Package: BaseSpaceR

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BaseSpaceR_1.26.0.tar.gz

StartedAt: 2019-04-15 22:28:27 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:29:54 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 86.8 seconds

RetCode: 0

Status:  OK

CheckDir: BaseSpaceR.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BaseSpaceR_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BaseSpaceR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK
* this is package ‘BaseSpaceR’ version ‘1.26.0’
* 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 ‘BaseSpaceR’ 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
'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: no visible global function definition for
  ‘basicHeaderGatherer’
GET,ServiceURI: no visible global function definition for
  ‘basicTextGatherer’
GET,ServiceURI: no visible global function definition for ‘getForm’
GET,ServiceURI: no visible global function definition for ‘curlOptions’
POST,ServiceURI: no visible global function definition for
  ‘basicHeaderGatherer’
POST,ServiceURI: no visible global function definition for
  ‘basicTextGatherer’
POST,ServiceURI: no visible global function definition for
  ‘curlPerform’
POSTForm,ServiceURI: no visible global function definition for
  ‘basicHeaderGatherer’
POSTForm,ServiceURI: no visible global function definition for
  ‘basicTextGatherer’
POSTForm,ServiceURI: no visible global function definition for
  ‘postForm’
POSTForm,ServiceURI: no visible global function definition for
  ‘curlOptions’
getBAMs,AppResults: no visible binding for global variable
  ‘BamFileList’
getFiles,AppAuth : .toDisk: no visible global function definition for
  ‘CFILE’
getFiles,AppAuth : .toDisk: no visible global function definition for
  ‘curlPerform’
getFiles,AppAuth : .toMem: no visible global function definition for
  ‘getURLContent’
getFiles,AppAuth : .toMem: no visible binding for global variable
  ‘dsize’
Undefined global functions or variables:
  BamFile BamFileList CFILE basicHeaderGatherer basicTextGatherer
  curlOptions curlPerform dsize getForm getURLContent postForm
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
AppAuth-class  0.261  0.017   6.820
Runs-class     0.173  0.010  15.701
Projects-class 0.141  0.009   6.889
Samples-class  0.141  0.006   6.232
Files-class    0.080  0.009   5.657
* 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-3.8-bioc/meat/BaseSpaceR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BaseSpaceR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BaseSpaceR’ ...
** R
** data
** inst
** byte-compile and prepare 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	0.261	0.017	6.820
AppResults-class	0.001	0.000	0.001
AppSessionAuth	0.001	0.000	0.002
AppSessions-class	0.001	0.000	0.001
Coverage	0.013	0.002	0.014
Error	0.000	0.000	0.001
Files-class	0.080	0.009	5.657
FilesExtra	0.080	0.010	1.545
Genomes-class	0.125	0.014	4.853
Projects-class	0.141	0.009	6.889
Response-class	0.003	0.001	0.004
Runs-class	0.173	0.010	15.701
Samples-class	0.141	0.006	6.232
ServiceURI-class	0.000	0.001	0.001
Users-class	0.077	0.005	3.905
Variants	0.062	0.004	2.482
data-aAuth	0.035	0.004	0.584