Package: pathprint

Version: 1.12.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings pathprint_1.12.0.tar.gz

StartedAt: 2019-04-16 01:58:47 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:03:27 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 280.1 seconds

RetCode: 0

Status:  OK

CheckDir: pathprint.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings pathprint_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/pathprint.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
single.chip.enrichment 67.208  0.576  67.874
diffPathways           44.536  0.444  45.069
pathprint-package      23.788  0.704  24.558
consensusDistance      22.632  1.236  23.991
thresholdFingerprint   20.568  0.656  21.245
pluripotents.frame     16.372  0.728  17.214
exprs2fingerprint      16.424  0.468  16.982
customCDFAnn           15.756  0.432  16.237
consensusFingerprint   15.172  0.628  15.850
platform.thresholds    14.056  0.580  14.819
* 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-3.8-bioc/meat/pathprint.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL pathprint
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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	22.632	1.236	23.991
consensusFingerprint	15.172	0.628	15.850
customCDFAnn	15.756	0.432	16.237
diffPathways	44.536	0.444	45.069
exprs2fingerprint	16.424	0.468	16.982
genesets	0.004	0.000	0.002
pathprint-package	23.788	0.704	24.558
pathprint.Ce.gs	0.032	0.016	0.061
pathprint.Dm.gs	0.040	0.024	0.062
pathprint.Dr.gs	0.124	0.012	0.138
pathprint.Hs.gs	0.032	0.000	0.034
pathprint.Mm.gs	0.132	0.056	0.191
pathprint.Rn.gs	0.108	0.076	0.184
platform.thresholds	14.056	0.580	14.819
pluripotents.frame	16.372	0.728	17.214
single.chip.enrichment	67.208	0.576	67.874
thresholdFingerprint	20.568	0.656	21.245