Package: pathprint

Version: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2019-04-16 01:47:08 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:53:32 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 383.3 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/pathprint.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.0’
* 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 84.351 13.798  98.936
diffPathways           50.148  9.298  60.332
consensusDistance      28.138  2.447  38.908
thresholdFingerprint   25.641  3.006  28.833
pathprint-package      24.518  2.738  27.567
consensusFingerprint   19.357  1.943  22.016
pluripotents.frame     19.327  1.758  21.288
customCDFAnn           17.594  1.641  19.475
exprs2fingerprint      17.127  1.142  18.504
platform.thresholds    15.342  1.619  17.405
* 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-3.8-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	28.138	2.447	38.908
consensusFingerprint	19.357	1.943	22.016
customCDFAnn	17.594	1.641	19.475
diffPathways	50.148	9.298	60.332
exprs2fingerprint	17.127	1.142	18.504
genesets	0.002	0.001	0.003
pathprint-package	24.518	2.738	27.567
pathprint.Ce.gs	0.030	0.002	0.033
pathprint.Dm.gs	0.037	0.001	0.037
pathprint.Dr.gs	0.085	0.003	0.087
pathprint.Hs.gs	0.059	0.004	0.063
pathprint.Mm.gs	0.110	0.002	0.114
pathprint.Rn.gs	0.113	0.002	0.115
platform.thresholds	15.342	1.619	17.405
pluripotents.frame	19.327	1.758	21.288
single.chip.enrichment	84.351	13.798	98.936
thresholdFingerprint	25.641	3.006	28.833