Jose Marugan
| Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/ArrayExpress |
| git_branch: devel |
| git_last_commit: d308412 |
| git_last_commit_date: 2025-04-15 09:43:08 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-20 12:05 -0400 (Sat, 20 Sep 2025).
| 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" | 4814 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
| 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 94/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ArrayExpress 1.69.0 (landing page) Jose Marugan
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the ArrayExpress package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ArrayExpress.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. |
| Package: ArrayExpress |
| Version: 1.69.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ArrayExpress_1.69.0.tar.gz |
| StartedAt: 2025-09-19 18:12:54 -0400 (Fri, 19 Sep 2025) |
| EndedAt: 2025-09-19 18:16:26 -0400 (Fri, 19 Sep 2025) |
| EllapsedTime: 211.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ArrayExpress.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ArrayExpress_1.69.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ArrayExpress.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.69.0’
* 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 ‘ArrayExpress’ 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'ArrayExpress.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'ae2bioc.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'procset.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ArrayExpress-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ArrayExpress
> ### Title: R objects from ArrayExpress collection
> ### Aliases: ArrayExpress
> ### Keywords: datasets
>
> ### ** Examples
>
> ETABM25.affybatch = ArrayExpress("E-TABM-25")
Downloading file: cp7.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp7.CEL'
Content type 'unknown' length 9583464 bytes (9.1 MB)
==================================================
Downloading file: cp4.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp4.CEL'
Content type 'unknown' length 9552987 bytes (9.1 MB)
==================================================
Downloading file: cx2.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx2.CEL'
Content type 'unknown' length 9593339 bytes (9.1 MB)
==================================================
Downloading file: cc2.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc2.CEL'
Content type 'unknown' length 9620339 bytes (9.2 MB)
==================================================
Downloading file: cc4.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc4.CEL'
Content type 'unknown' length 4096 bytes
==================================================
Downloading file: cx1.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx1.CEL'
Content type 'unknown' length 9613953 bytes (9.2 MB)
==================================================
Downloading file: cp3.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp3.CEL'
Content type 'unknown' length 9574729 bytes (9.1 MB)
==================================================
Downloading file: cp6.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp6.CEL'
Content type 'unknown' length 9599435 bytes (9.2 MB)
==================================================
Downloading file: cp5.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp5.CEL'
Content type 'unknown' length 9608514 bytes (9.2 MB)
==================================================
Downloading file: cc6.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc6.CEL'
Content type 'unknown' length 9583909 bytes (9.1 MB)
==================================================
Downloading file: cx4.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx4.CEL'
Content type 'unknown' length 9566430 bytes (9.1 MB)
==================================================
Downloading file: cp2.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp2.CEL'
Content type 'unknown' length 9565364 bytes (9.1 MB)
==================================================
Downloading file: cc3.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc3.CEL'
Content type 'unknown' length 9753457 bytes (9.3 MB)
==================================================
Downloading file: cp1.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp1.CEL'
Content type 'unknown' length 4096 bytes
==================================================
Downloading file: cx3.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx3.CEL'
Content type 'unknown' length 9582638 bytes (9.1 MB)
==================================================
Downloading file: cc5.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc5.CEL'
Content type 'unknown' length 9578927 bytes (9.1 MB)
==================================================
Downloading file: cx5.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx5.CEL'
Content type 'unknown' length 9593453 bytes (9.1 MB)
==================================================
Downloading file: cc1.CEL
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc1.CEL'
Content type 'unknown' length 9594808 bytes (9.2 MB)
==================================================
Downloading file: E-TABM-25.idf.txt
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.idf.txt'
Content type 'unknown' length 2965 bytes
==================================================
Downloading file: E-TABM-25.sdrf.txt
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.sdrf.txt'
Content type 'unknown' length 9769 bytes
==================================================
Downloading file: A-AFFY-1.adf.txt
trying URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-1/A-AFFY-1.adf.txt'
Content type 'text/plain; charset=UTF-8' length 1547751 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
Unpacking data files
ArrayExpress: Reading pheno data from SDRF
ArrayExpress: Reading data files
Loading required package: pd.hg.u95av2
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
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: IRanges
Loading required package: XVector
Loading required package: Seqinfo
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.71.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.73.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Reading in : /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp1C0eqX/cp7.CEL
Reading in : /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp1C0eqX/cp4.CEL
Reading in : /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp1C0eqX/cx2.CEL
Reading in : /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp1C0eqX/cc2.CEL
Reading in : /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp1C0eqX/cc4.CEL
Error in read_abatch(filenames, FALSE, FALSE, FALSE, headdetails[[1]], :
End of file reached unexpectedly. Perhaps this file is truncated.
Error in readAEdata(path = path, files = dataFiles, dataCols = dataCols, :
Unable to read cel files in /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp1C0eqX
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) :
ArrayExpress: Unable to read assay data
> print(ETABM25.affybatch)
NULL
> sampleNames(ETABM25.affybatch)
Error: unable to find an inherited method for function ‘sampleNames’ for signature ‘object = "NULL"’
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: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.
ArrayExpress.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ArrayExpress ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘ArrayExpress’ ... ** this is package ‘ArrayExpress’ version ‘1.69.0’ ** 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 (ArrayExpress)
ArrayExpress.Rcheck/ArrayExpress-Ex.timings
| name | user | system | elapsed |