Package: pathprint

Version: 1.16.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pathprint_1.16.0.tar.gz

StartedAt: 2020-04-15 04:39:53 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:45:34 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 341.1 seconds

RetCode: 0

Status:  OK

CheckDir: pathprint.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pathprint_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/pathprint.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.0’
* 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 81.068  0.680  82.773
diffPathways           50.204  0.584  52.582
consensusDistance      28.036  1.532  30.021
thresholdFingerprint   26.576  0.676  27.459
pathprint-package      25.048  0.672  25.866
consensusFingerprint   19.948  0.820  21.078
customCDFAnn           19.836  0.564  20.766
pluripotents.frame     19.192  0.736  20.064
exprs2fingerprint      19.088  0.568  20.263
platform.thresholds    14.040  0.544  15.056
* 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-3.10-bioc/meat/pathprint.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL pathprint
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* installing to library ‘/home/biocbuild/bbs-3.10-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	28.036	1.532	30.021
consensusFingerprint	19.948	0.820	21.078
customCDFAnn	19.836	0.564	20.766
diffPathways	50.204	0.584	52.582
exprs2fingerprint	19.088	0.568	20.263
genesets	0.000	0.000	0.001
pathprint-package	25.048	0.672	25.866
pathprint.Ce.gs	0.028	0.016	0.044
pathprint.Dm.gs	0.040	0.020	0.085
pathprint.Dr.gs	0.096	0.044	0.141
pathprint.Hs.gs	0.052	0.000	0.051
pathprint.Mm.gs	0.128	0.044	0.173
pathprint.Rn.gs	0.120	0.060	0.178
platform.thresholds	14.040	0.544	15.056
pluripotents.frame	19.192	0.736	20.064
single.chip.enrichment	81.068	0.680	82.773
thresholdFingerprint	26.576	0.676	27.459