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 11:39:50 -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: /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_2.37.0.tar.gz |
| StartedAt: 2024-03-27 23:22:28 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 23:28:31 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 362.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: qpgraph.Rcheck |
| Warnings: 1 |
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### 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_2.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/qpgraph.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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:6149:23: warning: data argument not used by format string [-Wformat-extra-args]
qpgraph.c:6827:23: warning: data argument not used by format string [-Wformat-extra-args]
qpgraph.c:7115:25: warning: data argument not used by format string [-Wformat-extra-args]
qpgraph.c:7373:25: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/qpgraph.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 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 ... 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-3.19-bioc/meat/qpgraph.Rcheck/00check.log’
for details.
qpgraph.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qpgraph
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘qpgraph’ ...
** using staged installation
checking for gcc... clang -arch x86_64
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 clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ANSI C... none needed
checking build system type... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_FC_LEN_T -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c cliquer.c -o cliquer.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_FC_LEN_T -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c graph.c -o graph.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_FC_LEN_T -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -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
^
qpgraph.c:6149:23: warning: data argument not used by format string [-Wformat-extra-args]
Rprintf(".",pct);
~~~ ^
qpgraph.c:6827:23: warning: data argument not used by format string [-Wformat-extra-args]
Rprintf(".",pct);
~~~ ^
qpgraph.c:7090:44: warning: invalid conversion specifier ')' [-Wformat-invalid-specifier]
Rprintf("Iterating through cliques (%): ");
~^
qpgraph.c:7115:25: warning: data argument not used by format string [-Wformat-extra-args]
Rprintf(".",pct);
~~~ ^
qpgraph.c:7373:25: warning: data argument not used by format string [-Wformat-extra-args]
Rprintf(".",pct);
~~~ ^
6 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DUSE_FC_LEN_T -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c reorder.c -o reorder.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/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
** 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-apple-darwin20
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 -- Wed Mar 27 23:28:14 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
18.036 0.813 19.072
qpgraph.Rcheck/qpgraph-Ex.timings
| name | user | system | elapsed | |
| EcoliOxygen | 0.003 | 0.002 | 0.004 | |
| filterCollinearities | 0.069 | 0.008 | 0.080 | |
| qpAllCItests | 0.091 | 0.009 | 0.103 | |
| qpAnyGraph | 0.093 | 0.009 | 0.103 | |
| qpAvgNrr | 1.291 | 0.022 | 1.331 | |
| qpBoundary | 0.327 | 0.010 | 0.341 | |
| qpCItest | 0.113 | 0.014 | 0.130 | |
| qpClique | 0.348 | 0.009 | 0.362 | |
| qpCliqueNumber | 0.368 | 0.020 | 0.393 | |
| qpCov | 0.080 | 0.005 | 0.087 | |
| qpEdgeNrr | 0.079 | 0.002 | 0.083 | |
| qpFunctionalCoherence | 0.000 | 0.001 | 0.001 | |
| qpG2Sigma | 0.006 | 0.001 | 0.007 | |
| qpGenNrr | 0.544 | 0.008 | 0.558 | |
| qpGetCliques | 0.314 | 0.012 | 0.332 | |
| qpGraphDensity | 0.302 | 0.005 | 0.311 | |
| qpHTF | 0.086 | 0.006 | 0.093 | |
| qpHist | 0.201 | 0.004 | 0.208 | |
| qpIPF | 0.123 | 0.006 | 0.130 | |
| qpK2ParCor | 0.048 | 0.005 | 0.054 | |
| qpNrr | 0.160 | 0.004 | 0.166 | |
| qpPAC | 0.300 | 0.011 | 0.313 | |
| qpPCC | 0.083 | 0.005 | 0.089 | |
| qpPRscoreThreshold | 0.154 | 0.003 | 0.158 | |
| qpPathWeight | 0.059 | 0.002 | 0.061 | |
| qpPlotMap | 0.044 | 0.006 | 0.051 | |
| qpPlotNetwork | 0 | 0 | 0 | |
| qpPrecisionRecall | 0.209 | 0.005 | 0.215 | |
| qpRndGraph | 0.004 | 0.000 | 0.004 | |
| qpRndWishart | 0.006 | 0.001 | 0.007 | |
| qpTopPairs | 0.003 | 0.000 | 0.003 | |
| qpUnifRndAssociation | 0.003 | 0.001 | 0.004 | |
| qpUpdateCliquesRemoving | 0 | 0 | 0 | |