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This page was generated on 2024-02-29 11:36:14 -0500 (Thu, 29 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1626/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.36.0  (landing page)
Robert Castelo
Snapshot Date: 2024-02-28 14:05:05 -0500 (Wed, 28 Feb 2024)
git_url: https://git.bioconductor.org/packages/qpgraph
git_branch: RELEASE_3_18
git_last_commit: 08faf23
git_last_commit_date: 2023-10-24 09:41:20 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for qpgraph on nebbiolo2


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: 2.36.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings qpgraph_2.36.0.tar.gz
StartedAt: 2024-02-29 01:25:19 -0500 (Thu, 29 Feb 2024)
EndedAt: 2024-02-29 01:33:11 -0500 (Thu, 29 Feb 2024)
EllapsedTime: 472.5 seconds
RetCode: 0
Status:   OK  
CheckDir: qpgraph.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings qpgraph_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/qpgraph.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ 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 ‘qpgraph’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 loading without being on the library search path ... OK
* checking 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘eQTLnetworks.Rnw’... OK
  ‘qpTxRegNet.Rnw’... OK
  ‘qpgraphSimulate.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/qpgraph.Rcheck/00check.log’
for details.



Installation output

qpgraph.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL qpgraph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘qpgraph’ ...
** using staged installation
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c cliquer.c -o cliquer.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c qpgraph.c -o qpgraph.o
qpgraph.c:24: warning: "USE_FC_LEN_T" redefined
   24 | #define USE_FC_LEN_T
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c reorder.c -o reorder.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -llapack -L/home/biocbuild/bbs-3.18-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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("qpgraph")
Using t tests for zero partial regression coefficients.
Using exact likelihood ratio tests.


RUNIT TEST PROTOCOL -- Thu Feb 29 01:30:25 2024 
*********************************************** 
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 
  14.49    0.65   15.13 

Example timings

qpgraph.Rcheck/qpgraph-Ex.timings

nameusersystemelapsed
EcoliOxygen0.0020.0000.002
filterCollinearities0.0510.0120.063
qpAllCItests0.0990.0120.111
qpAnyGraph0.0610.0040.066
qpAvgNrr1.2370.0081.245
qpBoundary0.2400.0080.248
qpCItest0.0870.0000.087
qpClique0.2350.0000.236
qpCliqueNumber0.3110.0240.334
qpCov0.0490.0000.049
qpEdgeNrr0.0590.0000.059
qpFunctionalCoherence0.0010.0000.000
qpG2Sigma0.0040.0000.004
qpGenNrr0.4910.0040.496
qpGetCliques0.2460.0000.247
qpGraphDensity0.2190.0000.218
qpHTF0.0600.0000.061
qpHist0.1670.0000.166
qpIPF0.0930.0000.093
qpK2ParCor0.0310.0040.035
qpNrr0.1180.0040.122
qpPAC0.2440.0000.243
qpPCC0.0750.0000.075
qpPRscoreThreshold0.1180.0000.117
qpPathWeight0.0700.0160.085
qpPlotMap0.0260.0000.026
qpPlotNetwork000
qpPrecisionRecall0.1620.0000.162
qpRndGraph0.0060.0000.006
qpRndWishart0.0050.0000.006
qpTopPairs0.0000.0020.002
qpUnifRndAssociation0.0020.0010.002
qpUpdateCliquesRemoving000