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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1762/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAsense 1.21.0  (landing page)
Marcus Rosenblatt
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/RNAsense
git_branch: devel
git_last_commit: e99ce3a
git_last_commit_date: 2024-10-29 10:41:44 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows 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 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for RNAsense on kunpeng2

To the developers/maintainers of the RNAsense package:
- 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 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: RNAsense
Version: 1.21.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RNAsense.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RNAsense_1.21.0.tar.gz
StartedAt: 2024-12-24 10:33:12 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 10:50:46 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 1053.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RNAsense.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RNAsense.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RNAsense_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RNAsense.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAsense/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAsense’ version ‘1.21.0’
* 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 ‘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 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 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
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 ... NOTE
checkRd: (-1) MZsox.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MZsox.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MZsox.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MZsox.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MZsox.Rd:13: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'getFC.Rd':
  ‘DataFrame’

Missing link(s) in Rd file 'getSwitch.Rd':
  ‘DataFrame’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MZsox.Rd: SummarizedExperiment
  getFC.Rd: SummarizedExperiment, DataFrame
  getSwitch.Rd: SummarizedExperiment, DataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
combineResults   222.539  1.358 224.294
outputGeneTables 217.122  1.673 219.163
plotSSGS         216.258  0.592 217.228
getSwitch        139.264  1.214 140.826
getFC             52.190  0.095  52.360
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RNAsense.Rcheck/00check.log’
for details.


Installation output

RNAsense.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL RNAsense
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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
combineResults222.539 1.358224.294
getFC52.190 0.09552.360
getSwitch139.264 1.214140.826
outputGeneTables217.122 1.673219.163
plotSSGS216.258 0.592217.228