Multiple platform build/check report for BioC 3.21 - CHECK results for ERSSA on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4349
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*

CHECK results for ERSSA on lconway

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: 1.25.0

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_1.25.0.tar.gz

StartedAt: 2024-11-24 21:43:42 -0500 (Sun, 24 Nov 2024)

EndedAt: 2024-11-24 21:51:57 -0500 (Sun, 24 Nov 2024)

EllapsedTime: 495.1 seconds

RetCode: 0

Status: OK

CheckDir: ERSSA.Rcheck

Warnings: 0

Command output

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### Running command:
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###   /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_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ERSSA.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘1.25.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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_parallel 27.212  0.413  27.782
erssa_deseq2          26.651  0.593  28.232
erssa                  8.431  0.250   9.382
* 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-3.21-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/4.5-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

name	user	system	elapsed
comb_gen	0.005	0.003	0.010
count_filter	0.004	0.001	0.005
erssa	8.431	0.250	9.382
erssa_deseq2	26.651	0.593	28.232
erssa_deseq2_parallel	27.212	0.413	27.782
erssa_edger	1.368	0.046	1.424
erssa_edger_parallel	2.999	0.082	3.107
ggplot2_TPR_FPRPlot	0.290	0.005	0.297
ggplot2_dotplot	0.337	0.004	0.342
ggplot2_intersectPlot	0.338	0.005	0.346
ggplot2_marginPlot	0.267	0.004	0.272