DESeq 1.28.0
Simon Anders
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/DESeq | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DESeq_1.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DESeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.28.0’
* 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 ... 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
nbinomTestForMatrices 21.232 0.000 21.251
nbinomTest 10.256 0.008 10.268
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/DESeq.Rcheck/00check.log’
for details.
* installing *source* package ‘DESeq’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pval.c -o pval.o
pval.c: In function ‘add_from_both_sides’:
pval.c:26:11: warning: unused variable ‘esttotalperlength’ [-Wunused-variable]
double esttotalperlength = total/2;
^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o DESeq.so pval.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/DESeq.Rcheck/DESeq/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq)