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CHECK report for BCRANK on riesling1

This page was generated on 2020-10-18 12:33:14 -0400 (Sun, 18 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BCRANK PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 123/1874HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BCRANK 1.51.0
Adam Ameur
Snapshot Date: 2020-10-17 14:41:49 -0400 (Sat, 17 Oct 2020)
URL: https://git.bioconductor.org/packages/BCRANK
Branch: master
Last Commit: 35c15f3
Last Changed Date: 2020-04-27 14:16:34 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BCRANK
Version: 1.51.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BCRANK.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BCRANK_1.51.0.tar.gz
StartedAt: 2020-10-17 19:51:00 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 19:52:20 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 79.4 seconds
RetCode: 0
Status:  OK  
CheckDir: BCRANK.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BCRANK.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BCRANK_1.51.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/BCRANK.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BCRANK/DESCRIPTION' ... OK
* this is package 'BCRANK' version '1.51.0'
* 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 whether package 'BCRANK' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'BCRANK/R/AllClasses.R':
  .onLoad calls:
    require("methods", quietly = TRUE)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

bcrankRun: no visible global function definition for 'flush.console'
getBCRANKScore: no visible global function definition for 't.test'
hitsForNeighboursInC: no visible global function definition for
  'flush.console'
plot,BCRANKsearch-missing: no visible global function definition for
  'rainbow'
plot,BCRANKsearch-missing: no visible binding for global variable
  'points'
plot,BCRANKsearch-missing: no visible global function definition for
  'legend'
Undefined global functions or variables:
  flush.console legend points rainbow t.test
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "t.test")
  importFrom("utils", "flush.console")
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 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 'D:/biocbuild/bbs-3.12-bioc/R/library/BCRANK/libs/i386/BCRANK.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbuild/bbs-3.12-bioc/R/library/BCRANK/libs/x64/BCRANK.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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
** 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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.12-bioc/meat/BCRANK.Rcheck/00check.log'
for details.



Installation output

BCRANK.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/BCRANK_1.51.0.tar.gz && rm -rf BCRANK.buildbin-libdir && mkdir BCRANK.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BCRANK.buildbin-libdir BCRANK_1.51.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BCRANK_1.51.0.zip && rm BCRANK_1.51.0.tar.gz BCRANK_1.51.0.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 2048k  100 2048k    0     0  31.7M      0 --:--:-- --:--:-- --:--:-- 31.7M

install for i386

* installing *source* package 'BCRANK' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_consensus.c -o match_consensus.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o BCRANK.dll tmp.def init.o match_consensus.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/BCRANK.buildbin-libdir/00LOCK-BCRANK/00new/BCRANK/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BCRANK'
    finding HTML links ... done
    BCRANK-internal                         html  
    BCRANKmatch-class                       html  
    BCRANKout                               html  
    BCRANKresult-class                      html  
    BCRANKsearch-class                      html  
    bcrank                                  html  
    matchingSites                           html  
** 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

install for x64

* installing *source* package 'BCRANK' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_consensus.c -o match_consensus.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o BCRANK.dll tmp.def init.o match_consensus.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/BCRANK.buildbin-libdir/BCRANK/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BCRANK' as BCRANK_1.51.0.zip
* DONE (BCRANK)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'BCRANK' successfully unpacked and MD5 sums checked

Tests output


Example timings

BCRANK.Rcheck/examples_i386/BCRANK-Ex.timings

nameusersystemelapsed
bcrank0.070.000.06

BCRANK.Rcheck/examples_x64/BCRANK-Ex.timings

nameusersystemelapsed
bcrank0.050.010.06