Package: DEGseq

Version: 1.32.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DEGseq_1.32.0.tar.gz

StartedAt: 2018-04-11 22:49:34 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:50:15 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 40.3 seconds

RetCode: 0

Status:  OK

CheckDir: DEGseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DEGseq_1.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DEGseq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEGseq/DESCRIPTION’ ... OK
* this is package ‘DEGseq’ version ‘1.32.0’
* 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 ‘DEGseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
    libs      1.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘methods’ ‘qvalue’ ‘samr’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘qvalue’ ‘samr’
  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
DEGexp: no visible global function definition for ‘dev.cur’
DEGexp2: no visible global function definition for ‘dev.cur’
getQvalue2: no visible global function definition for ‘qvalue’
samWrapper: no visible global function definition for ‘check.format’
samWrapper: no visible global function definition for ‘samr’
samWrapper: no visible global function definition for
  ‘samr.compute.delta.table’
samWrapper: no visible global function definition for
  ‘samr.compute.siggenes.table’
Undefined global functions or variables:
  check.format dev.cur qvalue samr samr.compute.delta.table
  samr.compute.siggenes.table
Consider adding
  importFrom("grDevices", "dev.cur")
to your NAMESPACE file.
* 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
* 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-3.6-bioc/meat/DEGseq.Rcheck/00check.log’
for details.

* installing *source* package ‘DEGseq’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c getGeneExp.cpp -o getGeneExp.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o DEGseq.so getGeneExp.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/DEGseq.Rcheck/DEGseq/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 (DEGseq)

name	user	system	elapsed
DEGexp	1.016	0.012	1.049
DEGexp2	1.920	0.004	1.925
DEGseq	0.684	0.004	0.687
getGeneExp	0.068	0.000	0.070
readGeneExp	0.020	0.000	0.019
samWrapper	1.580	0.024	1.603