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This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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 1723/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCSL 1.17.0  (landing page)
Qinglin Mei
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 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 nebbiolo2

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.

raw results


Summary

Package: RCSL
Version: 1.17.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RCSL.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RCSL_1.17.0.tar.gz
StartedAt: 2025-10-11 03:33:48 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 03:41:00 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 432.6 seconds
RetCode: 0
Status:   OK  
CheckDir: RCSL.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RCSL.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --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 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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
PlotMST            37.516  0.127  37.644
TrajectoryAnalysis 37.215  0.113  37.328
PlotTrajectory     36.236  0.143  36.378
BDSM               35.741  0.288  36.031
PlotPseudoTime     35.835  0.122  35.961
NeigRepresent      35.130  0.165  35.296
EstClusters        34.766  0.037  34.803
getLineage         34.590  0.028  34.621
SimS               34.278  0.045  34.324
GenesFilter        33.371  0.103  33.480
RCSL                8.472  0.095   8.567
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL RCSL
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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
BDSM35.741 0.28836.031
EstClusters34.766 0.03734.803
GenesFilter33.371 0.10333.480
NeigRepresent35.130 0.16535.296
PlotMST37.516 0.12737.644
PlotPseudoTime35.835 0.12235.961
PlotTrajectory36.236 0.14336.378
RCSL8.4720.0958.567
SimS34.278 0.04534.324
TrajectoryAnalysis37.215 0.11337.328
getLineage34.590 0.02834.621