Robert Castelo
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/qpgraph |
| git_branch: devel |
| git_last_commit: f681a6c |
| git_last_commit_date: 2023-10-24 09:41:20 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:41:09 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1624/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qpgraph 2.37.0 (landing page) Robert Castelo
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: qpgraph |
| Version: 2.37.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings qpgraph_2.37.0.tar.gz |
| StartedAt: 2024-03-28 08:36:20 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 08:43:02 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 401.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: qpgraph.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings qpgraph_2.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/qpgraph.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.37.0’
* 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 ... WARNING
Found the following significant warnings:
qpgraph.c:6149:19: warning: too many arguments for format [-Wformat-extra-args]
qpgraph.c:6827:19: warning: too many arguments for format [-Wformat-extra-args]
qpgraph.c:7090:44: warning: unknown conversion type character ‘)’ in format [-Wformat=]
qpgraph.c:7115:21: warning: too many arguments for format [-Wformat-extra-args]
qpgraph.c:7373:21: warning: too many arguments for format [-Wformat-extra-args]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/qpgraph.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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 ... 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 ... 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-3.19-bioc/meat/qpgraph.Rcheck/00check.log’
for details.
qpgraph.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL qpgraph
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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... 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: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/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
qpgraph.c: In function ‘qp_clique_number_lb’:
qpgraph.c:6149:19: warning: too many arguments for format [-Wformat-extra-args]
6149 | Rprintf(".",pct);
| ^~~
qpgraph.c: In function ‘qp_fast_update_cliques_removing’:
qpgraph.c:6827:19: warning: too many arguments for format [-Wformat-extra-args]
6827 | Rprintf(".",pct);
| ^~~
qpgraph.c: In function ‘qp_fast_ipf’:
qpgraph.c:7090:44: warning: unknown conversion type character ‘)’ in format [-Wformat=]
7090 | Rprintf("Iterating through cliques (%): ");
| ^
qpgraph.c:7115:21: warning: too many arguments for format [-Wformat-extra-args]
7115 | Rprintf(".",pct);
| ^~~
qpgraph.c: In function ‘qp_fast_htf’:
qpgraph.c:7373:21: warning: too many arguments for format [-Wformat-extra-args]
7373 | Rprintf(".",pct);
| ^~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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)
qpgraph.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-03-19 r86153) -- "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 -- Thu Mar 28 08:42:57 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
30.757 0.707 31.509
qpgraph.Rcheck/qpgraph-Ex.timings
| name | user | system | elapsed | |
| EcoliOxygen | 0.002 | 0.000 | 0.002 | |
| filterCollinearities | 1.063 | 0.040 | 1.103 | |
| qpAllCItests | 0.105 | 0.004 | 0.109 | |
| qpAnyGraph | 0.096 | 0.004 | 0.100 | |
| qpAvgNrr | 1.424 | 0.004 | 1.431 | |
| qpBoundary | 0.337 | 0.008 | 0.346 | |
| qpCItest | 0.102 | 0.032 | 0.135 | |
| qpClique | 0.327 | 0.005 | 0.333 | |
| qpCliqueNumber | 0.381 | 0.013 | 0.395 | |
| qpCov | 0.082 | 0.000 | 0.082 | |
| qpEdgeNrr | 0.116 | 0.000 | 0.116 | |
| qpFunctionalCoherence | 0 | 0 | 0 | |
| qpG2Sigma | 0.006 | 0.000 | 0.006 | |
| qpGenNrr | 0.570 | 0.000 | 0.571 | |
| qpGetCliques | 0.276 | 0.004 | 0.281 | |
| qpGraphDensity | 0.316 | 0.000 | 0.317 | |
| qpHTF | 0.171 | 0.000 | 0.171 | |
| qpHist | 0.234 | 0.000 | 0.235 | |
| qpIPF | 0.138 | 0.000 | 0.138 | |
| qpK2ParCor | 0.05 | 0.00 | 0.05 | |
| qpNrr | 0.168 | 0.000 | 0.168 | |
| qpPAC | 0.231 | 0.004 | 0.235 | |
| qpPCC | 0.089 | 0.004 | 0.093 | |
| qpPRscoreThreshold | 0.158 | 0.000 | 0.159 | |
| qpPathWeight | 0.076 | 0.007 | 0.083 | |
| qpPlotMap | 0.033 | 0.001 | 0.033 | |
| qpPlotNetwork | 0 | 0 | 0 | |
| qpPrecisionRecall | 0.213 | 0.004 | 0.217 | |
| qpRndGraph | 0.008 | 0.000 | 0.008 | |
| qpRndWishart | 0.005 | 0.003 | 0.008 | |
| qpTopPairs | 0.003 | 0.000 | 0.003 | |
| qpUnifRndAssociation | 0.004 | 0.000 | 0.004 | |
| qpUpdateCliquesRemoving | 0.001 | 0.000 | 0.000 | |