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BioC 3.4: CHECK report for EDDA on morelia

This page was generated on 2017-04-15 16:25:19 -0400 (Sat, 15 Apr 2017).

Package 365/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EDDA 1.12.0
Chia Kuan Hui Burton , Niranjan Nagarajan
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/EDDA
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: EDDA
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EDDA_1.12.0.tar.gz
StartedAt: 2017-04-15 01:25:02 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:28:20 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 198.3 seconds
RetCode: 0
Status:  OK 
CheckDir: EDDA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EDDA_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/EDDA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.12.0’
* 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 ... 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
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 ‘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 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", "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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
testDATs     17.007  1.201  14.453
generateData  5.524  0.160   5.692
* 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/EDDA.Rcheck/00check.log’
for details.


EDDA.Rcheck/00install.out:

* installing *source* package ‘EDDA’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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 /Users/biocbuild/bbs-3.4-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-package0.9710.3430.998
computeAUC0.4920.2480.614
generateData5.5240.1605.692
plotPRC0.9520.3280.930
plotROC0.9400.3850.919
testDATs17.007 1.20114.453