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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 712/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FEAST 1.12.0  (landing page)
Kenong Su
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/FEAST
git_branch: RELEASE_3_19
git_last_commit: adbdda9
git_last_commit_date: 2024-04-30 11:33:40 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for FEAST on nebbiolo1

To the developers/maintainers of the FEAST package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FEAST.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: FEAST
Version: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FEAST.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FEAST_1.12.0.tar.gz
StartedAt: 2024-06-19 23:10:10 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 23:14:02 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 232.5 seconds
RetCode: 0
Status:   OK  
CheckDir: FEAST.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FEAST.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FEAST_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FEAST.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘FEAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FEAST’ version ‘1.12.0’
* 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 ‘FEAST’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
* 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
FEAST: multiple local function definitions for ‘bp_fun’ with different
  formal arguments
SC3_Clust: no visible global function definition for ‘metadata’
Visual_Rslt: no visible global function definition for ‘ggbarplot’
Visual_Rslt: no visible global function definition for ‘theme’
Visual_Rslt: no visible global function definition for ‘element_text’
Visual_Rslt: no visible global function definition for ‘ggline’
Visual_Rslt: no visible global function definition for ‘get_palette’
Visual_Rslt: no visible global function definition for
  ‘scale_y_continuous’
Visual_Rslt: no visible global function definition for ‘guides’
Visual_Rslt: no visible global function definition for ‘guide_legend’
Visual_Rslt: no visible global function definition for ‘ggarrange’
aricode_NMI : entropy: no visible global function definition for
  ‘sortPairs’
Undefined global functions or variables:
  element_text get_palette ggarrange ggbarplot ggline guide_legend
  guides metadata scale_y_continuous sortPairs theme
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.19-bioc/meat/FEAST.Rcheck/00check.log’
for details.


Installation output

FEAST.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL FEAST
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘FEAST’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cal_3_metrics.c -o cal_3_metrics.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o FEAST.so cal_3_metrics.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-FEAST/00new/FEAST/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FEAST)

Tests output


Example timings

FEAST.Rcheck/FEAST-Ex.timings

nameusersystemelapsed
Consensus1.9120.5472.460
FEAST0.9370.0610.998
FEAST_fast1.4630.0831.547
Norm_Y0.1410.0160.157
Select_Model_short_SC30.9770.0451.021
Select_Model_short_TSCAN0.8930.0280.922
TSCAN_Clust0.0000.0010.001
Visual_Rslt1.1940.0821.276
Y0.0580.0400.098
align_CellType0.0010.0000.001
cal_F20.3510.4400.791
cal_MSE0.7760.0880.865
eval_Cluster0.0050.0000.006
process_Y0.1040.0080.112
setUp_BPPARAM0.5560.0080.563
trueclass0.0020.0010.002