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This page was generated on 2023-04-12 11:05:49 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 RNAsense on palomino4


To the developers/maintainers of the RNAsense package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAsense.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1706/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAsense 1.12.0  (landing page)
Marcus Rosenblatt
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/RNAsense
git_branch: RELEASE_3_16
git_last_commit: 296c1de
git_last_commit_date: 2022-11-01 11:20:57 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RNAsense
Version: 1.12.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAsense.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings RNAsense_1.12.0.tar.gz
StartedAt: 2023-04-11 05:21:46 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 05:34:26 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 760.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RNAsense.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAsense.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings RNAsense_1.12.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/RNAsense.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RNAsense/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAsense' version '1.12.0'
* 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 whether package 'RNAsense' 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 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
combineResults: no visible binding for global variable 'resultSwitch'
combineResults: no visible binding for global variable 'resultFC'
combineResults : getFCupdown: no visible binding for global variable
  'resultFC'
combineResults : getFCupdown: no visible binding for global variable
  'name'
combineResults : getFCupdown: no visible binding for global variable
  'FCdetect'
getFC: no visible binding for global variable 'mydata'
getFC: no visible binding for global variable 'analyzeConditions'
getFC: no visible binding for global variable 'times'
getSwitch: no visible binding for global variable 'mydata'
getSwitch: no visible binding for global variable 'times'
outputGeneTables: no visible binding for global variable
  'resultCombined'
outputGeneTables: no visible binding for global variable 'times'
outputGeneTables: no visible binding for global variable
  'analyzeConditions'
outputGeneTables: no visible binding for global variable 'timepoint'
outputGeneTables: no visible binding for global variable 'FCdown'
outputGeneTables: no visible binding for global variable 'FCup'
outputGeneTables: no visible binding for global variable 'experiment'
plotSSGS: no visible binding for global variable 'resultCombined'
plotSSGS: no visible binding for global variable 'times'
plotSSGS: no visible binding for global variable 'analyzeConditions'
plotSSGS : getFT: no visible binding for global variable 'result'
plotSSGS : getFT: no visible binding for global variable 'timepoint'
plotSSGS : getFT: no visible binding for global variable 'FCdown'
plotSSGS : getFT: no visible binding for global variable 'FCup'
plotSSGS : <anonymous> : <anonymous> : <anonymous> : <anonymous>: no
  visible binding for global variable 'experiment'
plotSSGS: no visible binding for global variable 'xaxis'
plotSSGS: no visible binding for global variable 'cluster'
Undefined global functions or variables:
  FCdetect FCdown FCup analyzeConditions cluster experiment mydata name
  result resultCombined resultFC resultSwitch timepoint times xaxis
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'getFC.Rd':
  'DataFrame'

Missing link or links in documentation object 'getSwitch.Rd':
  'DataFrame'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
outputGeneTables 161.70   2.34  164.12
combineResults   159.22   3.05  162.27
plotSSGS         156.75   2.30  159.10
getSwitch         79.97   1.04   81.08
getFC             52.14   0.57   52.71
* 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-3.16-bioc/meat/RNAsense.Rcheck/00check.log'
for details.



Installation output

RNAsense.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL RNAsense
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'RNAsense' ...
** 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 (RNAsense)

Tests output


Example timings

RNAsense.Rcheck/RNAsense-Ex.timings

nameusersystemelapsed
combineResults159.22 3.05162.27
getFC52.14 0.5752.71
getSwitch79.97 1.0481.08
outputGeneTables161.70 2.34164.12
plotSSGS156.75 2.30159.10