Package: pathprint

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathprint.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathprint_1.13.0.tar.gz

StartedAt: 2019-04-09 02:44:37 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:50:38 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 361.0 seconds

RetCode: 0

Status:  OK

CheckDir: pathprint.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathprint.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathprint_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pathprint.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathprint/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathprint’ version ‘1.13.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pathprint’ 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
exprs2fingerprint: no visible binding for global variable ‘chipframe’
exprs2fingerprint: no visible binding for global variable ‘genesets’
thresholdFingerprint: no visible binding for global variable
  ‘platform.thresholds’
Undefined global functions or variables:
  chipframe genesets platform.thresholds
* 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
single.chip.enrichment 73.254 13.791  87.761
diffPathways           51.883  8.277  61.026
pathprint-package      25.906  2.779  28.916
consensusDistance      26.314  2.212  31.035
thresholdFingerprint   23.898  2.953  27.020
consensusFingerprint   18.772  2.052  21.020
exprs2fingerprint      18.357  1.339  19.965
pluripotents.frame     18.006  1.516  19.763
customCDFAnn           17.494  1.521  19.198
platform.thresholds    14.020  1.508  15.625
* 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-3.9-bioc/meat/pathprint.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 pathprint
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘pathprint’ ...
** 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 (pathprint)

name	user	system	elapsed
consensusDistance	26.314	2.212	31.035
consensusFingerprint	18.772	2.052	21.020
customCDFAnn	17.494	1.521	19.198
diffPathways	51.883	8.277	61.026
exprs2fingerprint	18.357	1.339	19.965
genesets	0.002	0.001	0.003
pathprint-package	25.906	2.779	28.916
pathprint.Ce.gs	0.032	0.002	0.036
pathprint.Dm.gs	0.038	0.001	0.040
pathprint.Dr.gs	0.096	0.002	0.104
pathprint.Hs.gs	0.051	0.005	0.061
pathprint.Mm.gs	0.115	0.002	0.117
pathprint.Rn.gs	0.107	0.004	0.118
platform.thresholds	14.020	1.508	15.625
pluripotents.frame	18.006	1.516	19.763
single.chip.enrichment	73.254	13.791	87.761
thresholdFingerprint	23.898	2.953	27.020