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This page was generated on 2024-06-11 14:44 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1862/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
saseR 1.0.0  (landing page)
Alexandre Segers
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/saseR
git_branch: RELEASE_3_19
git_last_commit: 83a2bb6
git_last_commit_date: 2024-04-30 11:53:31 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for saseR on kjohnson3

To the developers/maintainers of the saseR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/saseR.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: saseR
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:saseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings saseR_1.0.0.tar.gz
StartedAt: 2024-06-11 04:07:01 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 04:20:02 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 781.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: saseR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:saseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings saseR_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/saseR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘saseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘saseR’ version ‘1.0.0’
* 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 ‘saseR’ 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 ... WARNING
'::' or ':::' imports not declared from:
  'ensembldb' 'pbmcapply'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.ASpligenerateSamplesNames : my.make.unique: no visible global function
  definition for 'setNames'
.bamToCounts: no visible binding for global variable 'i'
.createGRangesGenes.getLocusOverlap: no visible global function
  definition for 'packageVersion'
.locusPValues: no visible binding for global variable 'locus'
jcounts: no visible binding for global variable 'df0'
jcounts: no visible global function definition for '.junctionsDiscover'
jcounts: no visible global function definition for '.e1e2JPIR'
binGenome,TxDb: no visible global function definition for 'seqlevels'
binGenome,TxDb: no visible global function definition for
  'as.data.table'
binGenome,TxDb: no visible global function definition for 'rbindlist'
Undefined global functions or variables:
  .e1e2JPIR .junctionsDiscover as.data.table df0 i locus packageVersion
  rbindlist seqlevels setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "packageVersion")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
BamtoAspliCounts 228.667   4.87 155.092
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/saseR.Rcheck/00check.log’
for details.


Installation output

saseR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘saseR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
** testing if installed package keeps a record of temporary installation path
* DONE (saseR)

Tests output


Example timings

saseR.Rcheck/saseR-Ex.timings

nameusersystemelapsed
BamtoAspliCounts228.667 4.870155.092
calculateOffsets0.5270.0180.967
convertASpli0.1820.0170.353
saseRfindEncodingDim0.3940.0430.781
saseRfit2.2850.0832.677