Package: pathprint

Version: 1.17.0

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_1.17.0.tar.gz

StartedAt: 2020-01-16 07:16:05 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:24:40 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 514.7 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 --install=check:pathprint.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathprint_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/pathprint.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.17.0’
* 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 ... OK
* 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 (user + system) or elapsed time > 5s
                          user system elapsed
single.chip.enrichment 111.120 29.054 140.297
diffPathways            67.575 15.423  83.632
consensusDistance       34.751  4.721  46.591
thresholdFingerprint    31.073  5.792  36.865
pathprint-package       28.182  4.836  33.117
consensusFingerprint    22.622  4.317  26.942
pluripotents.frame      22.106  3.108  25.799
customCDFAnn            21.491  3.365  24.859
exprs2fingerprint       21.251  2.949  24.223
platform.thresholds     15.898  3.015  19.192
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/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	34.751	4.721	46.591
consensusFingerprint	22.622	4.317	26.942
customCDFAnn	21.491	3.365	24.859
diffPathways	67.575	15.423	83.632
exprs2fingerprint	21.251	2.949	24.223
genesets	0.003	0.002	0.005
pathprint-package	28.182	4.836	33.117
pathprint.Ce.gs	0.029	0.002	0.032
pathprint.Dm.gs	0.039	0.003	0.041
pathprint.Dr.gs	0.102	0.004	0.106
pathprint.Hs.gs	0.056	0.005	0.061
pathprint.Mm.gs	0.113	0.003	0.116
pathprint.Rn.gs	0.131	0.002	0.133
platform.thresholds	15.898	3.015	19.192
pluripotents.frame	22.106	3.108	25.799
single.chip.enrichment	111.120	29.054	140.297
thresholdFingerprint	31.073	5.792	36.865