BioC 3.2: CHECK report for EDDA on linux1.bioconductor.org

Package: EDDA

Version: 1.8.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings EDDA_1.8.0.tar.gz

StartedAt: 2015-10-27 03:09:33 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:11:56 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 142.8 seconds

RetCode: 0

Status:  OK

CheckDir: EDDA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings EDDA_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/EDDA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘EDDA’ can be installed ... [17s/17s] OK
* 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 loading without being on the library search path ... 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
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 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’
learn_parameter_DESeq: no visible global function definition for
  ‘fData’
learn_parameter_edgeR: no visible binding for global variable
  ‘mean_fc_relation’
run_Cuffdiff_Mode: no visible global function definition for
  ‘Cuffdiff_Mode’
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/27s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
testDATs 20.666  0.761  13.754
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/EDDA.Rcheck/00check.log’
for details.

* installing *source* package ‘EDDA’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c cuffdiff.cpp -o cuffdiff.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o EDDA.so cuffdiff.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/EDDA.Rcheck/EDDA/libs
** R
** data
** inst
** preparing package for lazy loading
No methods found in "baySeq" for requests: rbind
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "baySeq" for requests: rbind
* DONE (EDDA)

name	user	system	elapsed
EDDA-package	1.471	0.360	1.276
computeAUC	0.685	0.242	0.763
generateData	4.924	0.064	4.993
plotPRC	0.893	0.219	0.726
plotROC	1.004	0.223	0.867
testDATs	20.666	0.761	13.754