Back to Build/check report for BioC 3.19 experimental data
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This page was generated on 2024-05-16 14:51:32 -0400 (Thu, 16 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
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 1.18.0  (landing page)
Brendan Gongol
Snapshot Date: 2024-05-16 07:30:03 -0400 (Thu, 16 May 2024)
git_url: https://git.bioconductor.org/packages/signatureSearchData
git_branch: RELEASE_3_19
git_last_commit: 975c34b
git_last_commit_date: 2024-04-30 11:06:46 -0400 (Tue, 30 Apr 2024)
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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2024-05-16 12:04:55 -0400 (Thu, 16 May 2024)
EndedAt: 2024-05-16 12:05:54 -0400 (Thu, 16 May 2024)
EllapsedTime: 59.3 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_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/signatureSearchData.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘1.18.0’
* 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 4.65  0.519   5.603
* 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
###
##############################################################################
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* 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_NULL4.6500.5195.603
GO_DATA0.9810.2041.401
GO_DATA_drug0.6910.0640.932
cmap0.0530.0000.052
cmap_expr0.0340.0030.037
cmap_rank0.0380.0000.039
combineNormRes0.0000.0010.000
combineResults0.0000.0010.000
dtlink_db_clue_sti0.6550.0850.816
getCmapCEL0.0010.0000.000
goAnno0.4060.0520.634
goAnno_drug0.4150.0640.681
inst_filter0.0070.0040.011
lincs0.0370.0080.046
lincs_expr0.0350.0040.039
meanExpr0.0540.0080.063
normalizeCel000
probe2gene0.0010.0000.001
runLimma1.8950.1562.051
sampleList1.4790.0081.486
sig_filter0.0020.0040.005
signatureSearchData0.6780.0880.942
taurefList0.4130.0360.624