Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:01 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (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

Package 94/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.66.0  (landing page)
Jose Marugan
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/ArrayExpress
git_branch: RELEASE_3_20
git_last_commit: d1e37af
git_last_commit_date: 2024-10-29 09:30:05 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for ArrayExpress on teran2

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: 1.66.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ArrayExpress_1.66.0.tar.gz
StartedAt: 2024-11-19 22:53:29 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 22:57:25 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 236.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ArrayExpress.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ArrayExpress_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ArrayExpress.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.66.0’
* 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 ... 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 ‘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 9580008 bytes (9.1 MB)
==================================================
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'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp1.CEL': 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-TABM-/025/E-TABM-25/Files/cp1.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp1.CEL  does not exist or is empty. 

Downloading file: cx3.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx3.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx3.CEL': 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-TABM-/025/E-TABM-25/Files/cx3.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx3.CEL  does not exist or is empty. 

Downloading file: cc5.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc5.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc5.CEL': 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-TABM-/025/E-TABM-25/Files/cc5.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc5.CEL  does not exist or is empty. 

Downloading file: cx5.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx5.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx5.CEL': 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-TABM-/025/E-TABM-25/Files/cx5.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx5.CEL  does not exist or is empty. 

Downloading file: cc1.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc1.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc1.CEL': 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-TABM-/025/E-TABM-25/Files/cc1.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc1.CEL  does not exist or is empty. 

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'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.idf.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-TABM-/025/E-TABM-25/Files/E-TABM-25.idf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.idf.txt  does not exist or is empty. 

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'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.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-TABM-/025/E-TABM-25/Files/E-TABM-25.sdrf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.sdrf.txt  does not exist or is empty. 

Downloading file: A-AFFY-1.adf.txt

trying URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-1/A-AFFY-1.adf.txt'
Warning in download.file(url, filedest) :
  URL 'https://ftp.ebi.ac.uk/biostudies/fire/A-AFFY-/001/A-AFFY-1/Files/A-AFFY-1.adf.txt': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-1/A-AFFY-1.adf.txt'
Warning in getAE(accession, path = path, type = "full") :
  https://www.ebi.ac.uk/biostudies/files/A-AFFY-1/A-AFFY-1.adf.txt  does not exist or is empty. 

Unpacking data files
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : 
  No SDRF file found.
> 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.


Installation output

ArrayExpress.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ArrayExpress
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ArrayExpress’ ...
** 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)

Tests output


Example timings

ArrayExpress.Rcheck/ArrayExpress-Ex.timings

nameusersystemelapsed