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CHECK report for EDDA on tokay1

This page was generated on 2019-04-13 11:23:35 -0400 (Sat, 13 Apr 2019).

Package 456/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EDDA 1.20.1
Chia Kuan Hui Burton , Niranjan Nagarajan
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/EDDA
Branch: RELEASE_3_8
Last Commit: 1328485
Last Changed Date: 2019-01-04 13:30:40 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: EDDA
Version: 1.20.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EDDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings EDDA_1.20.1.tar.gz
StartedAt: 2019-04-13 01:59:39 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:04:39 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 299.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: EDDA.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EDDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings EDDA_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/EDDA.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.20.1'
* 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'
 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) 
See 'C:/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
* 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 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-3.8-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)

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 or elapsed time > 5s
          user system elapsed
testDATs 17.64   0.06   18.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
testDATs 20.6   0.06   21.24
* 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-3.8-bioc/meat/EDDA.Rcheck/00check.log'
for details.



Installation output

EDDA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/EDDA_1.20.1.tar.gz && rm -rf EDDA.buildbin-libdir && mkdir EDDA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EDDA.buildbin-libdir EDDA_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL EDDA_1.20.1.zip && rm EDDA_1.20.1.tar.gz EDDA_1.20.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1789k  100 1789k    0     0  10.4M      0 --:--:-- --:--:-- --:--:-- 10.7M

install for i386

* installing *source* package 'EDDA' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cuffdiff.cpp -o cuffdiff.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o EDDA.dll tmp.def cuffdiff.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/EDDA.buildbin-libdir/EDDA/libs/i386
** 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
  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
No methods found in package 'baySeq' for request: 'rbind' when loading 'EDDA'
In R CMD INSTALL

install for x64

* installing *source* package 'EDDA' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cuffdiff.cpp -o cuffdiff.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o EDDA.dll tmp.def cuffdiff.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/EDDA.buildbin-libdir/EDDA/libs/x64
** testing if installed package can be loaded
No methods found in package 'baySeq' for request: 'rbind' when loading 'EDDA'
* MD5 sums
packaged installation of 'EDDA' as EDDA_1.20.1.zip
* DONE (EDDA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'EDDA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

EDDA.Rcheck/examples_i386/EDDA-Ex.timings

nameusersystemelapsed
EDDA-package0.960.002.08
computeAUC0.50.00.5
generateData3.520.193.70
plotPRC0.750.050.80
plotROC0.730.010.75
testDATs17.64 0.0618.12

EDDA.Rcheck/examples_x64/EDDA-Ex.timings

nameusersystemelapsed
EDDA-package0.850.030.89
computeAUC0.580.000.58
generateData3.560.213.77
plotPRC0.660.030.68
plotROC0.680.000.69
testDATs20.60 0.0621.24