Package: pathprint

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pathprint_1.6.0.tar.gz

StartedAt: 2018-04-12 07:26:48 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:30:57 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 248.7 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 --no-vignettes --timings pathprint_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/pathprint.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
single.chip.enrichment 56.503 13.078  71.010
diffPathways           36.598  6.288  43.763
pathprint-package      16.496  2.055  18.872
consensusDistance      17.091  1.188  18.664
thresholdFingerprint   12.638  1.984  14.800
consensusFingerprint   12.436  1.319  14.008
pluripotents.frame     11.864  1.263  13.362
customCDFAnn            9.190  0.999  10.395
exprs2fingerprint       8.830  0.868   9.884
platform.thresholds     5.791  0.962   6.883
* 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-3.6-bioc/meat/pathprint.Rcheck/00check.log’
for details.

* installing *source* package ‘pathprint’ ...
** 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 (pathprint)

name	user	system	elapsed
chipframe	2.326	0.058	2.426
consensusDistance	17.091	1.188	18.664
consensusFingerprint	12.436	1.319	14.008
customCDFAnn	9.190	0.999	10.395
diffPathways	36.598	6.288	43.763
exprs2fingerprint	8.830	0.868	9.884
genesets	0.002	0.001	0.003
pathprint-package	16.496	2.055	18.872
pathprint.Ce.gs	0.024	0.002	0.026
pathprint.Dm.gs	0.032	0.001	0.032
pathprint.Dr.gs	0.073	0.002	0.074
pathprint.Hs.gs	0.042	0.003	0.045
pathprint.Mm.gs	0.088	0.002	0.094
pathprint.Rn.gs	0.083	0.002	0.086
platform.thresholds	5.791	0.962	6.883
pluripotents.frame	11.864	1.263	13.362
single.chip.enrichment	56.503	13.078	71.010
thresholdFingerprint	12.638	1.984	14.800