Multiple platform build/check report for BioC 3.23 - BUILD results for ArrayExpress on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4866
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4614
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4571
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*

BUILD results for ArrayExpress on lconway

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.

raw results

Summary

Package: ArrayExpress

Version: 1.71.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpress

StartedAt: 2025-11-27 16:04:05 -0500 (Thu, 27 Nov 2025)

EndedAt: 2025-11-27 16:06:41 -0500 (Thu, 27 Nov 2025)

EllapsedTime: 155.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpress
###
##############################################################################
##############################################################################


* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* preparing ‘ArrayExpress’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘ArrayExpress.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Downloading file: 1203aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel'
Content type 'unknown' length 7317392 bytes (7.0 MB)
==================================================
Downloading file: E-MEXP-21-processed-data-2487199618.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': status was 'Failure when receiving data from the peer'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt  does not exist or is empty. 

Downloading file: 1205aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel'
Content type 'unknown' length 7340006 bytes (7.0 MB)
==================================================
Downloading file: 1202aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel'
Content type 'unknown' length 7329097 bytes (7.0 MB)
==================================================
Downloading file: 1204aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel'
Content type 'unknown' length 7343156 bytes (7.0 MB)
==================================================
Downloading file: E-MEXP-21-processed-data-2487199618.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt'
Content type 'unknown' length 1683750 bytes (1.6 MB)
==================================================
Downloading file: E-MEXP-21.idf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt'
Content type 'unknown' length 7299 bytes
==================================================
Downloading file: E-MEXP-21.sdrf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt': status was 'Failure when receiving data from the peer'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt  does not exist or is empty. 

Downloading file: A-AFFY-32.adf.txt

trying URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-32/A-AFFY-32.adf.txt'
Content type 'text/plain; charset=UTF-8' length 790789 bytes (772 KB)
==================================================
downloaded 772 KB

Unpacking data files
Warning in file(file, "rt") :
  'raw = FALSE' but '/tmp/RtmpfTgAlB/' is not a regular file
Warning in file(file, "rt") :
  cannot open file '/tmp/RtmpfTgAlB/': it is a directory
Error in file(file, "rt") : cannot open the connection
Downloading file: 30_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr'
Content type 'unknown' length 5350610 bytes (5.1 MB)
==================================================
Downloading file: 13_v3_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr'
Content type 'unknown' length 5277770 bytes (5.0 MB)
==================================================
Downloading file: 31_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr'
Content type 'unknown' length 5264983 bytes (5.0 MB)
==================================================
Downloading file: 45_4_4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr'
Content type 'unknown' length 5493312 bytes (5.2 MB)
==================================================
Downloading file: 47_3_4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr'
Content type 'unknown' length 5335570 bytes (5.1 MB)
==================================================
Downloading file: 11_v4_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr'
Content type 'unknown' length 5385618 bytes (5.1 MB)
==================================================
Downloading file: 46_3_3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr': status was 'Failure when receiving data from the peer'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr  does not exist or is empty. 

Downloading file: 12_v4_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr'
Content type 'unknown' length 5358829 bytes (5.1 MB)
==================================================
Downloading file: 29_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr'
Content type 'unknown' length 5344579 bytes (5.1 MB)
==================================================
Downloading file: E-MEXP-1870.idf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt'
Content type 'unknown' length 17908 bytes (17 KB)
==================================================
Downloading file: E-MEXP-1870.sdrf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt': status was 'Failure when receiving data from the peer'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt  does not exist or is empty. 

Downloading file: A-MEXP-1425.adf.txt

trying URL 'https://www.ebi.ac.uk/biostudies/files/A-MEXP-1425/A-MEXP-1425.adf.txt'
Content type 'text/plain; charset=UTF-8' length 768845 bytes (750 KB)
==================================================
downloaded 750 KB

Unpacking data files
Warning in file(file, "rt") :
  'raw = FALSE' but '/tmp/RtmpfTgAlB/' is not a regular file
Warning in file(file, "rt") :
  cannot open file '/tmp/RtmpfTgAlB/': it is a directory
Error in file(file, "rt") : cannot open the connection
Downloading file: 30_v4_v4.gpr

/tmp/RtmpfTgAlB/30_v4_v4.gpr already exists, skipping.
Downloading file: 13_v3_v3.gpr

/tmp/RtmpfTgAlB/13_v3_v3.gpr already exists, skipping.
Downloading file: 31_v4_v4.gpr

/tmp/RtmpfTgAlB/31_v4_v4.gpr already exists, skipping.
Downloading file: 45_4_4.gpr

/tmp/RtmpfTgAlB/45_4_4.gpr already exists, skipping.
Downloading file: 47_3_4.gpr

/tmp/RtmpfTgAlB/47_3_4.gpr already exists, skipping.
Downloading file: 11_v4_v3.gpr

/tmp/RtmpfTgAlB/11_v4_v3.gpr already exists, skipping.
Downloading file: 46_3_3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Content type 'unknown' length 5304968 bytes (5.1 MB)
==================================================
Downloading file: 12_v4_v3.gpr

/tmp/RtmpfTgAlB/12_v4_v3.gpr already exists, skipping.
Downloading file: 29_v4_v4.gpr

/tmp/RtmpfTgAlB/29_v4_v4.gpr already exists, skipping.
Downloading file: E-MEXP-1870.idf.txt

/tmp/RtmpfTgAlB/E-MEXP-1870.idf.txt already exists, skipping.
Downloading file: E-MEXP-1870.sdrf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt'
Content type 'unknown' length 14207 bytes (13 KB)
==================================================
Downloading file: A-MEXP-1425.adf.txt

/tmp/RtmpfTgAlB/A-MEXP-1425.adf.txt already exists, skipping.
Unpacking data files
Duplicates found in SDRF file
Removed duplicates in SDRF file
ArrayExpress: Reading pheno data from SDRF
Warning: non-unique values when setting 'row.names': ‘11_v4_v3.gpr’, ‘12_v4_v3.gpr’, ‘13_v3_v3.gpr’, ‘29_v4_v4.gpr’, ‘30_v4_v4.gpr’, ‘31_v4_v4.gpr’, ‘45_4_4.gpr’, ‘46_3_3.gpr’, ‘47_3_4.gpr’
Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
Downloading file: 1203aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel'
Content type 'unknown' length 7317392 bytes (7.0 MB)
==================================================
Downloading file: E-MEXP-21-processed-data-2487199618.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt'
Content type 'unknown' length 1683750 bytes (1.6 MB)
==================================================
Downloading file: 1205aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel'
Content type 'unknown' length 7340006 bytes (7.0 MB)
==================================================
Downloading file: 1202aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel'
Content type 'unknown' length 7329097 bytes (7.0 MB)
==================================================
Downloading file: 1204aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel'
Content type 'unknown' length 7343156 bytes (7.0 MB)
==================================================
Downloading file: E-MEXP-21-processed-data-2487199618.txt

/private/tmp/Rtmph3Ggq8/Rbuild872f2f00c70/ArrayExpress/vignettes/E-MEXP-21-processed-data-2487199618.txt already exists, skipping.
Downloading file: E-MEXP-21.idf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt'
Content type 'unknown' length 7299 bytes
==================================================
Downloading file: E-MEXP-21.sdrf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt': status was 'Failure when receiving data from the peer'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt'
Warning in getAE("E-MEXP-21", type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt  does not exist or is empty. 

Downloading file: A-AFFY-32.adf.txt

trying URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-32/A-AFFY-32.adf.txt'
Content type 'text/plain; charset=UTF-8' length 790789 bytes (772 KB)
==================================================
downloaded 772 KB

Unpacking data files
Warning in file(file, "rt") :
  'raw = FALSE' but '/private/tmp/Rtmph3Ggq8/Rbuild872f2f00c70/ArrayExpress/vignettes/' is not a regular file
Warning in file(file, "rt") :
  cannot open file '/private/tmp/Rtmph3Ggq8/Rbuild872f2f00c70/ArrayExpress/vignettes/': it is a directory

Error: processing vignette 'ArrayExpress.Rnw' failed with diagnostics:
 chunk 6 (label = ae2bioc-full) 
Error in file(file, "rt") : cannot open the connection

--- failed re-building ‘ArrayExpress.Rnw’

SUMMARY: processing the following file failed:
  ‘ArrayExpress.Rnw’

Error: Vignette re-building failed.
Execution halted