Back to Build/check report for BioC 3.19 experimental data |
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This page was generated on 2024-07-11 14:51 -0400 (Thu, 11 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
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 191/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
homosapienDEE2CellScore 1.0.0 (landing page) Justin Marsh
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||
To the developers/maintainers of the homosapienDEE2CellScore package: - 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: homosapienDEE2CellScore |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:homosapienDEE2CellScore.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings homosapienDEE2CellScore_1.0.0.tar.gz |
StartedAt: 2024-07-11 11:31:12 -0400 (Thu, 11 Jul 2024) |
EndedAt: 2024-07-11 11:52:22 -0400 (Thu, 11 Jul 2024) |
EllapsedTime: 1269.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: homosapienDEE2CellScore.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:homosapienDEE2CellScore.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings homosapienDEE2CellScore_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/homosapienDEE2CellScore.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘homosapienDEE2CellScore/DESCRIPTION’ ... OK * this is package ‘homosapienDEE2CellScore’ version ‘1.0.0’ * package encoding: UTF-8 * 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 ‘homosapienDEE2CellScore’ 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 whether startup messages can be suppressed ... 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 ‘homosapienDEE2CellScore-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: buildRaw > ### Title: buildRaw gets the raw data in SummarizedExperiment format > ### Aliases: buildRaw > > ### ** Examples > > # To get a few accessions and package them into a SummarizedExperiment > accessions_of_interest <- buildRaw(accessions=as.list(unique(cols$SRR_accession)[c(1,3)])) Warning in FUN(URL, ...) : downloaded length 53690368 != reported length 60367518 Warning in FUN(URL, ...) : URL 'https://dee2.io/metadata/hsapiens_metadata.tsv.cut': Timeout of 600 seconds was reached Error in getURL(URL = metadataURL, FUN = download.file, N.TRIES = 1L, : 'getURL()' failed: URL: http://dee2.io/metadata/hsapiens_metadata.tsv.cut error: download from 'http://dee2.io/metadata/hsapiens_metadata.tsv.cut' failed Calls: buildRaw ... lapply -> FUN -> <Anonymous> -> getDEE2Metadata -> getURL 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 ‘/home/biocbuild/bbs-3.19-data-experiment/meat/homosapienDEE2CellScore.Rcheck/00check.log’ for details.
homosapienDEE2CellScore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL homosapienDEE2CellScore ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘homosapienDEE2CellScore’ ... ** 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 (homosapienDEE2CellScore)
homosapienDEE2CellScore.Rcheck/homosapienDEE2CellScore-Ex.timings
name | user | system | elapsed | |
HomosapienDEE2_QC_WARN_Raw | 0.692 | 0.052 | 0.894 | |
buildData | 15.427 | 1.297 | 305.113 | |