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BioC 3.5: CHECK report for sva on malbec2

This page was generated on 2017-08-16 13:14:13 -0400 (Wed, 16 Aug 2017).

Package 1291/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sva 3.24.4
Jeffrey T. Leek , John D. Storey
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/sva
Last Changed Rev: 130529 / Revision: 131943
Last Changed Date: 2017-06-19 11:01:16 -0400 (Mon, 19 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sva
Version: 3.24.4
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sva_3.24.4.tar.gz
StartedAt: 2017-08-16 02:34:13 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:36:44 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 151.2 seconds
RetCode: 0
Status:  OK 
CheckDir: sva.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sva_3.24.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/sva.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 ‘sva/DESCRIPTION’ ... OK
* this is package ‘sva’ version ‘3.24.4’
* 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 ‘sva’ 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
sva.check  6.4  0.012    6.42
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: OK

sva.Rcheck/00install.out:

* installing *source* package ‘sva’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sva.c -o sva.o
sva.c:27:34: warning: missing braces around initializer [-Wmissing-braces]
 R_CallMethodDef callMethods[]  = {
                                  ^
sva.c:27:34: note: (near initialization for ‘callMethods’)
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o sva.so sva.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/sva.Rcheck/sva/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 (sva)

sva.Rcheck/sva-Ex.timings:

nameusersystemelapsed
ComBat1.1000.0721.184
empirical.controls2.0320.0482.081
f.pvalue0.2520.0000.251
fstats0.2520.0040.256
fsva1.0680.0081.100
irwsva.build1.3520.0041.356
num.sv0.8200.0080.827
psva0.4120.0040.418
qsva0.2440.0601.822
read.degradation.matrix0.2320.1003.344
ssva0.8680.0600.928
sva1.4040.0041.408
sva.check6.4000.0126.420
svaseq0.7200.0040.726
twostepsva.build2.8600.0082.870