Package: pathprint

Version: 1.6.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings pathprint_1.6.0.tar.gz

StartedAt: 2018-04-12 01:41:01 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:43:57 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 176.0 seconds

RetCode: 0

Status:  OK

CheckDir: pathprint.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings pathprint_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/pathprint.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 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 43.716  0.296  44.044
diffPathways           26.548  0.504  27.079
consensusDistance      14.244  0.704  14.987
pathprint-package      13.172  0.528  13.711
thresholdFingerprint   12.444  0.428  12.887
consensusFingerprint    9.824  0.520  10.351
pluripotents.frame      9.592  0.356   9.957
customCDFAnn            7.652  0.400   8.064
exprs2fingerprint       7.496  0.400   7.905
platform.thresholds     4.856  0.400   5.264
* 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
  ‘/home/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	2.128	0.040	2.171
consensusDistance	14.244	0.704	14.987
consensusFingerprint	9.824	0.520	10.351
customCDFAnn	7.652	0.400	8.064
diffPathways	26.548	0.504	27.079
exprs2fingerprint	7.496	0.400	7.905
genesets	0.004	0.000	0.002
pathprint-package	13.172	0.528	13.711
pathprint.Ce.gs	0.032	0.008	0.039
pathprint.Dm.gs	0.044	0.008	0.052
pathprint.Dr.gs	0.060	0.048	0.105
pathprint.Hs.gs	0.032	0.000	0.032
pathprint.Mm.gs	0.104	0.040	0.143
pathprint.Rn.gs	0.124	0.024	0.148
platform.thresholds	4.856	0.400	5.264
pluripotents.frame	9.592	0.356	9.957
single.chip.enrichment	43.716	0.296	44.044
thresholdFingerprint	12.444	0.428	12.887