Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-16 17:42 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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: 2024-07-14 14:00 -0400 (Sun, 14 Jul 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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 kjohnson1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FEAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FEAST_1.12.0.tar.gz
StartedAt: 2024-07-15 19:23:54 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 19:27:50 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 235.6 seconds
RetCode: 0
Status:   OK  
CheckDir: FEAST.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FEAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FEAST_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FEAST.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.5Mb
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/FEAST.Rcheck/00check.log’
for details.


Installation output

FEAST.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FEAST
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘FEAST’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cal_3_metrics.c -o cal_3_metrics.o
cal_3_metrics.c:42:22: warning: variable 'ni_2' set but not used [-Wunused-but-set-variable]
    double *nc, *nr, ni_2, n_j2, nt, nij_2;
                     ^
cal_3_metrics.c:42:28: warning: variable 'n_j2' set but not used [-Wunused-but-set-variable]
    double *nc, *nr, ni_2, n_j2, nt, nij_2;
                           ^
cal_3_metrics.c:42:34: warning: variable 'nt' set but not used [-Wunused-but-set-variable]
    double *nc, *nr, ni_2, n_j2, nt, nij_2;
                                 ^
cal_3_metrics.c:42:38: warning: variable 'nij_2' set but not used [-Wunused-but-set-variable]
    double *nc, *nr, ni_2, n_j2, nt, nij_2;
                                     ^
4 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o FEAST.so cal_3_metrics.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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
Consensus2.3980.0332.434
FEAST1.3630.0121.376
FEAST_fast2.8190.0292.848
Norm_Y0.2540.0230.276
Select_Model_short_SC31.4040.0171.420
Select_Model_short_TSCAN1.3700.0241.393
TSCAN_Clust0.0020.0030.004
Visual_Rslt1.6390.0491.687
Y0.1450.0120.159
align_CellType0.0010.0000.001
cal_F20.4830.3240.808
cal_MSE0.4560.0280.484
eval_Cluster0.0070.0000.007
process_Y1.0580.0221.083
setUp_BPPARAM0.8810.0040.886
trueclass0.0030.0030.006