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CHECK report for MatrixRider on tokay1

This page was generated on 2018-04-12 13:25:52 -0400 (Thu, 12 Apr 2018).

Package 792/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MatrixRider 1.10.0
Elena Grassi
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/MatrixRider
Branch: RELEASE_3_6
Last Commit: b24920f
Last Changed Date: 2017-10-30 12:40:49 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MatrixRider
Version: 1.10.0
Command: rm -rf MatrixRider.buildbin-libdir MatrixRider.Rcheck && mkdir MatrixRider.buildbin-libdir MatrixRider.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MatrixRider.buildbin-libdir MatrixRider_1.10.0.tar.gz >MatrixRider.Rcheck\00install.out 2>&1 && cp MatrixRider.Rcheck\00install.out MatrixRider-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MatrixRider.buildbin-libdir --install="check:MatrixRider-install.out" --force-multiarch --no-vignettes --timings MatrixRider_1.10.0.tar.gz
StartedAt: 2018-04-12 01:09:27 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:15:17 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 350.2 seconds
RetCode: 0
Status:  OK  
CheckDir: MatrixRider.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MatrixRider.buildbin-libdir MatrixRider.Rcheck && mkdir MatrixRider.buildbin-libdir MatrixRider.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MatrixRider.buildbin-libdir MatrixRider_1.10.0.tar.gz >MatrixRider.Rcheck\00install.out 2>&1 && cp MatrixRider.Rcheck\00install.out MatrixRider-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MatrixRider.buildbin-libdir --install="check:MatrixRider-install.out" --force-multiarch --no-vignettes --timings MatrixRider_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MatrixRider.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MatrixRider/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MatrixRider' version '1.10.0'
* 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 'MatrixRider' 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK
* 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-3.6-bioc/meat/MatrixRider.buildbin-libdir/MatrixRider/libs/i386/MatrixRider.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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/MatrixRider.Rcheck/00check.log'
for details.



Installation output

MatrixRider.Rcheck/00install.out


install for i386

* installing *source* package 'MatrixRider' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Biostring_stubs.c -o Biostring_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c CuTest.c -o CuTest.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_MatrixRider.c -o R_init_MatrixRider.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c RunCuTest.c -o RunCuTest.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c matrix_rider.c -o matrix_rider.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o MatrixRider.dll tmp.def Biostring_stubs.o CuTest.o R_init_MatrixRider.o RunCuTest.o XVector_stubs.o matrix_rider.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/MatrixRider.buildbin-libdir/MatrixRider/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MatrixRider'
    finding HTML links ... done
    MatrixRider-package                     html  
    getSeqOccupancy-method                  html  
    finding level-2 HTML links ... done

** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MatrixRider' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Biostring_stubs.c -o Biostring_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c CuTest.c -o CuTest.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_MatrixRider.c -o R_init_MatrixRider.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c RunCuTest.c -o RunCuTest.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c matrix_rider.c -o matrix_rider.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o MatrixRider.dll tmp.def Biostring_stubs.o CuTest.o R_init_MatrixRider.o RunCuTest.o XVector_stubs.o matrix_rider.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/MatrixRider.buildbin-libdir/MatrixRider/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MatrixRider' as MatrixRider_1.10.0.zip
* DONE (MatrixRider)
In R CMD INSTALL
In R CMD INSTALL

Tests output

MatrixRider.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("MatrixRider")

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit



RUNIT TEST PROTOCOL -- Thu Apr 12 01:14:54 2018 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MatrixRider RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  12.14    0.53   13.54 

MatrixRider.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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("MatrixRider")

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit



RUNIT TEST PROTOCOL -- Thu Apr 12 01:15:11 2018 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MatrixRider RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  15.85    0.46   16.32 

Example timings

MatrixRider.Rcheck/examples_i386/MatrixRider-Ex.timings

nameusersystemelapsed
MatrixRider-package0.230.010.56
getSeqOccupancy-method0.160.100.25

MatrixRider.Rcheck/examples_x64/MatrixRider-Ex.timings

nameusersystemelapsed
MatrixRider-package0.250.020.26
getSeqOccupancy-method0.310.000.31