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This page was generated on 2025-08-12 12:07 -0400 (Tue, 12 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 276/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CARDspa 1.1.0  (landing page)
Jing Fu
Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/CARDspa
git_branch: devel
git_last_commit: 8b194bb
git_last_commit_date: 2025-04-15 13:48:01 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CARDspa on palomino8

To the developers/maintainers of the CARDspa package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CARDspa.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: CARDspa
Version: 1.1.0
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CARDspa.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings CARDspa_1.1.0.tar.gz
StartedAt: 2025-08-12 00:18:12 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 00:27:38 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 565.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CARDspa.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CARDspa.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings CARDspa_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/CARDspa.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CARDspa/DESCRIPTION' ... OK
* this is package 'CARDspa' version '1.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 'CARDspa' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 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 whether startup messages can be suppressed ... 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/CARDspa/libs/x64/CARDspa.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
CARD_SCMapping          37.52   8.19   75.69
CARD_visualize_pie      15.18   0.46   15.61
CARD_refFree            11.31   0.52   11.82
CARD_deconvolution       8.96   0.42   10.10
CARD_visualize_prop      9.01   0.36    9.37
CARD_visualize_gene      8.58   0.39    8.98
CARD_imputation          7.55   0.50    8.29
CARD_visualize_prop_2CT  7.70   0.28    7.98
CARD_visualize_Cor       7.53   0.23    7.80
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.22-bioc/meat/CARDspa.Rcheck/00check.log'
for details.


Installation output

CARDspa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL CARDspa
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'CARDspa' ...
** this is package 'CARDspa' version '1.1.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c CARDfree.cpp -o CARDfree.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c CARDref.cpp -o CARDref.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -s -static-libgcc -o CARDspa.dll tmp.def CARDfree.o CARDref.o RcppExports.o -fopenmp -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-CARDspa/00new/CARDspa/libs/x64
** R
** data
** 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 (CARDspa)

Tests output

CARDspa.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CARDspa)
> test_check("CARDspa")
## QC on scRNASeq dataset! ...

## QC on spatially-resolved dataset! ...

## create reference matrix from scRNASeq...

## Select Informative Genes! ...

## Deconvolution Starts! ...

## Deconvolution Finish! ...

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
  73.03   11.67   83.57 

Example timings

CARDspa.Rcheck/CARDspa-Ex.timings

nameusersystemelapsed
CARD_SCMapping37.52 8.1975.69
CARD_deconvolution 8.96 0.4210.10
CARD_imputation7.550.508.29
CARD_refFree11.31 0.5211.82
CARD_visualize_Cor7.530.237.80
CARD_visualize_gene8.580.398.98
CARD_visualize_pie15.18 0.4615.61
CARD_visualize_prop9.010.369.37
CARD_visualize_prop_2CT7.700.287.98