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 04:13:54 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:21:59 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 484.5 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) (2019-03-18 r76245)
* 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 99.701 27.417 127.281
diffPathways           64.563 16.140  80.915
consensusDistance      31.921  4.423  42.250
pathprint-package      30.120  5.236  35.576
thresholdFingerprint   29.544  5.586  35.132
consensusFingerprint   22.219  3.999  26.221
pluripotents.frame     21.908  3.193  26.017
customCDFAnn           19.697  2.996  22.696
exprs2fingerprint      19.884  2.556  22.498
platform.thresholds    15.902  2.916  19.116
* 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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pathprint)

name	user	system	elapsed
consensusDistance	31.921	4.423	42.250
consensusFingerprint	22.219	3.999	26.221
customCDFAnn	19.697	2.996	22.696
diffPathways	64.563	16.140	80.915
exprs2fingerprint	19.884	2.556	22.498
genesets	0.002	0.001	0.003
pathprint-package	30.120	5.236	35.576
pathprint.Ce.gs	0.020	0.002	0.022
pathprint.Dm.gs	0.026	0.002	0.029
pathprint.Dr.gs	0.079	0.002	0.081
pathprint.Hs.gs	0.041	0.004	0.044
pathprint.Mm.gs	0.125	0.003	0.129
pathprint.Rn.gs	0.128	0.002	0.130
platform.thresholds	15.902	2.916	19.116
pluripotents.frame	21.908	3.193	26.017
single.chip.enrichment	99.701	27.417	127.281
thresholdFingerprint	29.544	5.586	35.132