Package: MatrixRider

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MatrixRider.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MatrixRider_1.14.0.tar.gz

StartedAt: 2019-04-13 03:33:13 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:39:19 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 365.2 seconds

RetCode: 0

Status:  OK

CheckDir: MatrixRider.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MatrixRider.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MatrixRider_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MatrixRider.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 'MatrixRider/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MatrixRider' version '1.14.0'
* 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 '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
* 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 ... 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-3.8-bioc/R/library/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 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-3.8-bioc/meat/MatrixRider.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MatrixRider_1.14.0.tar.gz && rm -rf MatrixRider.buildbin-libdir && mkdir MatrixRider.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MatrixRider.buildbin-libdir MatrixRider_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MatrixRider_1.14.0.zip && rm MatrixRider_1.14.0.tar.gz MatrixRider_1.14.0.zip
###
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100 22262  100 22262    0     0   751k      0 --:--:-- --:--:-- --:--:--  869k

install for i386

* installing *source* package 'MatrixRider' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c matrix_rider.c -o matrix_rider.o
C:/Rtools/mingw_32/bin/gcc -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:/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/MatrixRider.buildbin-libdir/MatrixRider/libs/i386
** R
** inst
** byte-compile and prepare 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c matrix_rider.c -o matrix_rider.o
C:/Rtools/mingw_64/bin/gcc -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:/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/MatrixRider.buildbin-libdir/MatrixRider/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MatrixRider' as MatrixRider_1.14.0.zip
* DONE (MatrixRider)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MatrixRider' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit



RUNIT TEST PROTOCOL -- Sat Apr 13 03:39:00 2019 
*********************************************** 
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 
  12.59    1.56   15.34 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit



RUNIT TEST PROTOCOL -- Sat Apr 13 03:39:15 2019 
*********************************************** 
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 
  13.31    0.68   13.98