##############################################################################
##############################################################################
###
### 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_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/qpgraph.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.40.0’
* 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:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  ./set.h:9:52: 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:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
  reorder.c:9:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/qpgraph.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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-3.20-bioc/meat/qpgraph.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qpgraph
###
##############################################################################
##############################################################################


* 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-1500.0.40.1)’
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:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
./set.h:9:52: 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:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
./set.h:9:52: 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
In file included from qpgraph.c:41:
In file included from ./cliquer.h:7:
./set.h:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
./set.h:9:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                                      ^
qpgraph.c:5154:10: warning: variable 'avgpr' set but not used [-Wunused-but-set-variable]
  double avgpr = 0;
         ^
3 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:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
reorder.c:9:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                                      ^
In file included from reorder.c:16:
In file included from ./reorder.h:5:
./set.h:9:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
./set.h:9:52: 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)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

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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 -- Sat Dec 21 05:44:59 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 
 16.879   0.485  17.356