Jose Marugan
| Snapshot Date: 2025-11-14 13:40 -0500 (Fri, 14 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/ArrayExpress |
| git_branch: devel |
| git_last_commit: 4a25159 |
| git_last_commit_date: 2025-10-29 10:01:28 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-15 11:34 -0500 (Sat, 15 Nov 2025).
| 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" | 4826 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4561 |
| 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 97/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ArrayExpress 1.71.0 (landing page) Jose Marugan
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.71.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ArrayExpress_1.71.0.tar.gz |
| StartedAt: 2025-11-14 21:04:10 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 21:11:07 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 416.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ArrayExpress.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ArrayExpress_1.71.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ArrayExpress.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.71.0’
* 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 loading without being on the library search path ... 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’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ArrayExpress 31.097 2.872 89.218
getAE 27.520 1.678 49.179
queryAE 0.788 0.039 14.959
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- 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'
Content type 'unknown' length 1683750 bytes (1.6 MB)
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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)
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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)
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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)
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Downloading file: E-MEXP-21-processed-data-2487199618.txt
/tmp/Rtmp34EFG9/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
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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'
Content type 'unknown' length 3791 bytes
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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)
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downloaded 772 KB
Unpacking data files
ArrayExpress: Reading pheno data from SDRF
ArrayExpress: Reading data files
Loading required package: pd.hu6800
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 1.73.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.75.0
================================================================================
Loading required package: DBI
Platform design info loaded.
Read 48 items
E-MEXP-21 was successfully loaded into ExpressionFeatureSet
Warning in file.remove(file.path(path, basename(mageFiles$processedFiles), :
cannot remove file '/tmp/Rtmp34EFG9/E-MEXP-21-processed-data-2487199618.txt', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
cannot remove file '/tmp/Rtmp34EFG9/1203aa.cel', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
cannot remove file '/tmp/Rtmp34EFG9/E-MEXP-21-processed-data-2487199618.txt', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
cannot remove file '/tmp/Rtmp34EFG9/1205aa.cel', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
cannot remove file '/tmp/Rtmp34EFG9/1202aa.cel', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
cannot remove file '/tmp/Rtmp34EFG9/1204aa.cel', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$processedArchive), :
cannot remove file '/tmp/Rtmp34EFG9/E-MEXP-21-processed-data-2487199618.txt', reason 'No such file or directory'
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)
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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'
Warning in download.file(url, filedest) :
URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.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/31_v4_v4.gpr'
Warning in getAE(accession, path = path, type = "full") :
ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr does not exist or is empty.
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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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downloaded 750 KB
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: 30_v4_v4.gpr
/tmp/Rtmp34EFG9/30_v4_v4.gpr already exists, skipping.
Downloading file: 13_v3_v3.gpr
/tmp/Rtmp34EFG9/13_v3_v3.gpr already exists, skipping.
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)
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Downloading file: 45_4_4.gpr
/tmp/Rtmp34EFG9/45_4_4.gpr already exists, skipping.
Downloading file: 47_3_4.gpr
/tmp/Rtmp34EFG9/47_3_4.gpr already exists, skipping.
Downloading file: 11_v4_v3.gpr
/tmp/Rtmp34EFG9/11_v4_v3.gpr already exists, skipping.
Downloading file: 46_3_3.gpr
/tmp/Rtmp34EFG9/46_3_3.gpr already exists, skipping.
Downloading file: 12_v4_v3.gpr
/tmp/Rtmp34EFG9/12_v4_v3.gpr already exists, skipping.
Downloading file: 29_v4_v4.gpr
/tmp/Rtmp34EFG9/29_v4_v4.gpr already exists, skipping.
Downloading file: E-MEXP-1870.idf.txt
/tmp/Rtmp34EFG9/E-MEXP-1870.idf.txt already exists, skipping.
Downloading file: E-MEXP-1870.sdrf.txt
/tmp/Rtmp34EFG9/E-MEXP-1870.sdrf.txt already exists, skipping.
Downloading file: A-MEXP-1425.adf.txt
/tmp/Rtmp34EFG9/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)
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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)
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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)
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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)
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Downloading file: E-MEXP-21-processed-data-2487199618.txt
/home/biocbuild/bbs-3.23-bioc/meat/ArrayExpress.Rcheck/vign_test/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
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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 '/home/biocbuild/bbs-3.23-bioc/meat/ArrayExpress.Rcheck/vign_test/ArrayExpress/vignettes/' is not a regular file
Warning in file(file, "rt") :
cannot open file '/home/biocbuild/bbs-3.23-bioc/meat/ArrayExpress.Rcheck/vign_test/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
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.
ArrayExpress.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ArrayExpress ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ArrayExpress’ ... ** this is package ‘ArrayExpress’ version ‘1.71.0’ ** 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 | |
| ArrayExpress | 31.097 | 2.872 | 89.218 | |
| ae2bioc | 0 | 0 | 0 | |
| getAE | 27.520 | 1.678 | 49.179 | |
| procset | 0 | 0 | 0 | |
| queryAE | 0.788 | 0.039 | 14.959 | |