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CHECK report for TransView on tokay1

This page was generated on 2019-04-13 11:22:26 -0400 (Sat, 13 Apr 2019).

Package 1581/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.26.1
Julius Muller
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/TransView
Branch: RELEASE_3_8
Last Commit: 4393040
Last Changed Date: 2019-01-04 13:52:57 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] 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: TransView
Version: 1.26.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TransView.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TransView_1.26.1.tar.gz
StartedAt: 2019-04-13 06:00:35 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:05:40 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 305.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: TransView.Rcheck
Warnings: 1

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:TransView.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TransView_1.26.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/TransView.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 'TransView/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TransView' version '1.26.1'
* 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 'TransView' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpSWLISW/R.INSTALL1a90252d3fd7/TransView/man/DensityContainer-class.Rd:137: file link 'slice1-methods' in package 'TransView' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpSWLISW/R.INSTALL1a90252d3fd7/TransView/man/DensityContainer-class.Rd:138: file link 'sliceN-methods' in package 'TransView' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpSWLISW/R.INSTALL1a90252d3fd7/TransView/man/DensityContainer-class.Rd:140: file link 'rmTV-methods' in package 'TransView' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpSWLISW/R.INSTALL1a90252d3fd7/TransView/man/TVResults-class.Rd:57: file link 'plotTVData-methods' in package 'TransView' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/TransView.Rcheck/00install.out' for details.
* 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 ... NOTE
'library' or 'require' call to 'RUnit' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.gene2window : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
.gene2window: no visible binding for global variable 'approx'
.onAttach: no visible global function definition for
  'packageDescription'
.test: no visible global function definition for 'defineTestSuite'
.test: no visible global function definition for 'runTestSuite'
.test: no visible global function definition for 'printTextProtocol'
annotatePeaks : <anonymous>: no visible global function definition for
  'median'
gtf2gr: no visible global function definition for 'read.table'
gtf2gr: no visible global function definition for 'ave'
macs2gr: no visible global function definition for 'read.delim'
meltPeak: no visible global function definition for 'approx'
meltPeak: no visible global function definition for 'lowess'
plotTV: no visible global function definition for 'quantile'
plotTV: no visible global function definition for 'kmeans'
plotTV: no visible global function definition for 'as.dendrogram'
plotTV: no visible global function definition for 'hclust'
plotTV: no visible global function definition for 'as.dist'
plotTV: no visible global function definition for 'dist'
plotTV: no visible global function definition for 'order.dendrogram'
plotTV: no visible global function definition for 'par'
plotTV: no visible global function definition for 'layout'
plotTV: no visible global function definition for 'image'
plotTV: no visible global function definition for 'hist'
plotTV: no visible global function definition for 'title'
plotTV: no visible global function definition for 'mtext'
plotTV: no visible global function definition for 'lines'
plotTV: no visible global function definition for 'axis'
plotTV: no visible global function definition for 'rainbow'
plotTV: no visible global function definition for 'plot'
plotTV: no visible global function definition for 'text'
plotTV: no visible global function definition for 'rgb'
plotTV: no visible global function definition for 'plot.new'
setTV: no visible global function definition for 'object.size'
.setTV,DensityContainer-character-character-numeric-numeric-numeric-logical-character-character-logical:
  no visible global function definition for 'object.size'
Undefined global functions or variables:
  approx as.dendrogram as.dist ave axis defineTestSuite dist hclust
  hist image kmeans layout lines lowess median mtext object.size
  order.dendrogram packageDescription par plot plot.new
  printTextProtocol quantile rainbow read.delim read.table rgb
  runTestSuite text title
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "axis", "hist", "image", "layout", "lines",
             "mtext", "par", "plot", "plot.new", "text", "title")
  importFrom("stats", "approx", "as.dendrogram", "as.dist", "ave",
             "dist", "hclust", "kmeans", "lowess", "median",
             "order.dendrogram", "quantile")
  importFrom("utils", "object.size", "packageDescription", "read.delim",
             "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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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/TransView/libs/i386/TransView.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (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
plotTV   1.44   3.82    5.25
meltPeak 1.74   3.44    5.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
plotTVData 1.75   4.09    6.35
meltPeak   2.02   3.72    5.73
slice1     1.69   4.04    6.67
plotTV     1.49   4.13    5.90
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'TransView_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'TransView_unit_tests.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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/TransView.Rcheck/00check.log'
for details.



Installation output

TransView.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/TransView_1.26.1.tar.gz && rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TransView.buildbin-libdir TransView_1.26.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL TransView_1.26.1.zip && rm TransView_1.26.1.tar.gz TransView_1.26.1.zip
###
##############################################################################
##############################################################################


  % 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  980k  100  980k    0     0  20.9M      0 --:--:-- --:--:-- --:--:-- 22.7M

install for i386

* installing *source* package 'TransView' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_TransView.c -o R_init_TransView.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bin_density.c -o bin_density.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c construct_dc.c -o construct_dc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c parse_sam.c -o parse_sam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:179:5: warning: 'slicep' may be used uninitialized in this function [-Wmaybe-uninitialized]
     shrink(slicep,new_vecp,rebuildc,wsize,summarizep);
     ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c visuals.c -o visuals.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/TransView.buildbin-libdir/TransView/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TransView'
    finding HTML links ... done
    DensityContainer-class                  html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpSWLISW/R.INSTALL1a90252d3fd7/TransView/man/DensityContainer-class.Rd:137: file link 'slice1-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpSWLISW/R.INSTALL1a90252d3fd7/TransView/man/DensityContainer-class.Rd:138: file link 'sliceN-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpSWLISW/R.INSTALL1a90252d3fd7/TransView/man/DensityContainer-class.Rd:140: file link 'rmTV-methods' in package 'TransView' does not exist and so has been treated as a topic
    TVResults-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpSWLISW/R.INSTALL1a90252d3fd7/TransView/man/TVResults-class.Rd:57: file link 'plotTVData-methods' in package 'TransView' does not exist and so has been treated as a topic
    TransView-package                       html  
    annotatePeaks                           html  
    finding level-2 HTML links ... done

    gtf2gr                                  html  
    histogram-methods                       html  
    macs2gr                                 html  
    meltPeak                                html  
    parseReads                              html  
    peak2tss                                html  
    plotTV                                  html  
    plotTVData                              html  
    rmTV                                    html  
    slice1                                  html  
    slice1T                                 html  
    tvStats-methods                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TransView' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_TransView.c -o R_init_TransView.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bin_density.c -o bin_density.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c construct_dc.c -o construct_dc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c parse_sam.c -o parse_sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:179:5: warning: 'slicep' may be used uninitialized in this function [-Wmaybe-uninitialized]
     shrink(slicep,new_vecp,rebuildc,wsize,summarizep);
     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c visuals.c -o visuals.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/TransView.buildbin-libdir/TransView/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TransView' as TransView_1.26.1.zip
* DONE (TransView)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'TransView' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

TransView.Rcheck/tests_i386/TransView_unit_tests.Rout


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.

> 
> 
> require("TransView") || stop("unable to load TransView package")
Loading required package: TransView
Loading required package: GenomicRanges
Loading required package: stats4
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

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: GenomeInfoDb
Welcome to TransView version 1.26.1

Attaching package: 'TransView'

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

    pos

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

    pos

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

    pos

[1] TRUE
> TransView:::.test()
Version 2.09+ detected
21 peaks matching
172 rows matching
2862 rows matching
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit
Successful annotation within -5kBps to 2kBps: NA, 21 peaks without hit
Successful annotation within -5kBps to 2kBps: 10, 11 peaks without hit
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit


RUNIT TEST PROTOCOL -- Sat Apr 13 06:05:12 2019 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TransView RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  12.54   12.17   25.35 
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.

TransView.Rcheck/tests_x64/TransView_unit_tests.Rout


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.

> 
> 
> require("TransView") || stop("unable to load TransView package")
Loading required package: TransView
Loading required package: GenomicRanges
Loading required package: stats4
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

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: GenomeInfoDb
Welcome to TransView version 1.26.1

Attaching package: 'TransView'

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

    pos

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

    pos

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

    pos

[1] TRUE
> TransView:::.test()
Version 2.09+ detected
21 peaks matching
172 rows matching
2862 rows matching
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit
Successful annotation within -5kBps to 2kBps: NA, 21 peaks without hit
Successful annotation within -5kBps to 2kBps: 10, 11 peaks without hit
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit


RUNIT TEST PROTOCOL -- Sat Apr 13 06:05:35 2019 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TransView RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  11.46   10.42   21.87 
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.

Example timings

TransView.Rcheck/examples_i386/TransView-Ex.timings

nameusersystemelapsed
DensityContainer-class000
TVResults-class000
TransView-package000
annotatePeaks1.820.002.05
gtf2gr0.080.000.08
macs2gr0.010.000.01
meltPeak1.743.445.44
parseReads0.651.342.00
peak2tss0.360.000.36
plotTV1.443.825.25
plotTVData1.393.184.57
rmTV0.911.462.36
slice11.502.724.22
slice1T0.620.010.67

TransView.Rcheck/examples_x64/TransView-Ex.timings

nameusersystemelapsed
DensityContainer-class000
TVResults-class000
TransView-package000
annotatePeaks1.530.051.58
gtf2gr0.060.000.06
macs2gr0.030.000.03
meltPeak2.023.725.73
parseReads0.811.872.69
peak2tss0.450.000.45
plotTV1.494.135.90
plotTVData1.754.096.35
rmTV1.362.123.49
slice11.694.046.67
slice1T0.860.042.00