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CHECK report for cisPath on tokay1

This page was generated on 2019-04-13 11:22:40 -0400 (Sat, 13 Apr 2019).

Package 265/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cisPath 1.22.0
Likun Wang
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/cisPath
Branch: RELEASE_3_8
Last Commit: b138f04
Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cisPath
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cisPath.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cisPath_1.22.0.tar.gz
StartedAt: 2019-04-13 01:14:50 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:16:31 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 101.1 seconds
RetCode: 0
Status:  OK  
CheckDir: cisPath.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cisPath.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cisPath_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/cisPath.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cisPath/DESCRIPTION' ... OK
* this is package 'cisPath' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* 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 ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/cisPath/libs/i386/cisPath.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
cisPath  1.7   1.01    5.03
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/cisPath.Rcheck/00check.log'
for details.



Installation output

cisPath.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/cisPath_1.22.0.tar.gz && rm -rf cisPath.buildbin-libdir && mkdir cisPath.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cisPath.buildbin-libdir cisPath_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL cisPath_1.22.0.zip && rm cisPath_1.22.0.tar.gz cisPath_1.22.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  716k  100  716k    0     0  14.8M      0 --:--:-- --:--:-- --:--:-- 16.2M

install for i386

* installing *source* package 'cisPath' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cisPath.cpp -o cisPath.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cisPath.dll tmp.def cisPath.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/cisPath.buildbin-libdir/cisPath/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cisPath'
    finding HTML links ... done
    cisPath                                 html  
    combinePPI                              html  
    easyEditor                              html  
    formatPINAPPI                           html  
    formatSIFfile                           html  
    formatSTRINGPPI                         html  
    formatiRefIndex                         html  
    getMappingFile                          html  
    networkView                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cisPath' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cisPath.cpp -o cisPath.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cisPath.dll tmp.def cisPath.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/cisPath.buildbin-libdir/cisPath/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cisPath' as cisPath_1.22.0.zip
* DONE (cisPath)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'cisPath' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

cisPath.Rcheck/examples_i386/cisPath-Ex.timings

nameusersystemelapsed
cisPath1.701.015.03
combinePPI0.000.020.86
easyEditor0.010.000.02
formatPINAPPI0.000.000.05
formatSIFfile0.020.010.28
formatSTRINGPPI0.020.000.11
formatiRefIndex0.010.000.04
getMappingFile0.000.020.02
networkView0.080.000.84

cisPath.Rcheck/examples_x64/cisPath-Ex.timings

nameusersystemelapsed
cisPath1.610.613.14
combinePPI0.010.000.01
easyEditor0.000.010.02
formatPINAPPI000
formatSIFfile0.000.020.01
formatSTRINGPPI000
formatiRefIndex0.000.010.02
getMappingFile000
networkView0.080.020.09