BioC 3.2: CHECK report for BaseSpaceR on zin1

Package: BaseSpaceR

Version: 1.13.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BaseSpaceR_1.13.2.tar.gz

StartedAt: 2015-08-23 21:49:23 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 21:49:53 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 30.4 seconds

RetCode: 0

Status:  OK

CheckDir: BaseSpaceR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BaseSpaceR_1.13.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BaseSpaceR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK
* this is package ‘BaseSpaceR’ version ‘1.13.2’
* 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 ‘BaseSpaceR’ can be installed ... [2s/2s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘Rsamtools’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
asBamFile: no visible global function definition for ‘BamFile’
GET,ServiceURI : .local: no visible global function definition for
  ‘basicHeaderGatherer’
GET,ServiceURI : .local: no visible global function definition for
  ‘basicTextGatherer’
GET,ServiceURI : .local: no visible global function definition for
  ‘getForm’
GET,ServiceURI : .local: no visible global function definition for
  ‘curlOptions’
POST,ServiceURI : .local: no visible global function definition for
  ‘basicHeaderGatherer’
POST,ServiceURI : .local: no visible global function definition for
  ‘basicTextGatherer’
POST,ServiceURI : .local: no visible global function definition for
  ‘curlPerform’
POSTForm,ServiceURI : .local: no visible global function definition for
  ‘basicHeaderGatherer’
POSTForm,ServiceURI : .local: no visible global function definition for
  ‘basicTextGatherer’
POSTForm,ServiceURI : .local: no visible global function definition for
  ‘postForm’
POSTForm,ServiceURI : .local: no visible global function definition for
  ‘curlOptions’
getBAMs,AppResults : .local: no visible binding for global variable
  ‘BamFileList’
getFiles,AppAuth : .local : .toDisk: no visible global function
  definition for ‘CFILE’
getFiles,AppAuth : .local : .toDisk: no visible global function
  definition for ‘curlPerform’
getFiles,AppAuth : .local : .toMem: no visible global function
  definition for ‘getURLContent’
getFiles,AppAuth : .local : .toMem: no visible binding for global
  variable ‘dsize’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/10s] 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-3.2-bioc/meat/BaseSpaceR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
AppAuth-class	0.108	0.008	0.856
AppResults-class	0.000	0.003	0.001
AppSessionAuth	0.000	0.000	0.002
AppSessions-class	0.002	0.000	0.002
Coverage	0.011	0.000	0.011
Error	0.001	0.000	0.001
Files-class	0.053	0.008	0.806
FilesExtra	0.037	0.003	0.689
Genomes-class	0.071	0.005	1.095
Projects-class	0.078	0.004	1.146
Response-class	0.003	0.000	0.003
Runs-class	0.124	0.004	2.037
Samples-class	0.071	0.004	1.140
ServiceURI-class	0.001	0.000	0.001
Users-class	0.040	0.007	0.661
Variants	0.047	0.000	0.715
data-aAuth	0.011	0.003	0.301