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This page was generated on 2024-03-27 11:37:11 -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 1911/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 2.36.0  (landing page)
Thomas J. Hardcastle
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/segmentSeq
git_branch: RELEASE_3_18
git_last_commit: 4116a42
git_last_commit_date: 2023-10-24 09:43:27 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for segmentSeq on palomino4


To the developers/maintainers of the segmentSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmentSeq.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: segmentSeq
Version: 2.36.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:segmentSeq.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings segmentSeq_2.36.0.tar.gz
StartedAt: 2024-03-26 05:04:44 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 05:11:13 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 388.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: segmentSeq.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:segmentSeq.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings segmentSeq_2.36.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/segmentSeq.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '2.36.0'
* 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 whether package 'segmentSeq' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'baySeq' is deprecated and will be removed from Bioconductor
See 'F:/biocbuild/bbs-3.18-bioc/meat/segmentSeq.Rcheck/00install.out' for details.
* 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 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
heuristicSeg : <anonymous>: no visible binding for global variable
  'sDP'
Undefined global functions or variables:
  sDP
* 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
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
classifySeg        38.03   0.18   38.25
lociLikelihoods    17.75   0.04   17.78
heuristicSeg       16.54   0.01   16.58
plotGenome          8.42   0.01    8.49
getCounts           6.42   0.00    6.44
processAD           5.41   0.00    5.42
segData-class       5.14   0.02    5.15
segmentSeq-package  5.07   0.00    5.15
* 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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.



Installation output

segmentSeq.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL segmentSeq
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'segmentSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'baySeq' is deprecated and will be removed from Bioconductor
  version 3.19 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'baySeq' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'baySeq' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (segmentSeq)

Tests output


Example timings

segmentSeq.Rcheck/segmentSeq-Ex.timings

nameusersystemelapsed
alignmentData-class3.970.003.98
classifySeg38.03 0.1838.25
findChunks4.010.024.03
getCounts6.420.006.44
getOverlaps4.210.004.20
heuristicSeg16.54 0.0116.58
lociLikelihoods17.75 0.0417.78
normaliseNC3.830.174.06
plotGenome8.420.018.49
processAD5.410.005.42
readMethods4.500.024.53
readMeths4.230.314.55
segData-class5.140.025.15
segmentSeq-package5.070.005.15
thresholdFinder4.110.294.84