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BioC 3.5: CHECK report for BeadDataPackR on veracruz2

This page was generated on 2017-10-18 14:29:01 -0400 (Wed, 18 Oct 2017).

Package 98/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BeadDataPackR 1.28.0
Mike Smith
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/BeadDataPackR
Branch: RELEASE_3_5
Last Commit: 21a8f40
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 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: BeadDataPackR
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BeadDataPackR_1.28.0.tar.gz
StartedAt: 2017-10-18 00:52:16 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:52:32 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 15.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BeadDataPackR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BeadDataPackR_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BeadDataPackR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.28.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/BeadDataPackR.Rcheck/00check.log’
for details.


BeadDataPackR.Rcheck/00install.out:

* installing *source* package ‘BeadDataPackR’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BeadDataPackR.c -o BeadDataPackR.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_BeadDataPackR.c -o R_init_BeadDataPackR.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BeadDataPackR.so BeadDataPackR.o R_init_BeadDataPackR.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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)

BeadDataPackR.Rcheck/BeadDataPackR-Ex.timings:

nameusersystemelapsed
compressBeadData0.0580.0040.062
decompressBeadData0.0360.0020.037
extractLocsFile0.0240.0000.024
readCompressedData0.0070.0010.008