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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1619/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.41.0  (landing page)
Robert Castelo
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/qpgraph
git_branch: devel
git_last_commit: 9b522d4
git_last_commit_date: 2024-10-29 09:30:44 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
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    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for qpgraph on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: qpgraph
Version: 2.41.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings qpgraph_2.41.0.tar.gz
StartedAt: 2024-12-23 10:59:43 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 11:06:33 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 409.4 seconds
RetCode: 0
Status:   OK  
CheckDir: qpgraph.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings qpgraph_2.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/qpgraph.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.41.0’
* 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: ‘aarch64-unknown-linux-gnu-gcc (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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  qpAllCItests.Rd: dspMatrix-class
  qpAvgNrr.Rd: dspMatrix-class
  qpCov.Rd: dspMatrix-class
  qpGenNrr.Rd: dspMatrix-class
  qpNrr.Rd: dspMatrix-class
  qpgraph-package.Rd: dspMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/qpgraph.Rcheck/00check.log’
for details.


Installation output

qpgraph.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL qpgraph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘qpgraph’ ...
** using staged installation
checking for gcc... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc accepts -g... yes
checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc option to accept ANSI C... none needed
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -Wall -pedantic -fPIC  -g -O2  -Wall -Werror=format-security -c cliquer.c -o cliquer.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -Wall -pedantic -fPIC  -g -O2  -Wall -Werror=format-security -c graph.c -o graph.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -Wall -pedantic -fPIC  -g -O2  -Wall -Werror=format-security -c qpgraph.c -o qpgraph.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -Wall -pedantic -fPIC  -g -O2  -Wall -Werror=format-security -c reorder.c -o reorder.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 -- Mon Dec 23 11:06:25 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 
 29.409   0.529  29.983 

Example timings

qpgraph.Rcheck/qpgraph-Ex.timings

nameusersystemelapsed
EcoliOxygen0.0020.0000.002
filterCollinearities0.0760.0040.080
qpAllCItests0.0960.0040.100
qpAnyGraph0.1050.0060.112
qpAvgNrr1.4080.0041.415
qpBoundary0.3400.0000.341
qpCItest0.1240.0080.132
qpClique0.3210.0040.326
qpCliqueNumber0.3840.0200.404
qpCov0.0910.0000.091
qpEdgeNrr0.0960.0080.104
qpFunctionalCoherence0.0000.0000.001
qpG2Sigma0.0060.0000.006
qpGenNrr0.5610.0000.561
qpGetCliques0.3450.0040.349
qpGraphDensity0.3080.0000.308
qpHTF0.1010.0040.106
qpHist0.2270.0000.227
qpIPF0.1370.0000.138
qpK2ParCor0.0620.0000.063
qpNrr0.160.000.16
qpPAC0.2130.0040.217
qpPCC0.0890.0000.088
qpPRscoreThreshold0.1510.0000.152
qpPathWeight0.0750.0000.075
qpPlotMap0.0390.0120.051
qpPlotNetwork000
qpPrecisionRecall0.2060.0030.209
qpRndGraph0.0070.0000.008
qpRndWishart0.0070.0000.007
qpTopPairs0.0030.0000.002
qpUnifRndAssociation0.0030.0000.003
qpUpdateCliquesRemoving000