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BioC 3.0: CHECK report for EDDA on zin1

This page was generated on 2015-04-10 09:41:44 -0700 (Fri, 10 Apr 2015).

Package 270/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EDDA 1.5.3
Chia Kuan Hui Burton , Niranjan Nagarajan
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/EDDA
Last Changed Rev: 98325 / Revision: 102249
Last Changed Date: 2015-01-13 23:07:42 -0800 (Tue, 13 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: EDDA
Version: 1.5.3
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings EDDA_1.5.3.tar.gz
StartedAt: 2015-04-09 23:31:30 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:35:08 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 218.7 seconds
RetCode: 0
Status:  OK 
CheckDir: EDDA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings EDDA_1.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/EDDA.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.5.3’
* 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 ... [20s/21s] 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 ... [38s/34s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
testDATs     17.705  0.552  14.909
generateData  6.436  0.048   6.651
* 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/EDDA.Rcheck/00check.log’
for details.

EDDA.Rcheck/00install.out:

* installing *source* package ‘EDDA’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c cuffdiff.cpp -o cuffdiff.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o EDDA.so cuffdiff.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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)

EDDA.Rcheck/EDDA-Ex.timings:

nameusersystemelapsed
EDDA-package1.3360.1921.379
computeAUC0.6160.2040.678
generateData6.4360.0486.651
plotPRC1.1280.2521.216
plotROC1.0960.2080.994
testDATs17.705 0.55214.909