Multiple platform build/check report for BioC 3.22 - CHECK results for BaseSpaceR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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: 1.53.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BaseSpaceR_1.53.0.tar.gz

StartedAt: 2025-10-24 21:22:29 -0400 (Fri, 24 Oct 2025)

EndedAt: 2025-10-24 21:28:19 -0400 (Fri, 24 Oct 2025)

EllapsedTime: 349.2 seconds

RetCode: 1

Status: ERROR

CheckDir: BaseSpaceR.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BaseSpaceR_1.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BaseSpaceR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK
* this is package ‘BaseSpaceR’ version ‘1.53.0’
* 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 ... 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 ... ERROR
Running examples in ‘BaseSpaceR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Projects-class
> ### Title: 'Projects' and 'ProjectsSummary' objects
> ### Aliases: projectItem projectItem-class projectCollection
> ###   projectCollection-class ProjectsSummary-class Projects-class Projects
> ###   Projects,missing-method Projects,AppAuth-method
> ###   Projects,ProjectsSummary-method listProjects
> ###   listProjects,AppAuth-method listProjects,Response-method
> ###   countProjects countProjects,AppAuth-method
> ###   countProjects,Response-method createProject
> ###   createProject,AppAuth-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> data(aAuth)
> 
> p <- listProjects(aAuth)
> p
ProjectsSummary object:
Collection with 7 projectItem objects (out of a total of 7 objects).
{
	"Id" : "21383369",
	"Name" : "MiSeq: TruSeq 2x151 (PhiX)",
	"Href" : "v1pre3/projects/21383369",
	"DateCreated" : "2015-03-31T07:11:09.0000000Z",
	"UserOwnedBy" : {
		"Id" : "1001",
		"Href" : "v1pre3/users/1001",
		"Name" : "Illumina Inc",
		"DateCreated" : "0001-01-01T00:00:00.0000000Z",
		"GravatarUrl" : "https://secure.gravatar.com/avatar/0646200388a465f27694d67b7aaea7cc.jpg?s=20&d=mm&r=PG"
	}
} 
{
	"Id" : "21450429",
	"Name" : "MiSeq: B cereus demo data",
	"Href" : "v1pre3/projects/21450429",
	"DateCreated" : "2015-03-31T18:43:38.0000000Z",
	"UserOwnedBy" : {
		"Id" : "1001",
		"Href" : "v1pre3/users/1001",
		"Name" : "Illumina Inc",
		"DateCreated" : "0001-01-01T00:00:00.0000000Z",
		"GravatarUrl" : "https://secure.gravatar.com/avatar/0646200388a465f27694d67b7aaea7cc.jpg?s=20&d=mm&r=PG"
	}
} 
{
	"Id" : "22006986",
	"Name" : "My Project X",
	"Href" : "v1pre3/projects/22006986",
	"DateCreated" : "2015-04-22T12:54:45.0000000Z",
	"UserOwnedBy" : {
		"Id" : "5638639",
		"Href" : "v1pre3/users/5638639",
		"Name" : "Illumina BaseSpaceR",
		"DateCreated" : "0001-01-01T00:00:00.0000000Z",
		"GravatarUrl" : "https://secure.gravatar.com/avatar/1f0003cc4474154aec01ca696bffded8.jpg?s=20&d=mm&r=PG"
	}
} 
{
	"Id" : "22011990",
	"Name" : "My New Project",
	"Href" : "v1pre3/projects/22011990",
	"DateCreated" : "2015-04-22T09:52:03.0000000Z",
	"UserOwnedBy" : {
		"Id" : "5638639",
		"Href" : "v1pre3/users/5638639",
		"Name" : "Illumina BaseSpaceR",
		"DateCreated" : "0001-01-01T00:00:00.0000000Z",
		"GravatarUrl" : "https://secure.gravatar.com/avatar/1f0003cc4474154aec01ca696bffded8.jpg?s=20&d=mm&r=PG"
	}
} 
{
	"Id" : "31422406",
	"Name" : "MyNewProj",
	"Href" : "v1pre3/projects/31422406",
	"DateCreated" : "2016-07-04T17:34:33.0000000Z",
	"UserOwnedBy" : {
		"Id" : "5638639",
		"Href" : "v1pre3/users/5638639",
		"Name" : "Illumina BaseSpaceR",
		"DateCreated" : "0001-01-01T00:00:00.0000000Z",
		"GravatarUrl" : "https://secure.gravatar.com/avatar/1f0003cc4474154aec01ca696bffded8.jpg?s=20&d=mm&r=PG"
	}
} 
{
	"Id" : "231781559",
	"Name" : "nhri_wes",
	"Href" : "v1pre3/projects/231781559",
	"DateCreated" : "2021-02-19T14:47:55.0000000Z",
	"UserOwnedBy" : {
		"Id" : "5638639",
		"Href" : "v1pre3/users/5638639",
		"Name" : "Illumina BaseSpaceR",
		"DateCreated" : "0001-01-01T00:00:00.0000000Z",
		"GravatarUrl" : "https://secure.gravatar.com/avatar/1f0003cc4474154aec01ca696bffded8.jpg?s=20&d=mm&r=PG"
	}
} 
{
	"Id" : "313239927",
	"Name" : "Test Apps",
	"Href" : "v1pre3/projects/313239927",
	"DateCreated" : "2021-12-09T08:48:19.0000000Z",
	"UserOwnedBy" : {
		"Id" : "5638639",
		"Href" : "v1pre3/users/5638639",
		"Name" : "Illumina BaseSpaceR",
		"DateCreated" : "0001-01-01T00:00:00.0000000Z",
		"GravatarUrl" : "https://secure.gravatar.com/avatar/1f0003cc4474154aec01ca696bffded8.jpg?s=20&d=mm&r=PG"
	}
} 

> 
> Projects(aAuth, id = c(2, 12, 1012))

  
 {
	"ResponseStatus" : {
		"ErrorCode" : "BASESPACE.COMMON.INSUFFICIENT_RESOURCE_PERMISSIONS",
		"Message" : "Sorry but this requires BROWSE access to this Project resource."
	},
	"Notifications" : [
		{
			"Type" : "error",
			"Item" : "Sorry but this requires BROWSE access to this Project resource."
		}
	]
} 

  
 {
	"ResponseStatus" : {
		"ErrorCode" : "BASESPACE.COMMON.INSUFFICIENT_RESOURCE_PERMISSIONS",
		"Message" : "Sorry but this requires BROWSE access to this Project resource."
	},
	"Notifications" : [
		{
			"Type" : "error",
			"Item" : "Sorry but this requires BROWSE access to this Project resource."
		}
	]
} 

  
 {
	"ResponseStatus" : {
		"ErrorCode" : "BASESPACE.COMMON.INSUFFICIENT_RESOURCE_PERMISSIONS",
		"Message" : "Sorry but this requires BROWSE access to this Project resource."
	},
	"Notifications" : [
		{
			"Type" : "error",
			"Item" : "Sorry but this requires BROWSE access to this Project resource."
		}
	]
} 
$`2`
NULL

$`12`
NULL

$`1012`
NULL

> Projects(p)
Error in file(con, "r") : cannot open the connection
Calls: Projects ... .local -> fromJSON -> fromJSON -> I -> unique.default
Execution halted
* 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 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BaseSpaceR.Rcheck/00check.log’
for details.

Installation output

BaseSpaceR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BaseSpaceR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BaseSpaceR’ ...
** this is package ‘BaseSpaceR’ version ‘1.53.0’
** 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	0.299	0.027	0.583
AppResults-class	0	0	0
AppSessionAuth	0.000	0.000	0.001
AppSessions-class	0	0	0
Coverage	0.007	0.001	0.008
Error	0.001	0.000	0.000
Files-class	0.113	0.017	0.617
FilesExtra	0.147	0.024	1.194
Genomes-class	0.207	0.004	0.731