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BioC 3.4: CHECK report for pdInfoBuilder on zin1

This page was generated on 2016-09-21 03:36:12 -0700 (Wed, 21 Sep 2016).

Package 883/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pdInfoBuilder 1.37.1
Benilton Carvalho
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pdInfoBuilder
Last Changed Rev: 120519 / Revision: 121152
Last Changed Date: 2016-08-26 12:00:42 -0700 (Fri, 26 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pdInfoBuilder
Version: 1.37.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings pdInfoBuilder_1.37.1.tar.gz
StartedAt: 2016-09-20 10:27:27 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:29:36 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 129.5 seconds
RetCode: 0
Status:  OK 
CheckDir: pdInfoBuilder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings pdInfoBuilder_1.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/pdInfoBuilder.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pdInfoBuilder/DESCRIPTION’ ... OK
* this is package ‘pdInfoBuilder’ version ‘1.37.1’
* 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 ‘pdInfoBuilder’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘IRanges’ ‘oligoClasses’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cdf2table: no visible global function definition for ‘getDoParWorkers’
cdf2table: no visible global function definition for ‘%dopar%’
cdf2table: no visible global function definition for ‘foreach’
cdf2table: no visible binding for global variable ‘unitLst’
cdfUnits2table: no visible global function definition for ‘%do%’
cdfUnits2table: no visible global function definition for ‘foreach’
cdfUnits2table: no visible binding for global variable ‘i’
createChrDict: no visible global function definition for ‘na.omit’
getAllFSetMpsTables: no visible global function definition for
  ‘%dopar%’
getAllFSetMpsTables: no visible global function definition for
  ‘foreach’
getAllFSetMpsTables: no visible binding for global variable ‘i’
parseBpmapCel: no visible global function definition for ‘aggregate’
parseCdfSeqAnnotSnp: no visible global function definition for
  ‘aggregate’
parseNgsTrio: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  %do% %dopar% aggregate foreach getDoParWorkers i na.omit unitLst
Consider adding
  importFrom("stats", "aggregate", "na.omit")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/pdInfoBuilder.Rcheck/00check.log’
for details.


pdInfoBuilder.Rcheck/00install.out:

* installing *source* package ‘pdInfoBuilder’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/pdInfoBuilder.Rcheck/pdInfoBuilder/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 (pdInfoBuilder)

pdInfoBuilder.Rcheck/pdInfoBuilder-Ex.timings:

nameusersystemelapsed
AffyClariomSPDInfoPkgSeed-class0.0080.0000.009
AffyExpressionPDInfoPkgSeed-class0.0000.0000.001
AffySNPCNVPDInfoPkgSeed-class0.0040.0000.001
AffySNPCNVPDInfoPkgSeed2-class0.0000.0000.001
AffySNPPDInfoPkgSeed-class0.3280.0000.328
AffySNPPDInfoPkgSeed2-class0.0000.0000.001
AffySTPDInfoPkgSeed-class0.0000.0000.001
AffyTilingPDInfoPkgSeed-class0.0000.0000.001
NgsExpressionPDInfoPkgSeed-class0.0000.0000.001
NgsTilingPDInfoPkgSeed-class0.0000.0000.001
NimbleGenPDInfoPkgSeed-class0.0000.0000.001
makePdInfoPackage0.0000.0040.002