Package: DESeq

Version: 1.35.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DESeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DESeq_1.35.1.tar.gz

StartedAt: 2019-04-09 00:26:05 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:28:55 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 170.5 seconds

RetCode: 0

Status:  OK

CheckDir: DESeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DESeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DESeq_1.35.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DESeq.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 ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.35.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘DESeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘locfit’
  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
estimateAndFitDispersionsWithCoxReid: no visible global function
  definition for ‘model.matrix’
estimateAndFitDispersionsWithCoxReid : <anonymous>: no visible global
  function definition for ‘glm.fit’
estimateAndFitDispersionsWithCoxReid : <anonymous>: no visible global
  function definition for ‘df.residual’
estimateAndFitDispersionsWithCoxReid : <anonymous>: no visible global
  function definition for ‘optimize’
estimateAndFitDispersionsWithCoxReid : <anonymous> : <anonymous>: no
  visible global function definition for ‘fitted.values’
estimateSizeFactorsForMatrix: no visible binding for global variable
  ‘median’
fitInfo: no visible global function definition for ‘is’
fitNbinomGLMs: no visible global function definition for ‘is’
fitNbinomGLMsForMatrix: no visible global function definition for ‘is’
fitNbinomGLMsForMatrix: no visible global function definition for
  ‘model.matrix’
fitNbinomGLMsForMatrix : <anonymous>: no visible global function
  definition for ‘glm.fit’
fitNbinomGLMsForMatrix : <anonymous>: no visible global function
  definition for ‘coefficients’
fitNbinomGLMsForMatrix : <anonymous>: no visible global function
  definition for ‘deviance’
fitNbinomGLMsForMatrix: no visible global function definition for
  ‘na.omit’
getVarianceStabilizedData: no visible global function definition for
  ‘is’
getVarianceStabilizedData: no visible global function definition for
  ‘splinefun’
getVarianceStabilizedData: no visible global function definition for
  ‘quantile’
makeExampleCountDataSet: no visible global function definition for
  ‘rexp’
makeExampleCountDataSet: no visible global function definition for
  ‘runif’
makeExampleCountDataSet: no visible global function definition for
  ‘rnorm’
makeExampleCountDataSet : <anonymous> : <anonymous>: no visible global
  function definition for ‘rnbinom’
nbinomGLMTest: no visible global function definition for ‘pchisq’
nbinomTest: no visible global function definition for ‘is’
nbinomTest: no visible global function definition for ‘p.adjust’
nbinomTestForMatrices : <anonymous>: no visible global function
  definition for ‘dnbinom’
newCountDataSet: no visible global function definition for ‘is’
newCountDataSet: no visible global function definition for ‘as’
newCountDataSet: no visible global function definition for ‘new’
newCountDataSetFromHTSeqCount : <anonymous>: no visible global function
  definition for ‘read.table’
parametricDispersionFit: no visible global function definition for
  ‘glm’
parametricDispersionFit: no visible global function definition for
  ‘Gamma’
parametricDispersionFit: no visible global function definition for
  ‘coefficients’
plotDispEsts: no visible global function definition for ‘plot’
plotDispEsts: no visible global function definition for ‘lines’
plotMA: no visible binding for global variable ‘baseMean’
plotMA: no visible global function definition for ‘quantile’
plotMA: no visible global function definition for ‘plot’
plotMA: no visible global function definition for ‘abline’
plotPCA: no visible global function definition for ‘prcomp’
prepareScvBiasCorrectionFits : <anonymous> : <anonymous>: no visible
  global function definition for ‘rnbinom’
prepareScvBiasCorrectionFits : <anonymous>: no visible global function
  definition for ‘locfit’
profileLogLikelihood : <anonymous>: no visible global function
  definition for ‘dnbinom’
safepredict: no visible global function definition for ‘predict’
varianceStabilizingTransformation: no visible global function
  definition for ‘new’
conditions<-,CountDataSet: no visible global function definition for
  ‘validObject’
counts<-,CountDataSet-matrix: no visible global function definition for
  ‘validObject’
dispTable<-,CountDataSet: no visible global function definition for
  ‘validObject’
estimateDispersions,CountDataSet: no visible global function definition
  for ‘is’
estimateDispersions,CountDataSet: no visible global function definition
  for ‘validObject’
estimateSizeFactors,CountDataSet: no visible binding for global
  variable ‘median’
sizeFactors<-,CountDataSet-numeric: no visible global function
  definition for ‘validObject’
Undefined global functions or variables:
  Gamma abline as baseMean coefficients deviance df.residual dnbinom
  fitted.values glm glm.fit is lines locfit median model.matrix na.omit
  new optimize p.adjust pchisq plot prcomp predict quantile read.table
  rexp rnbinom rnorm runif splinefun validObject
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("methods", "as", "is", "new", "validObject")
  importFrom("stats", "Gamma", "coefficients", "deviance", "df.residual",
             "dnbinom", "fitted.values", "glm", "glm.fit", "median",
             "model.matrix", "na.omit", "optimize", "p.adjust", "pchisq",
             "prcomp", "predict", "quantile", "rexp", "rnbinom", "rnorm",
             "runif", "splinefun")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... 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
nbinomTestForMatrices 23.183  0.147  23.539
nbinomTest            11.989  0.138  12.230
* 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-3.9-bioc/meat/DESeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DESeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DESeq’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pval.c -o pval.o
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
   double esttotalperlength = total/2;
          ^
1 warning generated.
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 DESeq.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/DESeq/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq)

name	user	system	elapsed
CountDataSet-class	0	0	0
adjustScvForBias	0.699	0.007	0.710
conditions	1.194	0.049	1.255
counts	1.082	0.024	1.120
dispTable	1.629	0.030	1.684
estimateDispersions	1.322	0.043	1.381
estimateSizeFactors	1.161	0.017	1.188
estimateSizeFactorsForMatrix	1.206	0.016	1.228
fitInfo	1.278	0.025	1.307
fitNbinomGLMs	0	0	0
fitNbinomGLMsForMatrix	0	0	0
getBaseMeansAndVariances	1.120	0.015	1.143
getVarianceStabilizedData	1.405	0.053	1.475
makeExampleCountDataSet	1.087	0.010	1.106
nbinomGLMTest	1.851	0.020	1.888
nbinomTest	11.989	0.138	12.230
nbinomTestForMatrices	23.183	0.147	23.539
newCountDataSet	1.235	0.007	1.261
plotDispEsts	1.446	0.029	1.486
plotMA	0	0	0
plotPCA	1.714	0.050	1.782
sizeFactors	1.128	0.010	1.152