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This page was generated on 2025-09-01 12:07 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1703/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCSL 1.17.0  (landing page)
Qinglin Mei
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025)
git_url: https://git.bioconductor.org/packages/RCSL
git_branch: devel
git_last_commit: d6ee94a
git_last_commit_date: 2025-04-15 12:33:13 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RCSL on taishan

To the developers/maintainers of the RCSL package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCSL.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: RCSL
Version: 1.17.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RCSL.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RCSL_1.17.0.tar.gz
StartedAt: 2025-08-29 10:37:51 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 10:49:21 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 689.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RCSL.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RCSL.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RCSL_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RCSL.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘RCSL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCSL’ version ‘1.17.0’
* 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 ‘RCSL’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘MatrixGenerics’ ‘Rcpp’ ‘SingleCellExperiment’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotMST: no visible binding for global variable ‘X1’
PlotMST: no visible binding for global variable ‘X2’
PlotMST: no visible binding for global variable ‘label’
PlotMST: no visible binding for global variable ‘from.x’
PlotMST: no visible binding for global variable ‘to.x’
PlotMST: no visible binding for global variable ‘from.y’
PlotMST: no visible binding for global variable ‘to.y’
PlotMST: no visible binding for global variable ‘V1’
PlotMST: no visible binding for global variable ‘V2’
PlotPseudoTime: no visible binding for global variable ‘x’
PlotPseudoTime: no visible binding for global variable ‘y’
PlotPseudoTime: no visible binding for global variable ‘Timepoint’
PlotTrajectory: no visible binding for global variable ‘X1’
PlotTrajectory: no visible binding for global variable ‘X2’
PlotTrajectory: no visible binding for global variable ‘label’
PlotTrajectory: no visible binding for global variable ‘x’
PlotTrajectory: no visible binding for global variable ‘y’
Undefined global functions or variables:
  Timepoint V1 V2 X1 X2 from.x from.y label to.x to.y x y
* checking Rd files ... NOTE
checkRd: (-1) BDSM.Rd:6: Lost braces; missing escapes or markup?
     6 | min_{B>=0, B*1=1, F'*F=I}  ||B - A||_1 + r*||B||^2 + 2*lambda*trace(F'*L*F)}
       |     ^
checkRd: (-1) BDSM.Rd:22: Lost braces; missing escapes or markup?
    22 | min_{B>=0, B*1=1, F'*F=I}  ||B - A||_1 + r*||B||^2 + 2*lambda*trace(F'*L*F)
       |     ^
* 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 LazyData ... 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
BDSM               64.468  0.196  64.865
PlotMST            64.164  0.032  64.376
TrajectoryAnalysis 63.335  0.108  63.606
EstClusters        62.968  0.008  63.158
PlotTrajectory     61.943  0.092  62.198
getLineage         61.076  0.120  61.360
NeigRepresent      61.067  0.024  61.265
PlotPseudoTime     60.749  0.032  60.956
SimS               59.651  0.319  60.116
GenesFilter        55.867  0.139  56.173
RCSL               14.639  0.259  14.939
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/RCSL.Rcheck/00check.log’
for details.


Installation output

RCSL.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL RCSL
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘RCSL’ ...
** this is package ‘RCSL’ version ‘1.17.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (RCSL)

Tests output


Example timings

RCSL.Rcheck/RCSL-Ex.timings

nameusersystemelapsed
BDSM64.468 0.19664.865
EstClusters62.968 0.00863.158
GenesFilter55.867 0.13956.173
NeigRepresent61.067 0.02461.265
PlotMST64.164 0.03264.376
PlotPseudoTime60.749 0.03260.956
PlotTrajectory61.943 0.09262.198
RCSL14.639 0.25914.939
SimS59.651 0.31960.116
TrajectoryAnalysis63.335 0.10863.606
getLineage61.076 0.12061.360