DESeq 1.24.0
Simon Anders
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/DESeq | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DESeq_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/DESeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.24.0’
* 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’
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
‘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 ‘p.adjust’
nbinomTestForMatrices : <anonymous>: no visible global function
definition for ‘dnbinom’
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’
estimateSizeFactors,CountDataSet: no visible binding for global
variable ‘median’
Undefined global functions or variables:
Gamma abline baseMean coefficients deviance df.residual dnbinom
fitted.values glm glm.fit lines locfit median model.matrix na.omit
optimize p.adjust pchisq plot prcomp predict quantile read.table rexp
rnbinom rnorm runif splinefun
Consider adding
importFrom("graphics", "abline", "lines", "plot")
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.
* 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 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
nbinomTestForMatrices 33.293 0.048 33.539
nbinomTest 17.608 0.008 17.759
* 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-3.3-bioc/meat/DESeq.Rcheck/00check.log’
for details.
* installing *source* package ‘DESeq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-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 -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o DESeq.so pval.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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)