##############################################################################
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###
### Running 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_2.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/STRINGdb.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.4.2’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
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 ‘STRINGdb’ 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
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’
Undefined global functions or variables:
  download.file read.table sd tail
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "download.file", "read.table", "tail")
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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/STRINGdb.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL STRINGdb
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘STRINGdb’ ...
** 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 (STRINGdb)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 'https://stringdb-static.org/download/protein.aliases.v11.0/9606.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 13253303 bytes (12.6 MB)
==================================================
downloaded 12.6 MB

trying URL 'https://stringdb-static.org/download/protein.info.v11.0/9606.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 1894048 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://stringdb-static.org/download/protein.info.v11.0/511145.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 276124 bytes (269 KB)
==================================================
downloaded 269 KB

trying URL 'https://stringdb-static.org/download/protein.links.v11.0/511145.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 5323410 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

Warning:  we couldn't map to STRING 15% of your identifierstrying URL 'https://stringdb-static.org/download/protein.links.v11.0/9606.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 71241372 bytes (67.9 MB)
==================================================
downloaded 67.9 MB



RUNIT TEST PROTOCOL -- Fri Oct 15 00:33:35 2021 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
STRINGdb RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
193.393   4.028 236.932