##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBSeq_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EBSeq.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBSeq’ version ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘EBSeq’ can be installed ... WARNING
Found the following significant warnings:
  /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/EBSeq.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 C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package 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 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 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 ... NOTE
DenNHist: no visible global function definition for ‘hist’
DenNHist: no visible global function definition for ‘lines’
DenNHist: no visible global function definition for ‘dbeta’
DenNHist: no visible global function definition for ‘legend’
EBMultiTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBMultiTest: no visible binding for global variable ‘var’
EBMultiTest: no visible binding for global variable ‘NumBin’
EBMultiTest: no visible global function definition for ‘quantile’
EBMultiTest: no visible binding for global variable ‘PoolLower’
EBMultiTest: no visible binding for global variable ‘PoolUpper’
EBMultiTest : <anonymous>: no visible binding for global variable ‘var’
EBMultiTest: no visible binding for global variable ‘Print’
EBTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBTest: no visible binding for global variable ‘var’
EBTest: no visible global function definition for ‘quantile’
EBTest: no visible binding for global variable ‘PoolLower’
EBTest: no visible binding for global variable ‘PoolUpper’
EBTest: no visible binding for global variable ‘Print’
GetDEResults: no visible binding for global variable ‘median’
LogN: no visible global function definition for ‘optim’
LogNMulti: no visible global function definition for ‘optim’
MedianNorm : <anonymous>: no visible global function definition for
  ‘median’
MedianNorm : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
PlotPattern: no visible global function definition for ‘par’
PlotPattern: no visible global function definition for ‘rainbow’
PlotPattern: no visible global function definition for ‘heatmap’
PlotPostVsRawFC: no visible global function definition for ‘par’
PlotPostVsRawFC: no visible global function definition for ‘abline’
PlotPostVsRawFC: no visible global function definition for ‘rect’
PolyFitPlot: no visible global function definition for ‘lm’
PolyFitPlot: no visible global function definition for ‘smoothScatter’
PolyFitPlot: no visible global function definition for ‘axis’
PolyFitPlot: no visible global function definition for ‘lines’
QQP: no visible global function definition for ‘rbeta’
QQP: no visible global function definition for ‘qqplot’
QQP: no visible global function definition for ‘lm’
QQP: no visible global function definition for ‘abline’
QuantileNorm : <anonymous>: no visible global function definition for
  ‘quantile’
beta.mom: no visible global function definition for ‘var’
Undefined global functions or variables:
  NumBin PoolLower PoolUpper Print abline axis dbeta heatmap hist
  legend lines lm median optim par qqplot quantile rainbow rbeta rect
  smoothScatter var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "par", "rect", "smoothScatter")
  importFrom("stats", "dbeta", "heatmap", "lm", "median", "optim",
             "qqplot", "quantile", "rbeta", "var")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) EBTest.Rd:56: Lost braces; missing escapes or markup?
    56 | X_{gis}|mu_{gi} ~ NB (r_{gi0} * l_s, q_{gi})
       |   ^
checkRd: (-1) EBTest.Rd:56: Lost braces; missing escapes or markup?
    56 | X_{gis}|mu_{gi} ~ NB (r_{gi0} * l_s, q_{gi})
       |            ^
checkRd: (-1) EBTest.Rd:56: Lost braces; missing escapes or markup?
    56 | X_{gis}|mu_{gi} ~ NB (r_{gi0} * l_s, q_{gi})
       |                         ^
checkRd: (-1) EBTest.Rd:56: Lost braces; missing escapes or markup?
    56 | X_{gis}|mu_{gi} ~ NB (r_{gi0} * l_s, q_{gi})
       |                                        ^
checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup?
    60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}."
       |                               ^
checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup?
    60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}."
       |                                    ^
checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup?
    60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}."
       |                                             ^
checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup?
    60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}."
       |                                                  ^
checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup?
    60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}."
       |                                                                   ^
checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup?
    60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}."
       |                                                                        ^
checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup?
    60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}."
       |                                                                                  ^
checkRd: (-1) EBTest.Rd:60: Lost braces; missing escapes or markup?
    60 | The function will test "H0: q_{gi}^{C1} = q_{gi}^{C2}" and "H1: q_{gi}^{C1} != q_{gi}^{C2}."
       |                                                                                       ^
checkRd: (-1) MedianNorm.Rd:21: Lost braces
    21 | hat{l_1} = median_g [ X_g1 / (X_g1*X_g2*...*X_gS)^{-S} ]     (1)
       |    ^
checkRd: (-1) MedianNorm.Rd:21: Lost braces; missing escapes or markup?
    21 | hat{l_1} = median_g [ X_g1 / (X_g1*X_g2*...*X_gS)^{-S} ]     (1)
       |                                                   ^
checkRd: (-1) MedianNorm.Rd:23: Lost braces; missing escapes or markup?
    23 | which estimates l_1 / (l_1 * l_2 * ... * l_S)^{-S}. 
       |                                               ^
checkRd: (-1) MedianNorm.Rd:27: Lost braces
    27 | hat{l_1}  = median_g [ (X_g1/X_g1 * X_g1/X_g2 * .... * X_g1/X_gS)^{-S}]
       |    ^
checkRd: (-1) MedianNorm.Rd:27: Lost braces; missing escapes or markup?
    27 | hat{l_1}  = median_g [ (X_g1/X_g1 * X_g1/X_g2 * .... * X_g1/X_gS)^{-S}]
       |                                                                   ^
checkRd: (-1) MedianNorm.Rd:31: Lost braces; missing escapes or markup?
    31 | Then estimate l_1 = l_1 / (l_1 * l_2 * ... * l_S)^{-S} by taking the
       |                                                   ^
checkRd: (-1) MedianNorm.Rd:34: Lost braces
    34 | hat{l_1} = [ median_g(X_g1/X_g1) * median_g(X_g1/X_g2) *
       |    ^
checkRd: (-1) MedianNorm.Rd:35: Lost braces; missing escapes or markup?
    35 | median_g(X_g1/X_g3) * ... * median_g(X_g1/X_gS) ] ^{-S}
       |                                                    ^
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'EBSeq_NingLeng-package.Rd':
  ‘EBSeq_NingLeng-package’
* 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 data for ASCII and uncompressed saves ... 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 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, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/EBSeq.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘EBSeq’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Rexport.cpp -o Rexport.o
In file included from Rexport.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from Rexport.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from Rexport.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from Rexport.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/series.hpp:16:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
#    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
     ^
In file included from Rexport.cpp:11:
./negativeBinomial.hpp:139:26: warning: variable 'maxholder' set but not used [-Wunused-but-set-variable]
                    auto maxholder = add.maxCoeff(&maxRow, &maxCol);
                         ^
7 warnings generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o EBSeq.so Rexport.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-EBSeq/00new/EBSeq/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** 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 (EBSeq)