Ernest Turro
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/bgx |
| git_branch: master |
| git_last_commit: 7c90642 |
| git_last_commit_date: 2021-10-26 11:51:11 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:00 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the bgx package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bgx.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 141/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bgx 1.61.0 (landing page) Ernest Turro
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: bgx |
| Version: 1.61.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bgx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings bgx_1.61.0.tar.gz |
| StartedAt: 2022-03-17 18:30:59 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:33:07 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 127.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bgx.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bgx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings bgx_1.61.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/bgx.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bgx/DESCRIPTION' ... OK
* this is package 'bgx' version '1.61.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'bgx' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'Rcpp'
All declared Imports should be used.
Packages in Depends field not imported from:
'Biobase' 'affy'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bgx: no visible global function definition for 'geneNames'
bgx: no visible global function definition for 'sampleNames'
bgx: no visible global function definition for 'new'
bgx: no visible global function definition for 'annotation'
bgx: no visible global function definition for 'description'
bgx: no visible global function definition for
'assayDataElementReplace'
loessNorm: no visible global function definition for 'loess'
loessNorm: no visible global function definition for 'predict'
plotDEDensity: no visible global function definition for 'density'
plotDEDensity: no visible global function definition for 'abline'
plotDEHistogram: no visible global function definition for 'hist'
plotDEHistogram: no visible global function definition for 'glm'
plotDEHistogram: no visible binding for global variable 'poisson'
plotDEHistogram: no visible global function definition for 'lines'
plotDEHistogram: no visible global function definition for 'points'
plotDiffRank: no visible global function definition for 'quantile'
plotDiffRank: no visible global function definition for 'sd'
plotDiffRank: no visible global function definition for 'segments'
plotDiffRank: no visible global function definition for 'abline'
plotExpressionDensity: no visible global function definition for
'density'
plotExpressionDensity: no visible global function definition for
'lines'
plotExpressionDensity: no visible global function definition for
'legend'
readSingle.bgx: no visible global function definition for 'read.delim'
saveAffinityPlot.bgx: no visible global function definition for 'pdf'
saveAffinityPlot.bgx: no visible global function definition for 'par'
saveAffinityPlot.bgx: no visible global function definition for
'dev.off'
setupVars.bgx : calcProbeAffCategories: no visible global function
definition for 'cdfName'
setupVars.bgx : calcProbeAffCategories: no visible global function
definition for 'median'
setupVars.bgx: no visible global function definition for 'pData'
setupVars.bgx: no visible global function definition for 'indexProbes'
standalone.bgx: no visible global function definition for 'write.table'
standalone.bgx: no visible global function definition for 'geneNames'
standalone.bgx: no visible global function definition for 'sampleNames'
Undefined global functions or variables:
abline annotation assayDataElementReplace cdfName density description
dev.off geneNames glm hist indexProbes legend lines loess median new
pData par pdf points poisson predict quantile read.delim sampleNames
sd segments write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "abline", "hist", "legend", "lines", "par",
"points", "segments")
importFrom("methods", "new")
importFrom("stats", "density", "glm", "loess", "median", "poisson",
"predict", "quantile", "sd")
importFrom("utils", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: analysis.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: mcmc.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: readOutput.bgx.Rd:23-24: Dropping empty section \examples
prepare_Rd: saveAffinityPlot.bgx.Rd:18-19: Dropping empty section \details
prepare_Rd: saveAffinityPlot.bgx.Rd:20-21: Dropping empty section \value
prepare_Rd: saveAffinityPlot.bgx.Rd:26-27: Dropping empty section \examples
prepare_Rd: setupVars.bgx.Rd:21-22: Dropping empty section \details
prepare_Rd: setupVars.bgx.Rd:43-44: Dropping empty section \examples
* 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 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/bgx/libs/x64/bgx.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bgx 41.72 0.25 41.97
* 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: 6 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/bgx.Rcheck/00check.log'
for details.
bgx.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL bgx
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'bgx' ...
** using staged installation
Untarring Boost header files...
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I ../boostIncl -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -DUSING_R -ffast-math -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c bgx.cc -o bgx.o
In file included from ../boostIncl/boost/config.hpp:57,
from ../boostIncl/boost/random/linear_congruential.hpp:22,
from ../boostIncl/boost/random.hpp:36,
from rand.hh:32,
from bgx.cc:32:
../boostIncl/boost/random/detail/const_mod.hpp: In static member function 'static IntType boost::random::const_mod<IntType, m>::invert_euclidian(IntType)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_148' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/detail/const_mod.hpp:148:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(m > 0);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_152' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/detail/const_mod.hpp:152:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(boost::integer_traits<IntType>::is_signed);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/linear_congruential.hpp: In constructor 'boost::random::linear_congruential<IntType, a, c, m, val>::linear_congruential(IntType)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_63' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/linear_congruential.hpp:63:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/inversive_congruential.hpp: In constructor 'boost::random::inversive_congruential<IntType, a, b, p, val>::inversive_congruential(IntType)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_50' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/inversive_congruential.hpp:50:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(b >= 0);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_51' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/inversive_congruential.hpp:51:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(p > 1);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_52' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/inversive_congruential.hpp:52:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(a >= 1);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/shuffle_output.hpp: In member function 'void boost::random::shuffle_output<UniformRandomNumberGenerator, k, val>::init()':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_124' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/shuffle_output.hpp:124:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/mersenne_twister.hpp: In member function 'void boost::random::mersenne_twister<UIntType, w, n, m, r, a, u, s, b, t, c, l, val>::seed(Generator&)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_99' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/mersenne_twister.hpp:99:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(!std::numeric_limits<result_type>::is_signed);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/subtract_with_carry.hpp: In constructor 'boost::random::subtract_with_carry<IntType, m, s, r, val>::subtract_with_carry()':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_83' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/subtract_with_carry.hpp:83:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_signed);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_84' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/subtract_with_carry.hpp:84:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/linear_feedback_shift.hpp: In constructor 'boost::random::linear_feedback_shift<UIntType, w, k, q, s, val>::linear_feedback_shift(UIntType)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_55' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/linear_feedback_shift.hpp:55:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<UIntType>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_56' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/linear_feedback_shift.hpp:56:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(!std::numeric_limits<UIntType>::is_signed);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/linear_feedback_shift.hpp: In constructor 'boost::random::linear_feedback_shift<UIntType, w, k, q, s, val>::linear_feedback_shift(It&, It)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_69' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/linear_feedback_shift.hpp:69:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<UIntType>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_70' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/linear_feedback_shift.hpp:70:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(!std::numeric_limits<UIntType>::is_signed);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/xor_combine.hpp: In member function 'boost::random::xor_combine<URNG1, s1, URNG2, s2, val>::result_type boost::random::xor_combine<URNG1, s1, URNG2, s2, val>::operator()()':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_67' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/xor_combine.hpp:67:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<typename base1_type::result_type>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_68' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/xor_combine.hpp:68:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<typename base2_type::result_type>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_69' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/xor_combine.hpp:69:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<typename base1_type::result_type>::digits >= std::numeric_limits<typename base2_type::result_type>::digits);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/uniform_smallint.hpp: In constructor 'boost::detail::uniform_smallint_float<UniformRandomNumberGenerator, IntType>::uniform_smallint_float(boost::detail::uniform_smallint_float<UniformRandomNumberGenerator, IntType>::base_type&, IntType, IntType)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_121' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/uniform_smallint.hpp:121:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_122' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/uniform_smallint.hpp:122:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(!std::numeric_limits<typename base_type::result_type>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/uniform_smallint.hpp: In constructor 'boost::uniform_smallint<IntType>::uniform_smallint(IntType, IntType)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_170' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/uniform_smallint.hpp:170:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/uniform_int.hpp: In constructor 'boost::uniform_int<IntType>::uniform_int(IntType, IntType)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_47' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/uniform_int.hpp:47:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/random_number_generator.hpp: In constructor 'boost::random_number_generator<UniformRandomNumberGenerator, IntType>::random_number_generator(boost::random_number_generator<UniformRandomNumberGenerator, IntType>::base_type&)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_38' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/random_number_generator.hpp:38:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<result_type>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/uniform_real.hpp: In constructor 'boost::uniform_real<RealType>::uniform_real(RealType, RealType)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_41' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/uniform_real.hpp:41:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(!std::numeric_limits<RealType>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/random/poisson_distribution.hpp: In constructor 'boost::poisson_distribution<IntType, RealType>::poisson_distribution(const RealType&)':
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_38' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/poisson_distribution.hpp:38:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(std::numeric_limits<IntType>::is_integer);
^~~~~~~~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:21: warning: typedef 'boost_static_assert_typedef_39' locally defined but not used [-Wunused-local-typedefs]
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../boostIncl/boost/config/suffix.hpp:523:32: note: in definition of macro 'BOOST_DO_JOIN2'
#define BOOST_DO_JOIN2( X, Y ) X##Y
^
../boostIncl/boost/config/suffix.hpp:521:28: note: in expansion of macro 'BOOST_DO_JOIN'
#define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )
^~~~~~~~~~~~~
../boostIncl/boost/static_assert.hpp:105:10: note: in expansion of macro 'BOOST_JOIN'
BOOST_JOIN(boost_static_assert_typedef_, __LINE__)
^~~~~~~~~~
../boostIncl/boost/random/poisson_distribution.hpp:39:5: note: in expansion of macro 'BOOST_STATIC_ASSERT'
BOOST_STATIC_ASSERT(!std::numeric_limits<RealType>::is_integer);
^~~~~~~~~~~~~~~~~~~
In file included from bgx.cc:32:
rand.hh: In member function 'RealType Rand<GenType, RealType>::Normal()':
rand.hh:399:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(u0<.5) return y; return -y;
^~
rand.hh:399:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(u0<.5) return y; return -y;
^~~~~~
rand.hh:406:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(u0<.5) return y; return -y;
^~
rand.hh:406:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(u0<.5) return y; return -y;
^~~~~~
rand.hh:413:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(u0<.5) return y; return -y;
^~
rand.hh:413:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(u0<.5) return y; return -y;
^~~~~~
rand.hh:420:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(u0<.5) return y; return -y;
^~
rand.hh:420:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(u0<.5) return y; return -y;
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I ../boostIncl -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -DUSING_R -ffast-math -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c bgx_frontend.cc -o bgx_frontend.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I ../boostIncl -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -DUSING_R -ffast-math -O3 -std=c99 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c qnorm.c -o qnorm.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I ../boostIncl -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -DUSING_R -ffast-math -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c rundir.cc -o rundir.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I ../boostIncl -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -DUSING_R -ffast-math -O3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c sokal.cc -o sokal.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o bgx.dll tmp.def bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-bgx/00new/bgx/libs/x64
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'bgx'
finding HTML links ... done
analysis.bgx html
bgx html
mcmc.bgx html
readOutput.bgx html
saveAffinityPlot.bgx html
setupVars.bgx html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bgx)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'sRACIPE' is missing or broken
done
bgx.Rcheck/bgx-Ex.timings
| name | user | system | elapsed | |
| bgx | 41.72 | 0.25 | 41.97 | |