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CHECK report for cisPath on merida2

This page was generated on 2018-10-17 08:51:16 -0400 (Wed, 17 Oct 2018).

Package 249/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cisPath 1.20.0
Likun Wang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/cisPath
Branch: RELEASE_3_7
Last Commit: 9d47152
Last Changed Date: 2018-04-30 10:35:29 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cisPath
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cisPath.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cisPath_1.20.0.tar.gz
StartedAt: 2018-10-16 20:29:55 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:30:20 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 25.6 seconds
RetCode: 0
Status:  OK 
CheckDir: cisPath.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cisPath.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cisPath_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/cisPath.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 ‘cisPath/DESCRIPTION’ ... OK
* this is package ‘cisPath’ 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 ‘cisPath’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
getResults: no visible global function definition for ‘read.table’
cisPath,character-character: no visible global function definition for
  ‘browseURL’
combinePPI,character-character: no visible global function definition
  for ‘browseURL’
easyEditor,character: no visible global function definition for
  ‘browseURL’
networkView,character-character-character: no visible global function
  definition for ‘browseURL’
Undefined global functions or variables:
  browseURL read.table
Consider adding
  importFrom("utils", "browseURL", "read.table")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/cisPath.Rcheck/00check.log’
for details.



Installation output

cisPath.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cisPath
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘cisPath’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cisPath.cpp -o cisPath.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cisPath.so cisPath.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/cisPath/libs
** R
** 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 (cisPath)

Tests output


Example timings

cisPath.Rcheck/cisPath-Ex.timings

nameusersystemelapsed
cisPath0.6550.9501.782
combinePPI0.0060.0010.009
easyEditor0.0050.0110.016
formatPINAPPI0.0070.0010.008
formatSIFfile0.0090.0020.011
formatSTRINGPPI0.0100.0020.011
formatiRefIndex0.0080.0010.010
getMappingFile0.0100.0010.011
networkView0.0580.0320.093