Back to Build/check report for BioC 3.21 experimental data
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This page was generated on 2025-01-02 15:01 -0500 (Thu, 02 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4755
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 364/430HostnameOS / ArchINSTALLBUILDCHECK
signatureSearchData 1.21.0  (landing page)
Brendan Gongol
Snapshot Date: 2025-01-02 07:30 -0500 (Thu, 02 Jan 2025)
git_url: https://git.bioconductor.org/packages/signatureSearchData
git_branch: devel
git_last_commit: 4d1195c
git_last_commit_date: 2024-10-29 09:50:38 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for signatureSearchData on nebbiolo1

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.

raw results


Summary

Package: signatureSearchData
Version: 1.21.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings signatureSearchData_1.21.0.tar.gz
StartedAt: 2025-01-02 12:39:53 -0500 (Thu, 02 Jan 2025)
EndedAt: 2025-01-02 12:40:51 -0500 (Thu, 02 Jan 2025)
EllapsedTime: 57.6 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearchData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings signatureSearchData_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/signatureSearchData.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘signatureSearchData/DESCRIPTION’ ... OK
* this is package ‘signatureSearchData’ version ‘1.21.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
ES_NULL 4.566  0.462   5.313
* 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-3.21-data-experiment/meat/signatureSearchData.Rcheck/00check.log’
for details.


Installation output

signatureSearchData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL signatureSearchData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘signatureSearchData’ ...
** 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)

Tests output


Example timings

signatureSearchData.Rcheck/signatureSearchData-Ex.timings

nameusersystemelapsed
ES_NULL4.5660.4625.313
GO_DATA0.7200.1190.989
GO_DATA_drug0.7080.0720.962
cmap0.0430.0010.044
cmap_expr0.0390.0030.042
cmap_rank0.0420.0010.043
combineNormRes0.0010.0000.000
combineResults0.0010.0000.000
dtlink_db_clue_sti0.6950.0600.905
getCmapCEL0.0010.0000.000
goAnno0.3960.0500.595
goAnno_drug0.4440.0490.644
inst_filter0.0060.0010.008
lincs0.0450.0020.048
lincs_expr0.0430.0020.045
meanExpr0.0430.0030.046
normalizeCel0.0000.0000.001
probe2gene0.0020.0000.002
runLimma2.0370.2902.328
sampleList1.5570.0671.624
sig_filter0.0050.0010.007
signatureSearchData0.6780.0930.921
taurefList0.4350.0520.637