label
checkRd: (5) Users-class.Rd:37-41: \item in \describe must have non-empty label
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BaseSpaceR.Rcheck/00check.log’
for details.

Installation output

BaseSpaceR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BaseSpaceR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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

name	user	system	elapsed
AppAuth-class	0.221	0.010	0.684
AppResults-class	0.001	0.000	0.000
AppSessionAuth	0.001	0.000	0.000
AppSessions-class	0.001	0.000	0.000
Coverage	0.007	0.002	0.007
Error	0.000	0.000	0.001
Files-class	0.103	0.012	0.551
FilesExtra	0.151	0.009	0.473
Genomes-class	0.140	0.003	2.354
Projects-class	0.178	0.003	0.811
Response-class	0.004	0.000	0.004
Runs-class	0.273	0.003	2.132
Samples-class	0.210	0.003	1.562
ServiceURI-class	0.000	0.000	0.001
Users-class	0.130	0.001	0.373
Variants	0.141	0.002	1.756
data-aAuth	0.094	0.000	1.331