Robert Castelo
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/qpgraph |
| git_branch: RELEASE_3_19 |
| git_last_commit: e551606 |
| git_last_commit_date: 2024-04-30 10:19:23 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:42 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 1645/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qpgraph 2.38.0 (landing page) Robert Castelo
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | 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: 2.38.0 |
| 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_2.38.0.tar.gz |
| StartedAt: 2024-05-07 00:06:18 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 00:08:12 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 114.3 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_2.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/qpgraph.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.38.0’
* 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:
cliquer.c:13:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
cliquer.c:13:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
./set.h:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
./set.h:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
graph.c:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
graph.c:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
reorder.c:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
reorder.c:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/qpgraph.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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-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/4.4-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-darwin22.6.0
checking host system type... aarch64-apple-darwin22.6.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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
cliquer.c:13:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
cliquer.c:13:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
./set.h:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
4 warnings 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 graph.c -o graph.o
graph.c:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
graph.c:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
./set.h:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
4 warnings 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 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
^
In file included from qpgraph.c:39:
In file included from ./cliquer.h:7:
./set.h:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
./set.h:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
qpgraph.c:5176:10: warning: variable 'avgpr' set but not used [-Wunused-but-set-variable]
double avgpr = 0;
^
4 warnings 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
reorder.c:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
reorder.c:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
./set.h:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
* Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
^
4 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -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
installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 -- Tue May 7 00:08:07 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
5.090 0.131 5.220
qpgraph.Rcheck/qpgraph-Ex.timings
| name | user | system | elapsed | |
| EcoliOxygen | 0.001 | 0.001 | 0.002 | |
| filterCollinearities | 0.018 | 0.002 | 0.019 | |
| qpAllCItests | 0.023 | 0.002 | 0.025 | |
| qpAnyGraph | 0.019 | 0.001 | 0.021 | |
| qpAvgNrr | 0.360 | 0.001 | 0.361 | |
| qpBoundary | 0.075 | 0.001 | 0.076 | |
| qpCItest | 0.026 | 0.003 | 0.028 | |
| qpClique | 0.072 | 0.001 | 0.073 | |
| qpCliqueNumber | 0.101 | 0.004 | 0.105 | |
| qpCov | 0.018 | 0.001 | 0.019 | |
| qpEdgeNrr | 0.018 | 0.001 | 0.018 | |
| qpFunctionalCoherence | 0 | 0 | 0 | |
| qpG2Sigma | 0.001 | 0.000 | 0.002 | |
| qpGenNrr | 0.132 | 0.001 | 0.132 | |
| qpGetCliques | 0.105 | 0.003 | 0.107 | |
| qpGraphDensity | 0.075 | 0.000 | 0.076 | |
| qpHTF | 0.021 | 0.001 | 0.022 | |
| qpHist | 0.058 | 0.001 | 0.059 | |
| qpIPF | 0.034 | 0.002 | 0.036 | |
| qpK2ParCor | 0.011 | 0.001 | 0.013 | |
| qpNrr | 0.040 | 0.001 | 0.041 | |
| qpPAC | 0.088 | 0.001 | 0.090 | |
| qpPCC | 0.021 | 0.001 | 0.022 | |
| qpPRscoreThreshold | 0.034 | 0.001 | 0.034 | |
| qpPathWeight | 0.015 | 0.000 | 0.015 | |
| qpPlotMap | 0.041 | 0.004 | 0.045 | |
| qpPlotNetwork | 0 | 0 | 0 | |
| qpPrecisionRecall | 0.054 | 0.001 | 0.055 | |
| qpRndGraph | 0.001 | 0.000 | 0.002 | |
| qpRndWishart | 0.002 | 0.001 | 0.002 | |
| qpTopPairs | 0.001 | 0.000 | 0.001 | |
| qpUnifRndAssociation | 0.001 | 0.000 | 0.001 | |
| qpUpdateCliquesRemoving | 0 | 0 | 0 | |