Back to Build/check report for BioC 3.19 experimental data
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This page was generated on 2024-03-26 14:51:27 -0400 (Tue, 26 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
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 360/425HostnameOS / ArchINSTALLBUILDCHECK
signatureSearchData 1.17.0  (landing page)
Brendan Gongol
Snapshot Date: 2024-03-26 07:30:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/signatureSearchData
git_branch: devel
git_last_commit: c4c36bb
git_last_commit_date: 2023-10-24 09:20:27 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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: 1.17.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings signatureSearchData_1.17.0.tar.gz
StartedAt: 2024-03-26 12:18:40 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 12:19:41 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 60.7 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearchData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings signatureSearchData_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/signatureSearchData.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘signatureSearchData/DESCRIPTION’ ... OK
* this is package ‘signatureSearchData’ version ‘1.17.0’
* 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 4.782  0.545    5.75
* 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-3.19-data-experiment/meat/signatureSearchData.Rcheck/00check.log’
for details.


Installation output

signatureSearchData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL signatureSearchData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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_NULL4.7820.5455.750
GO_DATA0.6880.1000.972
GO_DATA_drug0.7190.0890.993
cmap0.0350.0030.039
cmap_expr0.0330.0040.037
cmap_rank0.0370.0000.038
combineNormRes0.0000.0000.001
combineResults0.0000.0000.001
dtlink_db_clue_sti0.7100.0570.953
getCmapCEL0.0010.0000.000
goAnno0.4020.0560.648
goAnno_drug0.4280.0560.760
inst_filter0.0060.0040.009
lincs0.0430.0040.046
lincs_expr0.0320.0080.041
meanExpr0.0530.0080.062
normalizeCel000
probe2gene0.0020.0000.002
runLimma2.0080.1642.172
sampleList1.5690.0241.593
sig_filter0.0060.0000.006
signatureSearchData0.6850.0920.963
taurefList0.4080.0480.701