Package: BeadDataPackR

Version: 1.30.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BeadDataPackR_1.30.0.tar.gz

StartedAt: 2018-04-11 21:42:44 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 21:43:01 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 17.1 seconds

RetCode: 0

Status:  OK

CheckDir: BeadDataPackR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BeadDataPackR_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BeadDataPackR.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 ‘BeadDataPackR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BeadDataPackR’ version ‘1.30.0’
* 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 ‘BeadDataPackR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
combineFiles: no visible global function definition for
  ‘setTxtProgressBar’
compressBeadData: no visible global function definition for
  ‘txtProgressBar’
compressBeadData: no visible global function definition for
  ‘setTxtProgressBar’
createIndices: no visible global function definition for
  ‘setTxtProgressBar’
createIndices: no visible global function definition for ‘lm’
decodeIndices: no visible global function definition for
  ‘setTxtProgressBar’
decompressBeadData: no visible global function definition for
  ‘txtProgressBar’
decompressBeadData: no visible global function definition for
  ‘setTxtProgressBar’
decompressBeadData: no visible global function definition for
  ‘write.table’
numberOfChannels: no visible global function definition for
  ‘read.table’
writeBabBody: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  lm read.table setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("stats", "lm")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/BeadDataPackR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
compressBeadData	0.04	0.00	0.04
decompressBeadData	0.04	0.00	0.04
extractLocsFile	0.028	0.000	0.029
readCompressedData	0.008	0.000	0.006