Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOP[Q]RSTUVWXYZ

This page was generated on 2022-04-13 12:08:35 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 machv2


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 1499/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.28.2  (landing page)
Robert Castelo
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/qpgraph
git_branch: RELEASE_3_14
git_last_commit: b8a47b2
git_last_commit_date: 2022-04-05 03:47:17 -0400 (Tue, 05 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: qpgraph
Version: 2.28.2
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_2.28.2.tar.gz
StartedAt: 2022-04-12 17:10:45 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:17:50 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 425.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: qpgraph.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_2.28.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/qpgraph.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.28.2’
* 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 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 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
  ‘/Users/biocbuild/bbs-3.14-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/4.1/Resources/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-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include  -Wall -g -O2 -Wall -pedantic -Werror=implicit-function-declaration -fPIC  -Wall -g -O2  -c cliquer.c -o cliquer.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include  -Wall -g -O2 -Wall -pedantic -Werror=implicit-function-declaration -fPIC  -Wall -g -O2  -c graph.c -o graph.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include  -Wall -g -O2 -Wall -pedantic -Werror=implicit-function-declaration -fPIC  -Wall -g -O2  -c qpgraph.c -o qpgraph.o
qpgraph.c:24:9: warning: 'USE_FC_LEN_T' macro redefined [-Wmacro-redefined]
#define USE_FC_LEN_T
        ^
<command line>:2:9: note: previous definition is here
#define USE_FC_LEN_T 1
        ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DUSE_FC_LEN_T  -I/usr/local/include  -Wall -g -O2 -Wall -pedantic -Werror=implicit-function-declaration -fPIC  -Wall -g -O2  -c reorder.c -o reorder.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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
   ‘eQTLnetworks.Rnw’ 
   ‘qpTxRegNet.Rnw’ 
   ‘qpgraphSimulate.Rnw’ 
** 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 -- Tue Apr 12 17:17:39 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 
 22.512   0.746  23.257 

Example timings

qpgraph.Rcheck/qpgraph-Ex.timings

nameusersystemelapsed
EcoliOxygen0.0030.0010.004
filterCollinearities0.1670.0160.184
qpAllCItests0.3490.0100.360
qpAnyGraph0.1480.0060.154
qpAvgNrr2.0900.0062.098
qpBoundary1.4640.0051.468
qpCItest0.1560.0020.157
qpClique0.6600.0030.665
qpCliqueNumber0.4580.0230.481
qpCov0.1160.0110.127
qpEdgeNrr0.1360.0130.149
qpFunctionalCoherence0.0010.0010.001
qpG2Sigma0.0170.0030.020
qpGenNrr1.9370.0141.951
qpGetCliques0.2930.0060.299
qpGraphDensity0.5200.0030.522
qpHTF0.0930.0040.097
qpHist0.4440.0030.447
qpIPF0.1650.0060.170
qpK2ParCor0.0730.0040.078
qpNrr0.3410.0020.343
qpPAC0.4890.0090.498
qpPCC0.1330.0070.139
qpPRscoreThreshold0.3430.0020.344
qpPathWeight0.1130.0020.114
qpPlotMap0.0340.0070.041
qpPlotNetwork0.0010.0010.000
qpPrecisionRecall0.4140.0080.421
qpRndGraph0.0090.0010.010
qpRndWishart0.0150.0050.020
qpTopPairs0.0050.0010.006
qpUnifRndAssociation0.0040.0010.005
qpUpdateCliquesRemoving0.0000.0010.000