Multiple platform build/check report for BioC 3.8 - CHECK report for EDDA on merida1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EDDA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EDDA_1.20.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/EDDA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EDDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EDDA’ version ‘1.20.1’
* 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 for sufficient/correct file permissions ... 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) 
See ‘/Users/biocbuild/bbs-3.8-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
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
testDATs     25.472  1.647  23.149
generateData  6.079  0.387   6.511
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/EDDA.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EDDA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘EDDA’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c cuffdiff.cpp -o cuffdiff.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o EDDA.so cuffdiff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/EDDA/libs
** R
** data
** byte-compile and prepare package for lazy loading
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
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘baySeq’ for request: ‘rbind’ when loading ‘EDDA’
* DONE (EDDA)

name	user	system	elapsed
EDDA-package	1.322	0.633	1.347
computeAUC	0.640	0.360	0.855
generateData	6.079	0.387	6.511
plotPRC	0.919	0.422	0.861
plotROC	1.148	0.683	1.171
testDATs	25.472	1.647	23.149

CHECK report for EDDA on merida1

Summary

Command output

Installation output

Tests output

Example timings