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) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:48 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (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 | ||||
|
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. |
| Package 1499/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qpgraph 2.28.2 (landing page) Robert Castelo
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: qpgraph |
| Version: 2.28.2 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings qpgraph_2.28.2.tar.gz |
| StartedAt: 2022-04-12 08:53:18 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 08:57:29 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 251.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: qpgraph.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings qpgraph_2.28.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/qpgraph.Rcheck’ * using R version 4.1.3 (2022-03-10) * 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 ‘2.28.2’ * 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 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-3.14-bioc/meat/qpgraph.Rcheck/00check.log’ for details.
qpgraph.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL qpgraph
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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
‘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)
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-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 -- Tue Apr 12 08:57:25 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
13.684 0.649 14.317
qpgraph.Rcheck/qpgraph-Ex.timings
| name | user | system | elapsed | |
| EcoliOxygen | 0.002 | 0.000 | 0.002 | |
| filterCollinearities | 0.106 | 0.012 | 0.118 | |
| qpAllCItests | 0.282 | 0.000 | 0.282 | |
| qpAnyGraph | 0.091 | 0.000 | 0.091 | |
| qpAvgNrr | 1.244 | 0.012 | 1.256 | |
| qpBoundary | 1.093 | 0.060 | 1.153 | |
| qpCItest | 0.086 | 0.004 | 0.090 | |
| qpClique | 0.264 | 0.004 | 0.268 | |
| qpCliqueNumber | 0.293 | 0.028 | 0.321 | |
| qpCov | 0.052 | 0.008 | 0.060 | |
| qpEdgeNrr | 0.068 | 0.000 | 0.068 | |
| qpFunctionalCoherence | 0 | 0 | 0 | |
| qpG2Sigma | 0.01 | 0.00 | 0.01 | |
| qpGenNrr | 0.437 | 0.004 | 0.441 | |
| qpGetCliques | 0.25 | 0.00 | 0.25 | |
| qpGraphDensity | 0.217 | 0.004 | 0.221 | |
| qpHTF | 0.076 | 0.012 | 0.088 | |
| qpHist | 0.176 | 0.000 | 0.176 | |
| qpIPF | 0.097 | 0.004 | 0.101 | |
| qpK2ParCor | 0.041 | 0.000 | 0.041 | |
| qpNrr | 0.11 | 0.00 | 0.11 | |
| qpPAC | 0.212 | 0.008 | 0.218 | |
| qpPCC | 0.068 | 0.004 | 0.072 | |
| qpPRscoreThreshold | 0.116 | 0.000 | 0.116 | |
| qpPathWeight | 0.049 | 0.004 | 0.053 | |
| qpPlotMap | 0.036 | 0.008 | 0.044 | |
| qpPlotNetwork | 0 | 0 | 0 | |
| qpPrecisionRecall | 0.152 | 0.004 | 0.156 | |
| qpRndGraph | 0.009 | 0.000 | 0.009 | |
| qpRndWishart | 0.008 | 0.000 | 0.008 | |
| qpTopPairs | 0.000 | 0.003 | 0.002 | |
| qpUnifRndAssociation | 0.001 | 0.001 | 0.002 | |
| qpUpdateCliquesRemoving | 0 | 0 | 0 | |