Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 674/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ERSSA 1.24.0  (landing page)
Zixuan Shao
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ERSSA
git_branch: RELEASE_3_20
git_last_commit: 193c677
git_last_commit_date: 2024-10-29 10:31:30 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for ERSSA on merida1

To the developers/maintainers of the ERSSA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ERSSA.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: ERSSA
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ERSSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ERSSA_1.24.0.tar.gz
StartedAt: 2024-12-20 03:11:38 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 03:21:51 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 612.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ERSSA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ERSSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ERSSA_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ERSSA.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ERSSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ERSSA’ version ‘1.24.0’
* 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 ‘ERSSA’ 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
Namespace in Imports field not imported from: ‘apeglm’
  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 ... NOTE
checkRd: (-1) erssa.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:90-91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:92-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:95-97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:98-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_TPR_FPRPlot.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_TPR_FPRPlot.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_TPR_FPRPlot.Rd:35-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_dotplot.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_dotplot.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_dotplot.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_marginPlot.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_marginPlot.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
* 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 LazyData ... 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
erssa_deseq2          76.576  0.600  82.063
erssa_deseq2_parallel 76.314  0.531  80.164
erssa                 19.156  0.408  20.896
erssa_edger_parallel   5.759  0.088   5.996
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ERSSA.Rcheck/00check.log’
for details.

Installation output

ERSSA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ERSSA
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ERSSA’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (ERSSA)

Tests output


Example timings

ERSSA.Rcheck/ERSSA-Ex.timings

nameusersystemelapsed
comb_gen0.0130.0060.021
count_filter0.0060.0020.010
erssa19.156 0.40820.896
erssa_deseq276.576 0.60082.063
erssa_deseq2_parallel76.314 0.53180.164
erssa_edger3.2280.0523.391
erssa_edger_parallel5.7590.0885.996
ggplot2_TPR_FPRPlot0.7510.0070.797
ggplot2_dotplot0.9170.0070.980
ggplot2_intersectPlot0.8690.0110.896
ggplot2_marginPlot0.6580.0090.678