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This page was generated on 2023-10-24 11:41:29 -0400 (Tue, 24 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4724
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4459
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4473
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4461
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 1854/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SCATE 1.11.1  (landing page)
Wenpin Hou
Snapshot Date: 2023-10-23 14:05:08 -0400 (Mon, 23 Oct 2023)
git_url: https://git.bioconductor.org/packages/SCATE
git_branch: devel
git_last_commit: 7cfab20
git_last_commit_date: 2023-09-05 13:44:29 -0400 (Tue, 05 Sep 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.6.5 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson1macOS 13.3.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for SCATE on kunpeng2


To the developers/maintainers of the SCATE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SCATE.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: SCATE
Version: 1.11.1
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SCATE.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings SCATE_1.11.1.tar.gz
StartedAt: 2023-10-24 12:25:15 -0000 (Tue, 24 Oct 2023)
EndedAt: 2023-10-24 12:36:38 -0000 (Tue, 24 Oct 2023)
EllapsedTime: 683.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: SCATE.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SCATE.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings SCATE_1.11.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SCATE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘SCATE/DESCRIPTION’ ... OK
* this is package ‘SCATE’ version ‘1.11.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'parallel', 'preprocessCore', 'splines', 'splines2', 'xgboost',
  'SCATEData', 'Rtsne', 'mclust'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘SCATE’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'SCATE' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/SCATE.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘SCATEData’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SCATE : SCATEsingle: no visible global function definition for
  ‘IRanges’
cellcluster : <anonymous>: no visible global function definition for
  ‘IRanges’
extractfeature: no visible global function definition for ‘IRanges’
makedatabase: no visible global function definition for ‘IRanges’
makedatabase: no visible global function definition for ‘seqlevels’
peakcall: no visible global function definition for ‘IRanges’
Undefined global functions or variables:
  IRanges seqlevels
* checking Rd files ... OK
* 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
SCATEpipeline 125.704  1.381 106.989
SCATE         113.743  2.141  96.212
peakcall      105.214  0.914  87.828
cellcluster    21.127  0.372  21.534
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SCATE.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘SCATE.Rmd’ using rmarkdown
Error: processing vignette 'SCATE.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘SCATE.Rmd’

SUMMARY: processing the following file failed:
  ‘SCATE.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SCATE.Rcheck/00check.log’
for details.


Installation output

SCATE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL SCATE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘SCATE’ ...
** 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
Warning: Package 'SCATE' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'SCATE' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (SCATE)

Tests output


Example timings

SCATE.Rcheck/SCATE-Ex.timings

nameusersystemelapsed
SCATE113.743 2.141 96.212
SCATEpipeline125.704 1.381106.989
cellcluster21.127 0.37221.534
extractfeature0.0520.0000.053
peakcall105.214 0.914 87.828
satacprocess0.1050.0000.105