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BioC 3.2: CHECK report for DESeq on oaxaca

This page was generated on 2016-04-23 10:24:33 -0700 (Sat, 23 Apr 2016).

Package 268/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DESeq 1.22.1
Simon Anders
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DESeq
Last Changed Rev: 112514 / Revision: 116712
Last Changed Date: 2016-01-13 08:32:41 -0800 (Wed, 13 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DESeq
Version: 1.22.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DESeq_1.22.1.tar.gz
StartedAt: 2016-04-22 23:31:26 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:34:33 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 186.4 seconds
RetCode: 0
Status:  OK 
CheckDir: DESeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DESeq_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/DESeq.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.22.1’
* 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 ... [14s/14s] 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
plotMA: no visible binding for global variable ‘baseMean’
prepareScvBiasCorrectionFits : <anonymous>: no visible global function
  definition for ‘locfit’
* 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 ... [66s/66s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nbinomTestForMatrices 21.846  0.207  22.072
nbinomTest            12.028  0.155  12.195
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/DESeq.Rcheck/00check.log’
for details.


DESeq.Rcheck/00install.out:

* installing *source* package ‘DESeq’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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 /Users/biocbuild/bbs-3.2-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)

DESeq.Rcheck/DESeq-Ex.timings:

nameusersystemelapsed
CountDataSet-class0.0010.0000.001
adjustScvForBias0.5900.0290.619
conditions1.4140.0231.437
counts1.3000.0141.315
dispTable1.9060.0571.966
estimateDispersions1.7640.0161.783
estimateSizeFactors1.2400.0231.264
estimateSizeFactorsForMatrix1.2220.0171.239
fitInfo1.7060.0461.752
fitNbinomGLMs0.0010.0000.001
fitNbinomGLMsForMatrix000
getBaseMeansAndVariances1.3380.0131.352
getVarianceStabilizedData2.1140.0452.159
makeExampleCountDataSet1.2940.0091.304
nbinomGLMTest1.9340.0281.962
nbinomTest12.028 0.15512.195
nbinomTestForMatrices21.846 0.20722.072
newCountDataSet1.3090.0111.321
plotDispEsts1.7820.0331.817
plotMA0.0010.0000.000
plotPCA2.0850.0532.143
sizeFactors1.4210.0201.441