Package: pathprint

Version: 1.10.4

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pathprint_1.10.4.tar.gz

StartedAt: 2018-10-16 02:34:23 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 02:37:54 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 211.1 seconds

RetCode: 0

Status:  OK

CheckDir: pathprint.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pathprint.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pathprint_1.10.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/pathprint.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.4’
* 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 47.504  0.424  47.962
diffPathways           29.596  0.760  30.382
consensusDistance      18.328  1.140  19.576
pathprint-package      16.580  0.460  17.055
thresholdFingerprint   16.428  0.468  16.909
customCDFAnn           13.320  0.396  13.724
pluripotents.frame     13.236  0.420  13.674
consensusFingerprint   12.620  0.660  13.290
exprs2fingerprint      12.600  0.344  12.955
platform.thresholds     8.992  0.380   9.378
* 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-3.7-bioc/meat/pathprint.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL pathprint
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* installing to library ‘/home/biocbuild/bbs-3.7-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	18.328	1.140	19.576
consensusFingerprint	12.62	0.66	13.29
customCDFAnn	13.320	0.396	13.724
diffPathways	29.596	0.760	30.382
exprs2fingerprint	12.600	0.344	12.955
genesets	0.004	0.000	0.001
pathprint-package	16.580	0.460	17.055
pathprint.Ce.gs	0.032	0.016	0.062
pathprint.Dm.gs	0.028	0.020	0.048
pathprint.Dr.gs	0.108	0.036	0.147
pathprint.Hs.gs	0.052	0.000	0.052
pathprint.Mm.gs	0.104	0.036	0.141
pathprint.Rn.gs	0.10	0.04	0.15
platform.thresholds	8.992	0.380	9.378
pluripotents.frame	13.236	0.420	13.674
single.chip.enrichment	47.504	0.424	47.962
thresholdFingerprint	16.428	0.468	16.909