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This page was generated on 2025-08-06 13:55 -0400 (Wed, 06 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4813
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1642/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.43.1  (landing page)
Robert Castelo
Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 Aug 2025)
git_url: https://git.bioconductor.org/packages/qpgraph
git_branch: devel
git_last_commit: a352aa4
git_last_commit_date: 2025-07-23 14:16:18 -0400 (Wed, 23 Jul 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


CHECK results for qpgraph on lconway

To the developers/maintainers of the qpgraph package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qpgraph.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: qpgraph
Version: 2.43.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qpgraph_2.43.1.tar.gz
StartedAt: 2025-08-05 23:12:05 -0400 (Tue, 05 Aug 2025)
EndedAt: 2025-08-05 23:17:42 -0400 (Tue, 05 Aug 2025)
EllapsedTime: 336.2 seconds
RetCode: 0
Status:   OK  
CheckDir: qpgraph.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qpgraph_2.43.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/qpgraph.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.43.1’
* 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 ‘qpgraph’ 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 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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 ... 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-3.22-bioc/meat/qpgraph.Rcheck/00check.log’
for details.


Installation output

qpgraph.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘qpgraph’ ...
** this is package ‘qpgraph’ version ‘2.43.1’
** using staged installation
checking for gcc... clang -arch x86_64
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ANSI C... none needed
checking build system type... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_FC_LEN_T  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC  -falign-functions=64 -Wall -g -O2  -c cliquer.c -o cliquer.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_FC_LEN_T  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC  -falign-functions=64 -Wall -g -O2  -c graph.c -o graph.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_FC_LEN_T  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC  -falign-functions=64 -Wall -g -O2  -c qpgraph.c -o qpgraph.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_FC_LEN_T  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC  -falign-functions=64 -Wall -g -O2  -c reorder.c -o reorder.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-qpgraph/00new/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘det’ from package ‘Matrix’ in package ‘qpgraph’
** 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 (qpgraph)

Tests output

qpgraph.Rcheck/tests/runTests.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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("qpgraph")
Using t tests for zero partial regression coefficients.
Using exact likelihood ratio tests.


RUNIT TEST PROTOCOL -- Tue Aug  5 23:17:26 2025 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
qpgraph RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 16.144   0.638  16.889 

Example timings

qpgraph.Rcheck/qpgraph-Ex.timings

nameusersystemelapsed
EcoliOxygen0.0010.0010.003
filterCollinearities0.0780.0040.083
qpAllCItests0.0740.0040.078
qpAnyGraph0.1020.0090.111
qpAvgNrr1.1610.0101.178
qpBoundary0.3270.0070.340
qpCItest0.1060.0120.120
qpClique0.3290.0070.338
qpCliqueNumber0.3230.0180.343
qpCov0.0820.0060.091
qpEdgeNrr0.0810.0010.083
qpFunctionalCoherence0.0000.0000.001
qpG2Sigma0.0070.0010.007
qpGenNrr0.5220.0050.528
qpGetCliques0.3100.0110.323
qpGraphDensity0.2780.0030.281
qpHTF0.0950.0060.101
qpHist0.2010.0030.205
qpIPF0.1180.0060.124
qpK2ParCor0.0590.0050.065
qpNrr0.1600.0020.162
qpPAC0.2640.0050.272
qpPCC0.0970.0050.104
qpPRscoreThreshold0.1660.0020.169
qpPathWeight0.0700.0010.072
qpPlotMap0.0270.0050.033
qpPlotNetwork000
qpPrecisionRecall0.2140.0080.223
qpRndGraph0.0040.0010.004
qpRndWishart0.0050.0010.006
qpTopPairs0.0010.0000.002
qpUnifRndAssociation0.0020.0000.003
qpUpdateCliquesRemoving0.0000.0000.001