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This page was generated on 2024-03-27 11:37:31 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 514/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeconRNASeq 1.44.0  (landing page)
Ting Gong
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/DeconRNASeq
git_branch: RELEASE_3_18
git_last_commit: b74d94c
git_last_commit_date: 2023-10-24 09:51:21 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for DeconRNASeq on merida1


To the developers/maintainers of the DeconRNASeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeconRNASeq.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: DeconRNASeq
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeconRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeconRNASeq_1.44.0.tar.gz
StartedAt: 2024-03-26 01:28:50 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 01:29:56 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 66.4 seconds
RetCode: 0
Status:   OK  
CheckDir: DeconRNASeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeconRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeconRNASeq_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/DeconRNASeq.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘DeconRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeconRNASeq’ version ‘1.44.0’
* 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 ‘DeconRNASeq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
* 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 R 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
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggplot2’ ‘grid’ ‘pcaMethods’
  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
DeconRNASeq: no visible global function definition for ‘prep’
DeconRNASeq: no visible global function definition for ‘pca’
DeconRNASeq: no visible global function definition for ‘R2cum’
DeconRNASeq: no visible global function definition for ‘ggplot’
DeconRNASeq: no visible global function definition for ‘aes’
DeconRNASeq: no visible global function definition for ‘geom_point’
DeconRNASeq: no visible global function definition for ‘labs’
DeconRNASeq: no visible global function definition for ‘geom_abline’
DeconRNASeq: no visible global function definition for ‘xlab’
DeconRNASeq: no visible global function definition for ‘ylab’
condplot: no visible global function definition for ‘rainbow’
condplot: no visible global function definition for ‘lines’
condplot: no visible global function definition for ‘axis’
condplot: no visible global function definition for ‘title’
decon.bootstrap: no visible global function definition for ‘t.test’
multiplot: no visible global function definition for ‘grid.newpage’
multiplot: no visible global function definition for ‘pushViewport’
multiplot: no visible global function definition for ‘viewport’
multiplot: no visible global function definition for ‘grid.layout’
multiplot : vplayout: no visible global function definition for
  ‘viewport’
Undefined global functions or variables:
  R2cum aes axis geom_abline geom_point ggplot grid.layout grid.newpage
  labs lines pca prep pushViewport rainbow t.test title viewport xlab
  ylab
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "lines", "title")
  importFrom("stats", "t.test")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/DeconRNASeq.Rcheck/00check.log’
for details.



Installation output

DeconRNASeq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘DeconRNASeq’ ...
** using staged installation
** R
** data
** demo
** 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 (DeconRNASeq)

Tests output


Example timings

DeconRNASeq.Rcheck/DeconRNASeq-Ex.timings

nameusersystemelapsed
DeconRNASeq0.0000.0010.001
all.datasets0.0950.0120.108
array.proportions0.0650.0080.081
array.signatures0.0630.0070.070
condplot0.0630.0070.070
datasets0.1460.0100.162
fraction0.4090.0160.425
liver_kidney0.1340.0060.141
multi_tissue0.3810.0100.393
multiplot0.0030.0010.004
proportions0.1300.0050.138
signatures0.1380.0050.145
x.data0.3960.0120.411
x.signature0.4100.0110.423
x.signature.filtered0.4060.0120.419
x.signature.filtered.optimal0.4190.0150.436