Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2023-01-31 11:09:23 -0500 (Tue, 31 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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

CHECK results for FEAST on lconway


To the developers/maintainers of the FEAST package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 669/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FEAST 1.6.0  (landing page)
Kenong Su
Snapshot Date: 2023-01-30 14:00:05 -0500 (Mon, 30 Jan 2023)
git_url: https://git.bioconductor.org/packages/FEAST
git_branch: RELEASE_3_16
git_last_commit: 7d99b9d
git_last_commit_date: 2022-11-01 11:24:45 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FEAST
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2023-01-30 20:20:46 -0500 (Mon, 30 Jan 2023)
EndedAt: 2023-01-30 20:23:52 -0500 (Mon, 30 Jan 2023)
EllapsedTime: 185.4 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/FEAST.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FEAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FEAST’ version ‘1.6.0’
* 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
* 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 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 ... 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 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
  ‘/Users/biocbuild/bbs-3.16-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
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘FEAST’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.2/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
Consensus1.0680.0331.107
FEAST1.0240.0071.032
FEAST_fast1.5110.0481.564
Norm_Y0.1660.0040.172
Select_Model_short_SC31.0010.0161.021
Select_Model_short_TSCAN0.3850.0060.391
TSCAN_Clust0.0010.0010.002
Visual_Rslt0.7130.0240.743
Y0.0730.0020.074
align_CellType0.0010.0000.001
cal_F20.8600.2431.106
cal_MSE0.2200.0160.237
eval_Cluster0.0030.0000.004
process_Y0.1020.0100.114
setUp_BPPARAM0.0050.0000.006
trueclass0.0020.0010.003