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This page was generated on 2022-07-01 12:05:44 -0400 (Fri, 01 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 qpgraph on nebbiolo1


To the developers/maintainers of the qpgraph package:
- Please 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 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 1539/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.30.0  (landing page)
Robert Castelo
Snapshot Date: 2022-06-30 13:55:04 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/qpgraph
git_branch: RELEASE_3_15
git_last_commit: 58c292b
git_last_commit_date: 2022-04-26 11:02:28 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: qpgraph
Version: 2.30.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings qpgraph_2.30.0.tar.gz
StartedAt: 2022-06-30 21:27:01 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 21:31:34 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 273.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: qpgraph.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings qpgraph_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/qpgraph.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.30.0’
* 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
* 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 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 ... WARNING
Non-portable flags in variable 'PKG_CFLAGS':
  -Werror=implicit-function-declaration
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/qpgraph.Rcheck/00check.log’
for details.



Installation output

qpgraph.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL qpgraph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include  -g -O2 -Wall -Wall -pedantic -Werror=implicit-function-declaration -fpic  -g -O2  -Wall -c cliquer.c -o cliquer.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include  -g -O2 -Wall -Wall -pedantic -Werror=implicit-function-declaration -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include  -g -O2 -Wall -Wall -pedantic -Werror=implicit-function-declaration -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-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include  -g -O2 -Wall -Wall -pedantic -Werror=implicit-function-declaration -fpic  -g -O2  -Wall -c reorder.c -o reorder.o
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 Jun 30 21:31:29 2022 
*********************************************** 
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 
 14.201   0.579  14.766 

Example timings

qpgraph.Rcheck/qpgraph-Ex.timings

nameusersystemelapsed
EcoliOxygen0.0000.0030.003
filterCollinearities0.1140.0040.118
qpAllCItests0.2660.0150.282
qpAnyGraph0.0980.0000.099
qpAvgNrr1.2490.0041.253
qpBoundary0.2390.0000.238
qpCItest0.0880.0000.088
qpClique0.2310.0120.243
qpCliqueNumber1.3200.0881.407
qpCov0.0630.0070.071
qpEdgeNrr0.0530.0100.063
qpFunctionalCoherence0.0000.0010.001
qpG2Sigma0.0080.0020.009
qpGenNrr0.4110.0020.414
qpGetCliques0.2470.0040.250
qpGraphDensity0.2510.0000.252
qpHTF0.0640.0020.066
qpHist0.1700.0080.179
qpIPF0.1120.0020.114
qpK2ParCor0.0470.0000.047
qpNrr0.1080.0000.109
qpPAC0.2080.0040.213
qpPCC0.0820.0040.086
qpPRscoreThreshold0.1150.0000.115
qpPathWeight0.0500.0000.051
qpPlotMap0.0260.0040.029
qpPlotNetwork0.0010.0000.000
qpPrecisionRecall0.1640.0040.168
qpRndGraph0.0110.0000.011
qpRndWishart0.0100.0000.011
qpTopPairs0.0190.0040.023
qpUnifRndAssociation0.0030.0000.003
qpUpdateCliquesRemoving0.0000.0000.001