Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:36:55 -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. |
Package: qpgraph |
Version: 2.37.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings qpgraph_2.37.0.tar.gz |
StartedAt: 2024-03-28 01:43:32 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 01:49:58 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 386.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: qpgraph.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings qpgraph_2.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/qpgraph.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 ... 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 re-building of vignette outputs ... OK * 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
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL qpgraph ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/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) (2024-03-18 r86148) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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 01:48:25 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 14.012 0.672 14.676
qpgraph.Rcheck/qpgraph-Ex.timings
name | user | system | elapsed | |
EcoliOxygen | 0.003 | 0.000 | 0.002 | |
filterCollinearities | 0.815 | 0.068 | 0.884 | |
qpAllCItests | 0.074 | 0.000 | 0.074 | |
qpAnyGraph | 0.064 | 0.000 | 0.064 | |
qpAvgNrr | 1.257 | 0.000 | 1.257 | |
qpBoundary | 0.236 | 0.016 | 0.252 | |
qpCItest | 0.079 | 0.015 | 0.094 | |
qpClique | 0.232 | 0.008 | 0.240 | |
qpCliqueNumber | 0.305 | 0.020 | 0.325 | |
qpCov | 0.049 | 0.000 | 0.050 | |
qpEdgeNrr | 0.058 | 0.004 | 0.063 | |
qpFunctionalCoherence | 0.000 | 0.000 | 0.001 | |
qpG2Sigma | 0.005 | 0.000 | 0.005 | |
qpGenNrr | 0.407 | 0.000 | 0.406 | |
qpGetCliques | 0.242 | 0.000 | 0.243 | |
qpGraphDensity | 0.222 | 0.000 | 0.222 | |
qpHTF | 0.092 | 0.004 | 0.097 | |
qpHist | 0.164 | 0.012 | 0.176 | |
qpIPF | 0.092 | 0.008 | 0.101 | |
qpK2ParCor | 0.03 | 0.00 | 0.03 | |
qpNrr | 0.116 | 0.000 | 0.116 | |
qpPAC | 0.227 | 0.008 | 0.235 | |
qpPCC | 0.049 | 0.008 | 0.059 | |
qpPRscoreThreshold | 0.108 | 0.002 | 0.110 | |
qpPathWeight | 0.056 | 0.000 | 0.055 | |
qpPlotMap | 0.019 | 0.008 | 0.026 | |
qpPlotNetwork | 0.001 | 0.000 | 0.000 | |
qpPrecisionRecall | 0.148 | 0.004 | 0.153 | |
qpRndGraph | 0.005 | 0.001 | 0.006 | |
qpRndWishart | 0.004 | 0.003 | 0.007 | |
qpTopPairs | 0.000 | 0.002 | 0.003 | |
qpUnifRndAssociation | 0.002 | 0.001 | 0.002 | |
qpUpdateCliquesRemoving | 0 | 0 | 0 | |