Package: NCIgraph

Version: 1.30.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:NCIgraph.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings NCIgraph_1.30.0.tar.gz

StartedAt: 2019-04-16 01:44:41 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:45:22 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 41.3 seconds

RetCode: 0

Status:  OK

CheckDir: NCIgraph.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:NCIgraph.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings NCIgraph_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/NCIgraph.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 ‘NCIgraph/DESCRIPTION’ ... OK
* this is package ‘NCIgraph’ version ‘1.30.0’
* 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 ‘NCIgraph’ 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 ... NOTE
':::' call which should be '::': ‘RCy3:::existing.CytoscapeWindow’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
* 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/NCIgraph.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 NCIgraph
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘NCIgraph’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘RCy3’ for request: ‘getWindowList’ when loading ‘NCIgraph’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘RCy3’ for request: ‘getWindowList’ when loading ‘NCIgraph’
* DONE (NCIgraph)

name	user	system	elapsed
NCI.demo.cyList	0.344	0.004	0.350
getNCIPathways	2.416	0.024	2.442
getSubtype.NCIgraph	2.572	0.000	2.574
parseNCInetwork	0.152	0.000	0.149
translateNCI2GeneID	2.492	0.000	2.496