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This page was generated on 2024-07-11 14:51 -0400 (Thu, 11 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4675
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 363/425HostnameOS / ArchINSTALLBUILDCHECK
SingleCellMultiModal 1.17.3  (landing page)
Marcel Ramos
Snapshot Date: 2024-07-11 07:30 -0400 (Thu, 11 Jul 2024)
git_url: https://git.bioconductor.org/packages/SingleCellMultiModal
git_branch: devel
git_last_commit: 1ac9a1f
git_last_commit_date: 2024-06-18 16:54:35 -0400 (Tue, 18 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SingleCellMultiModal on nebbiolo2

To the developers/maintainers of the SingleCellMultiModal package:
- 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: SingleCellMultiModal
Version: 1.17.3
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SingleCellMultiModal.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SingleCellMultiModal_1.17.3.tar.gz
StartedAt: 2024-07-11 12:00:51 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 12:11:32 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 640.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SingleCellMultiModal.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SingleCellMultiModal.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SingleCellMultiModal_1.17.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/SingleCellMultiModal.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SingleCellMultiModal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SingleCellMultiModal’ version ‘1.17.3’
* 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 ‘SingleCellMultiModal’ 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
.CITEseqMaeToSce: no visible global function definition for ‘altExps<-’
.CITEseqMaeToSce: no visible global function definition for ‘altExp’
.CITEseqMaeToSce: no visible global function definition for ‘assays<-’
.CITEseqMaeToSce: no visible global function definition for ‘altExp<-’
.CITEseqMaeToSce: no visible global function definition for
  ‘SimpleList’
Undefined global functions or variables:
  SimpleList altExp altExp<- altExps<- assays<-
* checking Rd files ... NOTE
checkRd: (-1) scNMT.Rd:69: Lost braces
    69 | \item{met_}} - DNA methylation
       |      ^
checkRd: (-1) scNMT.Rd:82: Lost braces
    82 | url{https://github.com/BIRSBiointegration/Hackathon/tree/master/scNMT-seq}
       |    ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
CITEseq 11.863  1.604  14.128
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/SingleCellMultiModal.Rcheck/00check.log’
for details.


Installation output

SingleCellMultiModal.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SingleCellMultiModal
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘SingleCellMultiModal’ ...
** using staged installation
** R
** inst
** 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 (SingleCellMultiModal)

Tests output


Example timings

SingleCellMultiModal.Rcheck/SingleCellMultiModal-Ex.timings

nameusersystemelapsed
CITEseq11.863 1.60414.128
GTseq0.7960.0351.028
SCoPE20.9900.0631.246
SingleCellMultiModal-package0.0090.0000.010
SingleCellMultiModal3.8180.1354.805
ontomap0.0030.0000.003
scMultiome1.2550.0411.528
scNMT3.7390.3234.664
scmmCache0.0010.0000.001
seqFISH1.4420.0401.754