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This page was generated on 2023-06-20 11:38:03 -0400 (Tue, 20 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.0 RC (2023-04-18 r84287) -- "Already Tomorrow" 4602
palomino4Windows Server 2022 Datacenterx644.3.0 RC (2023-04-18 r84287 ucrt) -- "Already Tomorrow" 4352
lconwaymacOS 12.6.5 Montereyx86_644.3.0 RC (2023-04-13 r84266) -- "Already Tomorrow" 4359
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4383
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 1794/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SCATE 1.11.0  (landing page)
Wenpin Hou
Snapshot Date: 2023-06-19 14:00:08 -0400 (Mon, 19 Jun 2023)
git_url: https://git.bioconductor.org/packages/SCATE
git_branch: devel
git_last_commit: a5d9003
git_last_commit_date: 2023-04-25 11:22:07 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SCATEData' which is not available
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'SCATEData' which is not available
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    TIMEOUT  skipped

CHECK results for SCATE on palomino4


The builds on kunpeng2 (Linux ARM64) are experimental!
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.

raw results


Summary

Package: SCATE
Version: 1.11.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SCATE.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SCATE_1.11.0.tar.gz
StartedAt: 2023-06-20 06:01:48 -0400 (Tue, 20 Jun 2023)
EndedAt: 2023-06-20 06:10:57 -0400 (Tue, 20 Jun 2023)
EllapsedTime: 548.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SCATE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SCATE.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SCATE_1.11.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/SCATE.Rcheck'
* using R version 4.3.0 RC (2023-04-18 r84287 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SCATE/DESCRIPTION' ... OK
* this is package 'SCATE' version '1.11.0'
* 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 whether package 'SCATE' 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 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 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 121.59   2.70  108.75
SCATE         120.19   3.02  107.63
peakcall      110.60   2.44   96.39
cellcluster    20.73   0.73   21.49
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
  'F:/biocbuild/bbs-3.18-bioc/meat/SCATE.Rcheck/00check.log'
for details.



Installation output

SCATE.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL SCATE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SCATE)

Tests output


Example timings

SCATE.Rcheck/SCATE-Ex.timings

nameusersystemelapsed
SCATE120.19 3.02107.63
SCATEpipeline121.59 2.70108.75
cellcluster20.73 0.7321.49
extractfeature0.050.000.04
peakcall110.60 2.44 96.39
satacprocess0.090.000.10