Robert Castelo
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/qpgraph |
| git_branch: RELEASE_3_17 |
| git_last_commit: 521abb0 |
| git_last_commit_date: 2023-05-01 20:11:38 -0400 (Mon, 01 May 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1599/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qpgraph 2.34.2 (landing page) Robert Castelo
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the qpgraph package: - 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: 2.34.2 |
| 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_2.34.2.tar.gz |
| StartedAt: 2023-10-18 16:47:54 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 16:56:32 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 517.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qpgraph.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_2.34.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/qpgraph.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.34.2’
* 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
* 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 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 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 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 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/library’
* installing *source* package ‘qpgraph’ ...
** using staged installation
checking for gcc... clang -arch arm64
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 arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ANSI C... none needed
checking build system type... aarch64-apple-darwin21.6.0
checking host system type... aarch64-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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c cliquer.c -o cliquer.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c graph.c -o graph.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T -I/opt/R/arm64/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
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC -falign-functions=64 -Wall -g -O2 -c reorder.c -o reorder.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 -- Wed Oct 18 16:56:12 2023
***********************************************
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
16.397 0.594 26.166
qpgraph.Rcheck/qpgraph-Ex.timings
| name | user | system | elapsed | |
| EcoliOxygen | 0.002 | 0.001 | 0.006 | |
| filterCollinearities | 0.198 | 0.004 | 0.254 | |
| qpAllCItests | 0.098 | 0.004 | 0.131 | |
| qpAnyGraph | 0.099 | 0.006 | 0.133 | |
| qpAvgNrr | 1.372 | 0.012 | 1.772 | |
| qpBoundary | 0.329 | 0.006 | 0.443 | |
| qpCItest | 0.101 | 0.008 | 0.147 | |
| qpClique | 1.044 | 0.009 | 1.527 | |
| qpCliqueNumber | 0.359 | 0.010 | 0.539 | |
| qpCov | 0.088 | 0.006 | 0.135 | |
| qpEdgeNrr | 0.076 | 0.003 | 0.118 | |
| qpFunctionalCoherence | 0.000 | 0.001 | 0.001 | |
| qpG2Sigma | 0.006 | 0.001 | 0.012 | |
| qpGenNrr | 0.567 | 0.008 | 0.865 | |
| qpGetCliques | 0.295 | 0.007 | 0.449 | |
| qpGraphDensity | 0.306 | 0.003 | 0.452 | |
| qpHTF | 0.095 | 0.004 | 0.164 | |
| qpHist | 0.230 | 0.004 | 0.360 | |
| qpIPF | 0.132 | 0.005 | 0.211 | |
| qpK2ParCor | 0.055 | 0.003 | 0.088 | |
| qpNrr | 0.153 | 0.002 | 0.242 | |
| qpPAC | 0.302 | 0.006 | 0.470 | |
| qpPCC | 0.093 | 0.005 | 0.149 | |
| qpPRscoreThreshold | 0.144 | 0.003 | 0.226 | |
| qpPathWeight | 0.059 | 0.002 | 0.096 | |
| qpPlotMap | 0.025 | 0.003 | 0.040 | |
| qpPlotNetwork | 0 | 0 | 0 | |
| qpPrecisionRecall | 0.208 | 0.006 | 0.338 | |
| qpRndGraph | 0.004 | 0.001 | 0.009 | |
| qpRndWishart | 0.007 | 0.003 | 0.014 | |
| qpTopPairs | 0.002 | 0.001 | 0.007 | |
| qpUnifRndAssociation | 0.003 | 0.001 | 0.004 | |
| qpUpdateCliquesRemoving | 0.000 | 0.001 | 0.004 | |