Package: STRINGdb

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:STRINGdb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings STRINGdb_1.20.0.tar.gz

StartedAt: 2018-10-17 00:19:16 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:23:18 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 241.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: STRINGdb.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:STRINGdb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings STRINGdb_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/STRINGdb.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STRINGdb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STRINGdb’ version ‘1.20.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘STRINGdb’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'spinglass.community(get_subnetwork(string_ids), ': unused arguments (merges = TRUE, modularity = TRUE) 
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/STRINGdb.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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
coeffOfvar: no visible global function definition for ‘sd’
downloadAbsentFile: no visible global function definition for ‘tail’
downloadAbsentFile: no visible global function definition for
  ‘download.file’
downloadAbsentFileSTRING: no visible global function definition for
  ‘read.table’
downloadAbsentFileSTRING: no visible global function definition for
  ‘tail’
downloadAbsentFileSTRING: no visible global function definition for
  ‘download.file’
get_STRING_species: no visible global function definition for
  ‘read.table’
plot_ppi_enrichment_graph: no visible global function definition for
  ‘pdf’
plot_ppi_enrichment_graph: no visible global function definition for
  ‘jpeg’
plot_ppi_enrichment_graph: no visible global function definition for
  ‘plot’
plot_ppi_enrichment_graph: no visible global function definition for
  ‘abline’
plot_ppi_enrichment_graph: no visible global function definition for
  ‘dev.off’
ppi_enrichment: no visible global function definition for ‘ppois’
ppi_enrichment_full: no visible global function definition for
  ‘txtProgressBar’
ppi_enrichment_full: no visible global function definition for
  ‘setTxtProgressBar’
ppi_enrichment_full: no visible global function definition for ‘ppois’
Undefined global functions or variables:
  abline dev.off download.file jpeg pdf plot ppois read.table sd
  setTxtProgressBar tail txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf")
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "ppois", "sd")
  importFrom("utils", "download.file", "read.table", "setTxtProgressBar",
             "tail", "txtProgressBar")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/STRINGdb.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL STRINGdb
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘STRINGdb’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'spinglass.community(get_subnetwork(string_ids), ': unused arguments (merges = TRUE, modularity = TRUE) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (STRINGdb)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("STRINGdb")
trying URL 'http://string.uzh.ch/permanent/string/10/protein_aliases/9606__protein_aliases_tf.tsv.gz'
Content type 'application/x-gzip' length 13939907 bytes (13.3 MB)
==================================================
downloaded 13.3 MB

trying URL 'http://string.uzh.ch/permanent/string/10/proteins/9606__proteins.tsv.gz'
Content type 'application/x-gzip' length 1815122 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

Warning:  we couldn't map to STRING 14% of your identifiersWarning:  we couldn't map to STRING 14% of your identifiers

RUNIT TEST PROTOCOL -- Wed Oct 17 00:23:11 2018 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
STRINGdb RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
166.907   7.085 198.481 

name	user	system	elapsed
STRINGdb-class	0.002	0.000	0.002