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: 2017-10-16 01:06:04 -0400 (Mon, 16 Oct 2017)

EndedAt: 2017-10-16 01:08:59 -0400 (Mon, 16 Oct 2017)

EllapsedTime: 174.7 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 3.4.2 (2017-09-28)
* 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 41.932  1.128  43.086
diffPathways           26.712  0.836  27.578
consensusDistance      14.836  1.216  16.093
thresholdFingerprint   12.464  0.620  13.090
pathprint-package      12.600  0.308  12.913
consensusFingerprint    9.708  1.192  10.907
pluripotents.frame      9.956  0.712  10.677
customCDFAnn            7.448  0.568   8.023
exprs2fingerprint       7.116  0.188   7.312
* 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	2.084	0.008	2.093
consensusDistance	14.836	1.216	16.093
consensusFingerprint	9.708	1.192	10.907
customCDFAnn	7.448	0.568	8.023
diffPathways	26.712	0.836	27.578
exprs2fingerprint	7.116	0.188	7.312
genesets	0.000	0.000	0.001
pathprint-package	12.600	0.308	12.913
pathprint.Ce.gs	0.020	0.004	0.027
pathprint.Dm.gs	0.024	0.008	0.033
pathprint.Dr.gs	0.064	0.012	0.074
pathprint.Hs.gs	0.028	0.000	0.030
pathprint.Mm.gs	0.060	0.028	0.091
pathprint.Rn.gs	0.084	0.020	0.102
platform.thresholds	4.704	0.092	4.797
pluripotents.frame	9.956	0.712	10.677
single.chip.enrichment	41.932	1.128	43.086
thresholdFingerprint	12.464	0.620	13.090