| Back to Build/check report for BioC 3.23 experimental data |
|
This page was generated on 2025-10-30 15:01 -0400 (Thu, 30 Oct 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" | 4428 |
| 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 364/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| signatureSearchData 1.25.0 (landing page) Brendan Gongol
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
|
To the developers/maintainers of the signatureSearchData 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: signatureSearchData |
| Version: 1.25.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings signatureSearchData_1.25.0.tar.gz |
| StartedAt: 2025-10-30 12:45:52 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 12:46:51 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 58.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signatureSearchData.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings signatureSearchData_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-data-experiment/meat/signatureSearchData.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 ‘signatureSearchData/DESCRIPTION’ ... OK
* this is package ‘signatureSearchData’ version ‘1.25.0’
* 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 ‘signatureSearchData’ 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 ... NOTE
Namespaces in Imports field not imported from:
‘ExperimentHub’ ‘rhdf5’
All declared Imports should be used.
* 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 ... OK
* 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 NOTE
See
‘/home/biocbuild/bbs-3.23-data-experiment/meat/signatureSearchData.Rcheck/00check.log’
for details.
signatureSearchData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL signatureSearchData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘signatureSearchData’ ... ** this is package ‘signatureSearchData’ version ‘1.25.0’ ** 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 (signatureSearchData)
signatureSearchData.Rcheck/signatureSearchData-Ex.timings
| name | user | system | elapsed | |
| ES_NULL | 4.450 | 0.280 | 4.976 | |
| GO_DATA | 1.101 | 0.270 | 1.521 | |
| GO_DATA_drug | 0.743 | 0.085 | 0.981 | |
| cmap | 0.042 | 0.003 | 0.045 | |
| cmap_expr | 0.040 | 0.003 | 0.043 | |
| cmap_rank | 0.041 | 0.002 | 0.043 | |
| combineNormRes | 0.000 | 0.001 | 0.000 | |
| combineResults | 0.000 | 0.001 | 0.000 | |
| dtlink_db_clue_sti | 0.716 | 0.068 | 0.943 | |
| getCmapCEL | 0.000 | 0.000 | 0.001 | |
| goAnno | 0.389 | 0.054 | 0.594 | |
| goAnno_drug | 0.402 | 0.056 | 0.626 | |
| inst_filter | 0.006 | 0.002 | 0.007 | |
| lincs | 0.045 | 0.000 | 0.045 | |
| lincs_expr | 0.040 | 0.003 | 0.042 | |
| meanExpr | 0.042 | 0.004 | 0.046 | |
| normalizeCel | 0 | 0 | 0 | |
| probe2gene | 0.001 | 0.001 | 0.002 | |
| runLimma | 1.940 | 0.199 | 2.140 | |
| sampleList | 1.495 | 0.002 | 1.497 | |
| sig_filter | 0.005 | 0.000 | 0.006 | |
| signatureSearchData | 0.672 | 0.064 | 0.886 | |
| taurefList | 0.391 | 0.063 | 0.604 | |