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This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1805/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SANTA 2.36.0  (landing page)
Alex Cornish
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SANTA
git_branch: RELEASE_3_17
git_last_commit: d0a3108
git_last_commit_date: 2023-04-25 11:26:42 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for SANTA on kjohnson2


To the developers/maintainers of the SANTA package:
- 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: SANTA
Version: 2.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SANTA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SANTA_2.36.0.tar.gz
StartedAt: 2023-10-18 21:24:04 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 21:26:13 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 128.5 seconds
RetCode: 0
Status:   OK  
CheckDir: SANTA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SANTA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SANTA_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SANTA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SANTA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SANTA’ version ‘2.36.0’
* 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 ‘SANTA’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SANTA.Rcheck/00check.log’
for details.



Installation output

SANTA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘SANTA’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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 computenetK_fewzeros.c -o computenetK_fewzeros.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c computenodeAUK.c -o computenodeAUK.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c computeweights.c -o computeweights.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SANTA.so computenetK_fewzeros.o computenodeAUK.o computeweights.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-SANTA/00new/SANTA/libs
** 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
** 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 (SANTA)

Tests output

SANTA.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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.

> BiocGenerics:::testPackage("SANTA")

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... computing graph distance bins... computing graph distance bins... done
no edge attribute with name 'distance' found so all edge distances set to 1
computing graph distance matrix... done
no edge attribute with name 'distance' found so all edge distances set to 1
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
Warning: stack imbalance in '<-', 25 then 26
Warning: stack imbalance in '<-', 26 then 27
Warning: stack imbalance in '{', 21 then 23
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done


RUNIT TEST PROTOCOL -- Wed Oct 18 21:25:55 2023 
*********************************************** 
Number of test functions: 13 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SANTA RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In SANTA:::CheckAttributes(g, vertex.attr = "vertex.attr") :
  non-numeric/non-logical vertex weights found and converted to numerals
2: In SANTA:::CheckAttributes(g, vertex.attr = "vertex.attr") :
  NAs introduced by coercion
3: In SpreadHits(g, h = 2, clusters = 3, distance.cutoff = 20, lambda = 10,  :
  seed vertices not identified
> 
> proc.time()
   user  system elapsed 
  6.467   1.253  13.518 

Example timings

SANTA.Rcheck/SANTA-Ex.timings

nameusersystemelapsed
BinGraph0.1430.0170.285
CreateGrid0.0310.0030.060
DistGraph0.0230.0040.052
GraphDiffusion0.0110.0020.026
GraphMFPT0.0410.0050.085
Knet0.0620.0070.119
Knode0.0130.0020.023
SANTA.data0.0180.0040.038
SpreadHits0.0240.0030.045
plot.Knet0.0340.0040.072