Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:41:20 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 2073/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
subSeq 1.32.0  (landing page)
Andrew J. Bass , John D. Storey
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/subSeq
git_branch: RELEASE_3_18
git_last_commit: ada9c5b
git_last_commit_date: 2023-10-24 10:46:10 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 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
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for subSeq on kunpeng2


To the developers/maintainers of the subSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/subSeq.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: subSeq
Version: 1.32.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:subSeq.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings subSeq_1.32.0.tar.gz
StartedAt: 2023-11-02 14:42:49 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 14:45:45 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 175.3 seconds
RetCode: 0
Status:   OK  
CheckDir: subSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:subSeq.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings subSeq_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/subSeq.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘subSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘subSeq’ version ‘1.32.0’
* 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 ‘subSeq’ 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DESeq2: no visible global function definition for ‘selectMethod’
ccc: no visible global function definition for ‘cov’
ccc: no visible global function definition for ‘var’
generateSubsampledMatrix : <anonymous>: no visible global function
  definition for ‘rbinom’
plot.summary.subsamples: no visible binding for global variable
  ‘metric’
plot.summary.subsamples: no visible binding for global variable ‘value’
plot.summary.subsamples: no visible binding for global variable
  ‘significant’
plot.summary.subsamples: no visible binding for global variable
  ‘percent’
plot.summary.subsamples: no visible binding for global variable
  ‘method’
plot.summary.subsamples: no visible binding for global variable ‘depth’
plot.summary.subsamples: no visible binding for global variable
  ‘average.depth’
plot.summary.subsamples: no visible binding for global variable
  ‘average.value’
subsample: no visible binding for global variable ‘proportion’
subsample: no visible binding for global variable ‘replication’
subsample: no visible binding for global variable ‘.’
subsample: no visible binding for global variable ‘pvalue’
summary.subsamples: no visible binding for global variable ‘count’
summary.subsamples: no visible binding for global variable ‘method’
summary.subsamples: no visible binding for global variable ‘depth’
summary.subsamples: no visible binding for global variable ‘pvalue’
summary.subsamples: no visible binding for global variable ‘proportion’
summary.subsamples: no visible binding for global variable
  ‘replication’
summary.subsamples: no visible global function definition for
  ‘p.adjust’
summary.subsamples: no visible binding for global variable ‘ID’
summary.subsamples: no visible binding for global variable ‘padj’
summary.subsamples: no visible binding for global variable
  ‘coefficient’
summary.subsamples: no visible binding for global variable
  ‘o.coefficient’
summary.subsamples: no visible global function definition for ‘cor’
summary.subsamples: no visible binding for global variable ‘valid’
summary.subsamples: no visible binding for global variable ‘o.lfdr’
summary.subsamples: no visible binding for global variable ‘o.padj’
summary.subsamples: no visible binding for global variable
  ‘significant’
summary.subsamples: no visible binding for global variable ‘estFDP’
summary.subsamples: no visible binding for global variable ‘rFDP’
summary.subsamples: no visible binding for global variable ‘metric’
summary.subsamples: no visible binding for global variable ‘value’
summary.subsamples: no visible binding for global variable ‘percent’
voomLimma: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  . ID average.depth average.value coefficient cor count cov depth
  estFDP method metric model.matrix o.coefficient o.lfdr o.padj
  p.adjust padj percent proportion pvalue rFDP rbinom replication
  selectMethod significant valid value var
Consider adding
  importFrom("methods", "selectMethod")
  importFrom("stats", "cor", "cov", "model.matrix", "p.adjust", "rbinom",
             "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
generateSubsampledMatrix 43.912  0.691  44.692
getSeed                  33.771  0.267  34.104
subsample                33.126  0.152  33.341
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/subSeq.Rcheck/00check.log’
for details.



Installation output

subSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL subSeq
###
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##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘subSeq’ ...
** using staged installation
** R
** data
** 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 (subSeq)

Tests output


Example timings

subSeq.Rcheck/subSeq-Ex.timings

nameusersystemelapsed
combineSubsamples0.1960.0240.220
generateSubsampledMatrix43.912 0.69144.692
getSeed33.771 0.26734.104
plot.subsamples000
plot.summary.subsamples0.0010.0000.000
ss0.6900.0040.694
subsample33.126 0.15233.341
summary.subsamples1.4160.1081.527