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 01:20:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:24:08 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 217.9 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) (2019-03-18 r76245)
* 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 25.613  0.631  26.244
nbinomTest            12.250  0.496  12.748
* 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’ ...
** using staged installation
** 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/00LOCK-DESeq/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DESeq)

name	user	system	elapsed
CountDataSet-class	0.000	0.001	0.001
adjustScvForBias	0.819	0.017	0.835
conditions	1.592	0.128	1.719
counts	1.396	0.038	1.434
dispTable	2.154	0.014	2.169
estimateDispersions	1.565	0.072	1.637
estimateSizeFactors	1.462	0.087	1.550
estimateSizeFactorsForMatrix	1.684	0.109	1.794
fitInfo	1.914	0.138	2.054
fitNbinomGLMs	0	0	0
fitNbinomGLMsForMatrix	0.000	0.000	0.001
getBaseMeansAndVariances	1.865	0.090	1.954
getVarianceStabilizedData	1.701	0.102	1.804
makeExampleCountDataSet	2.152	0.115	2.267
nbinomGLMTest	2.925	0.202	3.129
nbinomTest	12.250	0.496	12.748
nbinomTestForMatrices	25.613	0.631	26.244
newCountDataSet	1.467	0.070	1.536
plotDispEsts	1.598	0.132	1.730
plotMA	0.001	0.000	0.001
plotPCA	2.125	0.171	2.297
sizeFactors	1.657	0.048	1.706