Package: pathprint

Version: 1.13.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pathprint_1.13.0.tar.gz

StartedAt: 2019-04-09 02:35:05 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:39:58 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 293.4 seconds

RetCode: 0

Status:  OK

CheckDir: pathprint.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pathprint_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/pathprint.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.13.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
single.chip.enrichment 70.077  0.732  70.842
diffPathways           43.096  0.710  43.883
pathprint-package      24.439  0.882  25.485
consensusDistance      23.346  1.436  25.376
thresholdFingerprint   21.815  0.592  22.411
customCDFAnn           17.388  0.668  18.061
pluripotents.frame     17.137  0.700  17.887
consensusFingerprint   16.451  0.848  17.300
exprs2fingerprint      14.503  0.563  15.123
platform.thresholds    12.657  0.635  13.339
* 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-3.9-bioc/meat/pathprint.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL pathprint
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	23.346	1.436	25.376
consensusFingerprint	16.451	0.848	17.300
customCDFAnn	17.388	0.668	18.061
diffPathways	43.096	0.710	43.883
exprs2fingerprint	14.503	0.563	15.123
genesets	0.001	0.000	0.001
pathprint-package	24.439	0.882	25.485
pathprint.Ce.gs	0.044	0.016	0.061
pathprint.Dm.gs	0.062	0.012	0.073
pathprint.Dr.gs	0.100	0.064	0.164
pathprint.Hs.gs	0.053	0.004	0.057
pathprint.Mm.gs	0.165	0.036	0.242
pathprint.Rn.gs	0.130	0.060	0.216
platform.thresholds	12.657	0.635	13.339
pluripotents.frame	17.137	0.700	17.887
single.chip.enrichment	70.077	0.732	70.842
thresholdFingerprint	21.815	0.592	22.411