BioC 3.5: CHECK report for pathprint on malbec2

Package: pathprint

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pathprint_1.4.0.tar.gz

StartedAt: 2017-08-13 01:10:57 -0400 (Sun, 13 Aug 2017)

EndedAt: 2017-08-13 01:13:51 -0400 (Sun, 13 Aug 2017)

EllapsedTime: 174.2 seconds

RetCode: 0

Status:  OK

CheckDir: pathprint.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pathprint_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/pathprint.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.4.0’
* 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 42.040  1.192  43.272
diffPathways           27.656  0.208  27.888
consensusDistance      14.696  0.956  15.696
pathprint-package      13.212  0.236  13.460
thresholdFingerprint   12.260  0.136  12.403
pluripotents.frame     10.644  0.172  10.826
consensusFingerprint    9.784  0.604  10.396
customCDFAnn            7.912  0.148   8.094
exprs2fingerprint       7.496  0.104   7.607
* 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-3.5-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	2.044	0.028	2.073
consensusDistance	14.696	0.956	15.696
consensusFingerprint	9.784	0.604	10.396
customCDFAnn	7.912	0.148	8.094
diffPathways	27.656	0.208	27.888
exprs2fingerprint	7.496	0.104	7.607
genesets	0.000	0.000	0.002
pathprint-package	13.212	0.236	13.460
pathprint.Ce.gs	0.024	0.000	0.025
pathprint.Dm.gs	0.016	0.016	0.030
pathprint.Dr.gs	0.056	0.024	0.079
pathprint.Hs.gs	0.032	0.000	0.032
pathprint.Mm.gs	0.084	0.016	0.099
pathprint.Rn.gs	0.076	0.016	0.095
platform.thresholds	4.684	0.108	4.796
pluripotents.frame	10.644	0.172	10.826
single.chip.enrichment	42.040	1.192	43.272
thresholdFingerprint	12.260	0.136	12.403