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This page was generated on 2024-05-21 11:38:16 -0400 (Tue, 21 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 1450/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
octad 1.6.0  (landing page)
E. Chekalin
Snapshot Date: 2024-05-20 14:00:15 -0400 (Mon, 20 May 2024)
git_url: https://git.bioconductor.org/packages/octad
git_branch: RELEASE_3_19
git_last_commit: 4228d89
git_last_commit_date: 2024-04-30 11:45:54 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for octad on lconway


To the developers/maintainers of the octad package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/octad.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: octad
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:octad.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings octad_1.6.0.tar.gz
StartedAt: 2024-05-20 22:37:38 -0400 (Mon, 20 May 2024)
EndedAt: 2024-05-20 22:51:09 -0400 (Mon, 20 May 2024)
EllapsedTime: 810.8 seconds
RetCode: 0
Status:   OK  
CheckDir: octad.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:octad.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings octad_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/octad.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘octad/DESCRIPTION’ ... OK
* this is package ‘octad’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'magrittr', 'dplyr', 'ggplot2', 'edgeR', 'RUVSeq', 'DESeq2', 'limma',
  'rhdf5', 'foreach', 'Rfast', 'octad.db', 'httr', 'qpdf',
  'ExperimentHub', 'AnnotationHub', 'Biobase', 'S4Vectors'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘octad’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘httr’ ‘qpdf’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
diffExp: no visible binding for global variable ‘case’
diffExp: no visible binding for global variable ‘control’
runsRGES: no visible binding for global variable ‘RGES’
topLineEval: no visible binding for global variable ‘sRGES’
topLineEval: no visible binding for global variable ‘medauc’
Undefined global functions or variables:
  RGES case control medauc sRGES
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
octadDrugEnrichment 77.955  8.952 168.771
computeCellLine     74.427  6.395 100.409
topLineEval         41.750  1.204  44.349
diffExp             35.731  3.302  48.351
computeRefTissue     6.913  0.546  14.856
loadOctadCounts      5.794  0.587  11.027
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/octad.Rcheck/00check.log’
for details.


Installation output

octad.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL octad
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘octad’ ...
** using staged installation
** R
** data
** 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 (octad)

Tests output


Example timings

octad.Rcheck/octad-Ex.timings

nameusersystemelapsed
computeCellLine 74.427 6.395100.409
computeRefTissue 6.913 0.54614.856
diffExp35.731 3.30248.351
loadOctadCounts 5.794 0.58711.027
octadDrugEnrichment 77.955 8.952168.771
runsRGES0.2040.0120.221
topLineEval41.750 1.20444.349