Package: pathprint

Version: 1.10.4

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_1.10.4.tar.gz

StartedAt: 2018-10-16 23:07:46 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:14:20 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 393.8 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_1.10.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/pathprint.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.4’
* 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 81.295 14.504  96.580
diffPathways           51.421  8.781  60.727
consensusDistance      29.805  2.667  43.746
pathprint-package      26.155  2.922  29.447
thresholdFingerprint   25.690  3.088  28.985
consensusFingerprint   20.415  1.962  27.325
customCDFAnn           20.052  1.719  22.005
pluripotents.frame     19.391  1.797  21.407
exprs2fingerprint      18.248  1.274  19.690
platform.thresholds    13.697  1.380  15.268
* 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-3.7-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/3.5/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	29.805	2.667	43.746
consensusFingerprint	20.415	1.962	27.325
customCDFAnn	20.052	1.719	22.005
diffPathways	51.421	8.781	60.727
exprs2fingerprint	18.248	1.274	19.690
genesets	0.003	0.001	0.003
pathprint-package	26.155	2.922	29.447
pathprint.Ce.gs	0.031	0.001	0.033
pathprint.Dm.gs	0.030	0.001	0.031
pathprint.Dr.gs	0.073	0.002	0.075
pathprint.Hs.gs	0.058	0.004	0.062
pathprint.Mm.gs	0.096	0.001	0.099
pathprint.Rn.gs	0.082	0.001	0.086
platform.thresholds	13.697	1.380	15.268
pluripotents.frame	19.391	1.797	21.407
single.chip.enrichment	81.295	14.504	96.580
thresholdFingerprint	25.690	3.088	28.985