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CHECK report for DEDS on malbec2

This page was generated on 2019-04-09 11:23:45 -0400 (Tue, 09 Apr 2019).

Package 396/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEDS 1.57.0
Yuanyuan Xiao
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/DEDS
Branch: master
Last Commit: e23381b
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: DEDS
Version: 1.57.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DEDS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DEDS_1.57.0.tar.gz
StartedAt: 2019-04-08 23:55:47 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:56:24 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 36.6 seconds
RetCode: 0
Status:  OK 
CheckDir: DEDS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DEDS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DEDS_1.57.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DEDS.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.57.0’
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  hist.DEDS pairs.DEDS qqnorm.DEDS
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ... NOTE
Note: information on .o files is not available
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/DEDS.Rcheck/00check.log’
for details.



Installation output

DEDS.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DEDS
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DEDS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c deds.c -o deds.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c distance.c -o distance.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c input.c -o input.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c manip.c -o manip.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c random.c -o random.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c sampling.c -o sampling.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-DEDS/00new/DEDS/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DEDS)

Tests output


Example timings

DEDS.Rcheck/DEDS-Ex.timings

nameusersystemelapsed
aggregateFun0.0060.0040.010
comp.B0.0000.0030.003
comp.F0.2070.0000.207
comp.FC0.0030.0000.003
comp.SAM0.7810.0080.788
comp.adjp0.0080.0000.008
comp.ebayes0.0020.0000.002
comp.fdr0.0090.0040.013
comp.modF0.0000.0020.002
comp.modt0.0010.0010.001
comp.stat0.0040.0000.004
comp.t0.0110.0000.011
comp.unadjp0.0070.0000.007
deds.chooseTest3.3800.0073.416
deds.genExtra0.0010.0000.000
deds.stat2.3210.0122.349
deds.stat.linkC0.0270.0000.027
pairs.DEDS0.1290.0000.130
qqnorm.DEDS0.0340.0080.042
topgenes0.0230.0040.027