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BioC 3.4: CHECK report for DEDS on zin1

This page was generated on 2016-09-21 03:35:50 -0700 (Wed, 21 Sep 2016).

Package 298/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEDS 1.47.0
Yuanyuan Xiao
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEDS
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEDS
Version: 1.47.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DEDS_1.47.0.tar.gz
StartedAt: 2016-09-20 05:24:43 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:25:07 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 24.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DEDS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DEDS_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DEDS.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 ‘DEDS/DESCRIPTION’ ... OK
* this is package ‘DEDS’ version ‘1.47.0’
* 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 ‘DEDS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
deds.stat.linkC: warning in matrix(res$t, byrow = FALSE, nc = newX$nT):
  partial argument match of 'nc' to 'ncol'
sam.multiclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nr' to 'nrow'
sam.multiclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nc' to 'ncol'
sam.oneclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nr' to 'nrow'
sam.oneclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nc' to 'ncol'
sam.twoclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nr' to 'nrow'
sam.twoclass.func: warning in matrix(nr = nrow(X), nc = B): partial
  argument match of 'nc' to 'ncol'
* checking Rd files ... NOTE
prepare_Rd: comp.fdr.Rd:52-54: Dropping empty section \details
prepare_Rd: deds.pval.Rd:65-68: Dropping empty section \examples
prepare_Rd: hist.DEDS.Rd:47-50: Dropping empty section \examples
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/DEDS.Rcheck/00check.log’
for details.


DEDS.Rcheck/00install.out:

* installing *source* package ‘DEDS’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c deds.c -o deds.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c distance.c -o distance.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c input.c -o input.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c manip.c -o manip.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c random.c -o random.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sampling.c -o sampling.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c stat_fun.c -o stat_fun.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o DEDS.so deds.o distance.o input.o manip.o random.o sampling.o stat_fun.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/DEDS.Rcheck/DEDS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEDS)

DEDS.Rcheck/DEDS-Ex.timings:

nameusersystemelapsed
aggregateFun0.0080.0000.006
comp.B0.0040.0000.004
comp.F0.1640.0000.163
comp.FC0.0040.0000.004
comp.SAM0.5640.0000.563
comp.adjp0.0080.0000.006
comp.ebayes0.0040.0000.003
comp.fdr0.0120.0000.011
comp.modF0.0000.0000.002
comp.modt0.0000.0000.002
comp.stat0.0040.0000.005
comp.t0.0120.0000.013
comp.unadjp0.0040.0000.005
deds.chooseTest2.6840.0162.703
deds.genExtra0.0040.0000.000
deds.stat2.0600.0122.073
deds.stat.linkC0.0160.0000.016
pairs.DEDS0.0840.0000.084
qqnorm.DEDS0.0280.0000.031
topgenes0.0160.0040.022