BioC 3.2: CHECK report for pdInfoBuilder on perceval

Package: pdInfoBuilder

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pdInfoBuilder_1.34.0.tar.gz

StartedAt: 2015-11-10 08:00:23 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 08:03:03 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 160.3 seconds

RetCode: 0

Status:  OK

CheckDir: pdInfoBuilder.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pdInfoBuilder_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/pdInfoBuilder.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pdInfoBuilder/DESCRIPTION’ ... OK
* this is package ‘pdInfoBuilder’ version ‘1.34.0’
* 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 ‘pdInfoBuilder’ can be installed ... [16s/16s] 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’
getAllFSetMpsTables: no visible global function definition for
  ‘%dopar%’
getAllFSetMpsTables: no visible global function definition for
  ‘foreach’
getAllFSetMpsTables: no visible binding for global variable ‘i’
* 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 ... [8s/8s] 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-3.2-bioc/meat/pdInfoBuilder.Rcheck/00check.log’
for details.

* installing *source* package ‘pdInfoBuilder’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pdInfoBuilder.c -o pdInfoBuilder.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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)

name	user	system	elapsed
AffyExpressionPDInfoPkgSeed-class	0.003	0.001	0.004
AffySNPCNVPDInfoPkgSeed-class	0.003	0.000	0.003
AffySNPCNVPDInfoPkgSeed2-class	0.003	0.000	0.002
AffySNPPDInfoPkgSeed-class	0.508	0.014	0.522
AffySNPPDInfoPkgSeed2-class	0.003	0.001	0.002
AffySTPDInfoPkgSeed-class	0.003	0.000	0.003
AffyTilingPDInfoPkgSeed-class	0.002	0.000	0.002
NgsExpressionPDInfoPkgSeed-class	0.002	0.001	0.002
NgsTilingPDInfoPkgSeed-class	0.002	0.000	0.003
NimbleGenPDInfoPkgSeed-class	0.002	0.000	0.002
makePdInfoPackage	0.002	0.000	0.002