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BioC 3.1: CHECK report for STRINGdb on moscato2

This page was generated on 2015-10-09 09:30:42 -0700 (Fri, 09 Oct 2015).

Package 957/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STRINGdb 1.8.1
Andrea Franceschini
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/STRINGdb
Last Changed Rev: 105174 / Revision: 109384
Last Changed Date: 2015-06-19 09:38:55 -0700 (Fri, 19 Jun 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: STRINGdb
Version: 1.8.1
Command: rm -rf STRINGdb.buildbin-libdir STRINGdb.Rcheck && mkdir STRINGdb.buildbin-libdir STRINGdb.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=STRINGdb.buildbin-libdir STRINGdb_1.8.1.tar.gz >STRINGdb.Rcheck\00install.out 2>&1 && cp STRINGdb.Rcheck\00install.out STRINGdb-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=STRINGdb.buildbin-libdir --install="check:STRINGdb-install.out" --force-multiarch --no-vignettes --timings STRINGdb_1.8.1.tar.gz
StartedAt: 2015-10-09 06:39:38 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 07:12:55 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 1996.7 seconds
RetCode: 0
Status:  OK  
CheckDir: STRINGdb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf STRINGdb.buildbin-libdir STRINGdb.Rcheck && mkdir STRINGdb.buildbin-libdir STRINGdb.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=STRINGdb.buildbin-libdir STRINGdb_1.8.1.tar.gz >STRINGdb.Rcheck\00install.out 2>&1 && cp STRINGdb.Rcheck\00install.out STRINGdb-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=STRINGdb.buildbin-libdir --install="check:STRINGdb-install.out" --force-multiarch --no-vignettes --timings STRINGdb_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/STRINGdb.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'STRINGdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'STRINGdb' version '1.8.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'png' 'sqldf' 'plyr' 'igraph' 'RCurl' 'plotrix' 'RColorBrewer'
  'gplots' 'hash'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'STRINGdb' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.3Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Packages in Depends field not imported from:
  'RColorBrewer' 'RCurl' 'gplots' 'hash' 'igraph' 'methods' 'plotrix'
  'plyr' 'png' 'sqldf'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_STRING_species: no visible binding for global variable
  'official_name'
postFormSmart: no visible global function definition for 'curlOptions'
postFormSmart: no visible global function definition for
  'getCurlHandle'
postFormSmart: no visible binding for global variable 'curlEscape'
postFormSmart: no visible global function definition for 'postForm'
ppi_enrichment: no visible global function definition for 'V'
ppi_enrichment: no visible global function definition for 'ecount'
ppi_enrichment: no visible global function definition for
  'induced.subgraph'
ppi_enrichment: no visible global function definition for 'degree'
ppi_enrichment_full: no visible global function definition for 'V'
ppi_enrichment_full: no visible global function definition for 'ecount'
ppi_enrichment_full: no visible global function definition for
  'induced.subgraph'
ppi_enrichment_full: no visible global function definition for 'degree'
ppie.getNumEdgesBetween: no visible global function definition for
  'neighborhood'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [11m] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
STRINGdb-package 242.01   3.03  376.52
STRINGdb         228.09   1.57  298.86
** running examples for arch 'x64' ... [11m] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
STRINGdb-package 248.71   4.04  387.22
STRINGdb         234.44   2.89  293.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [305s]
 [306s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [270s]
 [271s] 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: 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/STRINGdb.Rcheck/00check.log'
for details.


STRINGdb.Rcheck/00install.out:


install for i386

* installing *source* package 'STRINGdb' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'STRINGdb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STRINGdb' as STRINGdb_1.8.1.zip
* DONE (STRINGdb)

STRINGdb.Rcheck/examples_i386/STRINGdb-Ex.timings:

nameusersystemelapsed
STRINGdb-class000
STRINGdb-package242.01 3.03376.52
STRINGdb228.09 1.57298.86

STRINGdb.Rcheck/examples_x64/STRINGdb-Ex.timings:

nameusersystemelapsed
STRINGdb-class000
STRINGdb-package248.71 4.04387.22
STRINGdb234.44 2.89293.47