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CHECK report for EDDA on merida2

This page was generated on 2019-04-09 13:29:17 -0400 (Tue, 09 Apr 2019).

Package 477/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EDDA 1.21.1
Chia Kuan Hui Burton , Niranjan Nagarajan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/EDDA
Branch: master
Last Commit: b955462
Last Changed Date: 2019-01-04 13:30:38 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: EDDA
Version: 1.21.1
Command: /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_1.21.1.tar.gz
StartedAt: 2019-04-09 00:40:54 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:43:55 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 181.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: EDDA.Rcheck
Warnings: 1

Command output

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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_1.21.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/EDDA.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.21.1’
* 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-3.9-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     23.789  2.078  22.063
generateData  7.031  0.493   7.589
* 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-3.9-bioc/meat/EDDA.Rcheck/00check.log’
for details.



Installation output

EDDA.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EDDA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘EDDA’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c cuffdiff.cpp -o cuffdiff.o
clang++ -std=gnu++11 -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/3.6/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)

Tests output


Example timings

EDDA.Rcheck/EDDA-Ex.timings

nameusersystemelapsed
EDDA-package1.5050.5051.520
computeAUC1.0410.7501.640
generateData7.0310.4937.589
plotPRC0.9090.3950.831
plotROC0.9660.4210.935
testDATs23.789 2.07822.063