Multiple platform build/check report for BioC 3.20 - CHECK results for MsBackendMetaboLights on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 MsBackendMetaboLights on lconway

To the developers/maintainers of the MsBackendMetaboLights package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMetaboLights.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: MsBackendMetaboLights

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMetaboLights_1.0.0.tar.gz

StartedAt: 2024-11-20 00:17:34 -0500 (Wed, 20 Nov 2024)

EndedAt: 2024-11-20 00:23:25 -0500 (Wed, 20 Nov 2024)

EllapsedTime: 351.1 seconds

RetCode: 1

Status: ERROR

CheckDir: MsBackendMetaboLights.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMetaboLights_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsBackendMetaboLights.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendMetaboLights/DESCRIPTION’ ... OK
* this is package ‘MsBackendMetaboLights’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘MsBackendMetaboLights’ 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 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 dependencies in R code ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MsBackendMetaboLights-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MsBackendMetaboLights
> ### Title: MsBackend representing MS data from MetaboLights
> ### Aliases: MsBackendMetaboLights MsBackendMetaboLights-class
> ###   backendInitialize,MsBackendMetaboLights-method
> ###   backendMerge,MsBackendMetaboLights-method
> ###   backendRequiredSpectraVariables,MsBackendMetaboLights-method
> ###   mtbls_sync
> 
> ### ** Examples
> 
> 
> library(MsBackendMetaboLights)
> 
> ## List files of a MetaboLights data set
> mtbls_list_files("MTBLS39")
[1] "FILES"                                                                                                          
[2] "a_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry.txt"       
[3] "i_Investigation.txt"                                                                                            
[4] "m_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry_v2_maf.tsv"
[5] "metexplore_mapping.json"                                                                                        
[6] "s_MTBLS39.txt"                                                                                                  
> 
> ## Initialize a MsBackendMetaboLights representing all MS data files of
> ## the data set with the ID "MTBLS39". This will download and cache all
> ## files and subsequently load and represent them in R.
> 
> be <- backendInitialize(MsBackendMetaboLights(), "MTBLS39")
Used data files from the assay's column "Raw Spectral Data File" since none were available in column "Derived Spectral Data File".
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063B.cdf'
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063B.cdf' produced error:
  Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063C.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063C.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/CS063C.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3213
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063C.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063C.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063B.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063B.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/AM063B.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3214
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063B.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063B.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063C.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063C.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/AM063C.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3215
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063C.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063C.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073A.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073A.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/MN073A.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3216
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073A.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073A.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073B.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073B.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/MN073B.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3217
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073B.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073B.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073C.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073C.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/MN073C.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3218
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073C.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073C.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073A.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073A.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/CS073A.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3219
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073A.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073A.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073B.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073B.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/CS073B.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3220
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073B.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073B.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073C.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073C.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/CS073C.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3221
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073C.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073C.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073A.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073A.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/AM073A.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3222
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073A.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073A.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073B.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073B.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/AM073B.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3223
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073B.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073B.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073C.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073C.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/AM073C.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3224
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073C.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073C.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083A.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083A.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/MN083A.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3225
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083A.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083A.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083B.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083B.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/MN083B.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3226
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083B.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083B.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083C.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083C.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/MN083C.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3227
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083C.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083C.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083A.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083A.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/CS083A.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3228
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083A.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083A.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083B.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083B.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/CS083B.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3229
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083B.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083B.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083C.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083C.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/CS083C.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3230
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083C.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083C.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083A.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083A.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/AM083A.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3231
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083A.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083A.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083B.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083B.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/AM083B.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3232
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083B.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083B.cdf' produced error:
  bfcadd() failed; see warnings()
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083C.cdf'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083C.cdf’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/AM083C.cdf’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3233
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083C.cdf’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083C.cdf' produced error:
  bfcadd() failed; see warnings()
Error in bfcrpath(bfc, paste0(fpath, ffiles), fname = "exact") : 
  not all 'rnames' found or unique.
Calls: backendInitialize ... .local -> .mtbls_data_files -> bfcrpath -> bfcrpath
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_MsBackendMetaboLights.R:167:1'): (code run outside of `test_that()`) ──
  Error: Failed to connect to MetaboLights. No internet connection? Does the data set "MTBLS2" exist?
   - cannot open the connection
  Backtrace:
      ▆
   1. └─MsBackendMetaboLights:::.mtbls_assay_list("MTBLS2") at test_MsBackendMetaboLights.R:167:1
   2.   └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
   3.     └─base::tryCatch(...)
   4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.           └─value[[3L]](cond)
  
  [ FAIL 9 | WARN 9 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsBackendMetaboLights.Rcheck/00check.log’
for details.

Installation output

MsBackendMetaboLights.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘MsBackendMetaboLights’ ...
** using staged installation
** R
** 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 (MsBackendMetaboLights)

Tests output

MsBackendMetaboLights.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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'help.start()' for an HTML browser interface to help.
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> #' MetaboLights ID: MTBLS8735
> #' ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8735
> 
> library(testthat)
> library(MsBackendMetaboLights)
Loading required package: Spectra
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: BiocParallel
> 
> test_check("MsBackendMetaboLights")
[ FAIL 9 | WARN 9 | SKIP 0 | PASS 18 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_MsBackendMetaboLights.R:27:5'): backendInitialize,MsBackendMetaboLights works ──
`backendInitialize(MsBackendMetaboLights(), mtblsId = "MTBLS100")` threw an error with unexpected message.
Expected match: "No files matching"
Actual message: "Failed to connect to MetaboLights. No internet connection? Does the data set \"MTBLS100\" exist?\n - cannot open the connection"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_MsBackendMetaboLights.R:27:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─ProtGenerics::backendInitialize(MsBackendMetaboLights(), mtblsId = "MTBLS100")
  7. └─MsBackendMetaboLights::backendInitialize(...)
  8.   └─MsBackendMetaboLights (local) .local(object, ...)
  9.     └─MsBackendMetaboLights:::.mtbls_data_files(...)
 10.       └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
 11.         └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
 12.           └─base::tryCatch(...)
 13.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                 └─value[[3L]](cond)
── Error ('test_MsBackendMetaboLights.R:30:5'): backendInitialize,MsBackendMetaboLights works ──
Error: Failed to connect to MetaboLights. No internet connection? Does the data set "MTBLS39" exist?
 - cannot open the connection
Backtrace:
     ▆
  1. ├─ProtGenerics::backendInitialize(...) at test_MsBackendMetaboLights.R:30:5
  2. └─MsBackendMetaboLights::backendInitialize(...)
  3.   └─MsBackendMetaboLights (local) .local(object, ...)
  4.     └─MsBackendMetaboLights:::.mtbls_data_files(...)
  5.       └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
  6.         └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
  7.           └─base::tryCatch(...)
  8.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.                 └─value[[3L]](cond)
── Error ('test_MsBackendMetaboLights.R:65:5'): mtbls_sync works ───────────────
Error: Failed to connect to MetaboLights. No internet connection? Does the data set "MTBLS39" exist?
 - cannot open the connection
Backtrace:
     ▆
  1. └─MsBackendMetaboLights::mtbls_sync(x, offline = FALSE) at test_MsBackendMetaboLights.R:65:5
  2.   └─base::lapply(...)
  3.     └─MsBackendMetaboLights (local) FUN(X[[i]], ...)
  4.       └─MsBackendMetaboLights::mtbls_sync_data_files(...)
  5.         └─MsBackendMetaboLights:::.mtbls_data_files(...)
  6.           └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
  7.             └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
  8.               └─base::tryCatch(...)
  9.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                     └─value[[3L]](cond)
── Failure ('test_MsBackendMetaboLights.R:90:5'): .mtbls_data_files and .mtbls_data_files_offline works ──
`.mtbls_data_files(mtblsId = "MTBLS2", assayName = "does not exist")` threw an error with unexpected message.
Expected match: "Not all assay names"
Actual message: "Failed to connect to MetaboLights. No internet connection? Does the data set \"MTBLS2\" exist?\n - cannot open the connection"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_MsBackendMetaboLights.R:90:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─MsBackendMetaboLights:::.mtbls_data_files(...)
  7.   └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
  8.     └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
  9.       └─base::tryCatch(...)
 10.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.             └─value[[3L]](cond)
── Failure ('test_MsBackendMetaboLights.R:93:5'): .mtbls_data_files and .mtbls_data_files_offline works ──
`.mtbls_data_files(mtblsId = "MTBLS100")` threw an error with unexpected message.
Expected match: "No files matching"
Actual message: "Failed to connect to MetaboLights. No internet connection? Does the data set \"MTBLS100\" exist?\n - cannot open the connection"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_MsBackendMetaboLights.R:93:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─MsBackendMetaboLights:::.mtbls_data_files(mtblsId = "MTBLS100")
  7.   └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
  8.     └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
  9.       └─base::tryCatch(...)
 10.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.             └─value[[3L]](cond)
── Error ('test_MsBackendMetaboLights.R:106:5'): .mtbls_data_files and .mtbls_data_files_offline works ──
Error: Failed to connect to MetaboLights. No internet connection? Does the data set "MTBLS39" exist?
 - cannot open the connection
Backtrace:
    ▆
 1. └─MsBackendMetaboLights:::.mtbls_data_files("MTBLS39", pattern = "63A.cdf") at test_MsBackendMetaboLights.R:106:5
 2.   └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
 3.     └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
 4.       └─base::tryCatch(...)
 5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.             └─value[[3L]](cond)
── Error ('test_MsBackendMetaboLights.R:145:5'): mtbls_sync_data_files works ───
Error: Failed to connect to MetaboLights. No internet connection? Does the data set "MTBLS39" exist?
 - cannot open the connection
Backtrace:
    ▆
 1. └─MsBackendMetaboLights::mtbls_sync_data_files(...) at test_MsBackendMetaboLights.R:145:5
 2.   └─MsBackendMetaboLights:::.mtbls_data_files(...)
 3.     └─MsBackendMetaboLights:::.mtbls_assay_list(mtblsId)
 4.       └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
 5.         └─base::tryCatch(...)
 6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.               └─value[[3L]](cond)
── Error ('test_MsBackendMetaboLights.R:153:5'): mtbls_cached_data_files works ──
Error: No local MetaboLights cache available. Please re-run with 'offline = FALSE' first.
Backtrace:
    ▆
 1. └─MsBackendMetaboLights::mtbls_cached_data_files() at test_MsBackendMetaboLights.R:153:5
 2.   └─MsBackendMetaboLights:::.mtbls_data_files_offline(...)
── Error ('test_MsBackendMetaboLights.R:167:1'): (code run outside of `test_that()`) ──
Error: Failed to connect to MetaboLights. No internet connection? Does the data set "MTBLS2" exist?
 - cannot open the connection
Backtrace:
    ▆
 1. └─MsBackendMetaboLights:::.mtbls_assay_list("MTBLS2") at test_MsBackendMetaboLights.R:167:1
 2.   └─MsBackendMetaboLights::mtbls_list_files(x, pattern = "^a_")
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)

[ FAIL 9 | WARN 9 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted

Example timings

MsBackendMetaboLights.Rcheck/MsBackendMetaboLights-Ex.timings

name	user	system	elapsed
MetaboLights-utils	0.310	0.028	6.803