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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EDDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings EDDA_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/EDDA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EDDA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EDDA' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Rcpp', 'parallel', 'ROCR', 'DESeq', 'baySeq', 'snow', 'edgeR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'EDDA' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'exactTestByDeviance(y1, ': unused argument (big.count = big.count) 
  Note: possible error in 'exactTestBySmallP(y1, ': unused argument (big.count = big.count) 
  Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/EDDA.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'parallel' 'methods' 'ROCR' 'DESeq' 'baySeq' 'snow' 'edgeR'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Package in Depends field not imported from: 'Rcpp'
  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
DL.plot: no visible global function definition for 'na.omit'
DL.plot : <anonymous>: no visible global function definition for
  'median'
DL.plot : <anonymous>: no visible global function definition for
  'na.omit'
DL.plot: no visible global function definition for 'median'
DLbio.dat : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
DLbio.dat: no visible global function definition for 'median'
DLbio.dat: no visible global function definition for 'na.omit'
DLbio.plot: no visible global function definition for 'na.omit'
Lplot: no visible global function definition for 'na.omit'
Lplot: no visible global function definition for 'aggregate'
Lplot: no visible binding for global variable 'median'
Lplot2: no visible global function definition for 'na.omit'
Lplot2: no visible global function definition for 'aggregate'
Lplot2: no visible binding for global variable 'median'
MODEnormalization: no visible global function definition for 'median'
MODEnormalization: no visible global function definition for 'density'
UQNnormalization : <anonymous>: no visible global function definition
  for 'quantile'
calc_twosample_ts: no visible global function definition for 'var'
call_cuffdiff: no visible global function definition for 'var'
countbio.plot: no visible global function definition for 'na.omit'
countbio.plot: no visible global function definition for 'boxplot'
detect_differentially_abundant_feaTRUEs: no visible global function
  definition for 'var'
exactTestMode: possible error in exactTestByDeviance(y1, y2, dispersion
  = dispersion, big.count = big.count): unused argument (big.count =
  big.count)
exactTestMode: possible error in exactTestBySmallP(y1, y2, dispersion =
  dispersion, big.count = big.count): unused argument (big.count =
  big.count)
generateData: no visible global function definition for 'data'
generateData: no visible binding for global variable 'HBR'
generateData: no visible binding for global variable 'BP'
generateData: no visible binding for global variable 'Wu'
generateData: no visible binding for global variable 'SingleCell'
generateData: no visible global function definition for 'tail'
learn_parameter_DESeq: no visible global function definition for
  'fData'
learn_parameter_edgeR: no visible binding for global variable
  'mean_fc_relation'
outliers: no visible global function definition for 'quantile'
outliers: no visible global function definition for 'na.omit'
rpkm: no visible global function definition for 'na.omit'
run_Cuffdiff_Mode: no visible global function definition for
  'Cuffdiff_Mode'
run_NOISeq: no visible global function definition for 'na.omit'
run_NOISeq_Mode: no visible global function definition for 'na.omit'
run_NOISeq_nde: no visible global function definition for 'na.omit'
run_NOISeq_uqn: no visible global function definition for 'na.omit'
satur.plot2: no visible global function definition for 'na.omit'
saturbio.plot: no visible global function definition for 'na.omit'
tmm: no visible global function definition for 'install.packages'
tmm: no visible global function definition for 'na.omit'
uqua: no visible binding for global variable 'quantile'
uqua: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  BP Cuffdiff_Mode HBR SingleCell Wu aggregate boxplot data density
  fData install.packages mean_fc_relation median na.omit quantile tail
  var
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "aggregate", "density", "median", "na.omit",
             "quantile", "var")
  importFrom("utils", "data", "install.packages", "tail")
to your NAMESPACE file.
* 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/EDDA/libs/i386/EDDA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/EDDA/libs/x64/EDDA.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
testDATs 15.79   0.11   16.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
testDATs 14.14   0.16   14.72
* 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 WARNING, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/EDDA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/EDDA_1.28.0.tar.gz && rm -rf EDDA.buildbin-libdir && mkdir EDDA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EDDA.buildbin-libdir EDDA_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL EDDA_1.28.0.zip && rm EDDA_1.28.0.tar.gz EDDA_1.28.0.zip
###
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install for i386

* installing *source* package 'EDDA' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cuffdiff.cpp -o cuffdiff.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o EDDA.dll tmp.def cuffdiff.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/EDDA.buildbin-libdir/00LOCK-EDDA/00new/EDDA/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2 
No methods found in package 'baySeq' for request: 'rbind' when loading 'EDDA'
Note: possible error in 'exactTestByDeviance(y1, ': unused argument (big.count = big.count) 
Note: possible error in 'exactTestBySmallP(y1, ': unused argument (big.count = big.count) 
** help
*** installing help indices
  converting help for package 'EDDA'
    finding HTML links ... done
    BP                                      html  
    EDDA-package                            html  
    HBR                                     html  
    SingleCell                              html  
    Wu                                      html  
    computeAUC                              html  
    generateData                            html  
    plotPRC                                 html  
    plotROC                                 html  
    testDATs                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
No methods found in package 'baySeq' for request: 'rbind' when loading 'EDDA'
** testing if installed package can be loaded from final location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
No methods found in package 'baySeq' for request: 'rbind' when loading 'EDDA'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'EDDA' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cuffdiff.cpp -o cuffdiff.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o EDDA.dll tmp.def cuffdiff.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/EDDA.buildbin-libdir/EDDA/libs/x64
** testing if installed package can be loaded
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
No methods found in package 'baySeq' for request: 'rbind' when loading 'EDDA'
* MD5 sums
packaged installation of 'EDDA' as EDDA_1.28.0.zip
* DONE (EDDA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'EDDA' successfully unpacked and MD5 sums checked