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BioC 3.5: CHECK report for DEDS on malbec2

This page was generated on 2017-08-16 13:12:22 -0400 (Wed, 16 Aug 2017).

Package 325/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEDS 1.50.0
Yuanyuan Xiao
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/DEDS
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  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEDS
Version: 1.50.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DEDS_1.50.0.tar.gz
StartedAt: 2017-08-15 22:25:55 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:26:25 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 29.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DEDS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DEDS_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DEDS.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 ‘DEDS/DESCRIPTION’ ... OK
* this is package ‘DEDS’ version ‘1.50.0’
* 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 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-3.5-bioc/meat/DEDS.Rcheck/00check.log’
for details.


DEDS.Rcheck/00install.out:

* installing *source* package ‘DEDS’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c deds.c -o deds.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c distance.c -o distance.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c input.c -o input.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c manip.c -o manip.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c random.c -o random.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sampling.c -o sampling.o
gcc -I/home/biocbuild/bbs-3.5-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-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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
aggregateFun0.0360.0080.046
comp.B0.0120.0000.014
comp.F0.1720.0000.172
comp.FC0.0280.0000.025
comp.SAM0.5520.0000.555
comp.adjp0.0400.0000.043
comp.ebayes0.0120.0000.012
comp.fdr0.0480.0000.049
comp.modF0.0120.0000.011
comp.modt0.0040.0000.002
comp.stat0.0040.0000.003
comp.t0.0400.0000.041
comp.unadjp0.0080.0000.004
deds.chooseTest2.2200.0002.222
deds.genExtra000
deds.stat1.7280.0081.736
deds.stat.linkC0.0080.0040.013
pairs.DEDS0.2280.0000.229
qqnorm.DEDS0.10.00.1
topgenes0.0760.0000.075