BioC 3.3: CHECK report for AffyCompatible on zin2

Package: AffyCompatible

Version: 1.32.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AffyCompatible_1.32.0.tar.gz

StartedAt: 2016-10-12 23:16:36 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:18:41 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 124.5 seconds

RetCode: 0

Status:  OK

CheckDir: AffyCompatible.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AffyCompatible_1.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AffyCompatible.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 ‘AffyCompatible/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AffyCompatible’ 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 ‘AffyCompatible’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.readAnnotation: no visible global function definition for
  ‘download.file’
.readAnnotation: no visible global function definition for ‘read.csv’
.readAnnotation: no visible global function definition for ‘read.delim’
.readXmlAsClass: no visible global function definition for
  ‘xmlTreeParse’
.xassn: no visible global function definition for ‘xpathApply’
.xattrs: no visible global function definition for ‘xmlAttrs’
.xclass: no visible global function definition for ‘xmlName’
.xclass: no visible global function definition for ‘xpathApply’
.xclass: no visible binding for global variable ‘xmlName’
.xmlDoc: no visible global function definition for ‘xmlDoc’
.xpcdata: no visible global function definition for ‘xpathApply’
.xvalue: no visible global function definition for ‘xpathApply’
readXml: no visible global function definition for ‘xmlTreeParse’
xclass: no visible global function definition for ‘xpathApply’
Undefined global functions or variables:
  download.file read.csv read.delim xmlAttrs xmlDoc xmlName
  xmlTreeParse xpathApply
Consider adding
  importFrom("utils", "download.file", "read.csv", "read.delim")
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 R/sysdata.rda ... 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
Examples with CPU or elapsed time > 5s
                       user system elapsed
NetAffxResource-class 6.685  0.141  22.958
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/AffyCompatible.Rcheck/00check.log’
for details.

* installing *source* package ‘AffyCompatible’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AffyCompatible)

name	user	system	elapsed
AffyCompatible-class	0.001	0.000	0.001
NetAffxResource-class	6.685	0.141	22.958
readArr	0.415	0.000	0.414
readMage	1.174	0.004	1.191
readNetAffx	0.000	0.000	0.001
readXml	0.064	0.000	0.064
xclass	0.096	0.000	0.096
zzz-ARRCompatibility-class	0.002	0.000	0.002
zzz-DTTCompatibility-class	0.040	0.008	0.048
zzz-NetAffxCompatibility-class	0.002	0.000	0.002