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CHECK report for TSSi on tokay1

This page was generated on 2018-04-12 13:21:05 -0400 (Thu, 12 Apr 2018).

Package 1428/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TSSi 1.24.0
Julian Gehring
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/TSSi
Branch: RELEASE_3_6
Last Commit: 2da0aac
Last Changed Date: 2017-10-30 12:39:35 -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 [ WARNINGS ] 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: TSSi
Version: 1.24.0
Command: rm -rf TSSi.buildbin-libdir TSSi.Rcheck && mkdir TSSi.buildbin-libdir TSSi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TSSi.buildbin-libdir TSSi_1.24.0.tar.gz >TSSi.Rcheck\00install.out 2>&1 && cp TSSi.Rcheck\00install.out TSSi-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TSSi.buildbin-libdir --install="check:TSSi-install.out" --force-multiarch --no-vignettes --timings TSSi_1.24.0.tar.gz
StartedAt: 2018-04-12 03:43:25 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:46:31 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 186.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: TSSi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TSSi.buildbin-libdir TSSi.Rcheck && mkdir TSSi.buildbin-libdir TSSi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TSSi.buildbin-libdir TSSi_1.24.0.tar.gz >TSSi.Rcheck\00install.out 2>&1 && cp TSSi.Rcheck\00install.out TSSi-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TSSi.buildbin-libdir --install="check:TSSi-install.out" --force-multiarch --no-vignettes --timings TSSi_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TSSi.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 'TSSi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TSSi' version '1.24.0'
* 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 'TSSi' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TSSi-package.Rd:54: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TSSi-package.Rd:54: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TSSi-package.Rd:55: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TSSi-package.Rd:66: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssData-class.Rd:144: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssData-class.Rd:144: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssData-class.Rd:145: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssData-class.Rd:152: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssNorm-class.Rd:74: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssNorm-class.Rd:74: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssNorm-class.Rd:75: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssNorm-class.Rd:82: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssResult-class.Rd:86: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssResult-class.Rd:86: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssResult-class.Rd:87: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssResult-class.Rd:94: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/asRangedData-methods.Rd:89: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/asRangedData-methods.Rd:89: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/asRangedData-methods.Rd:90: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/asRangedData-methods.Rd:97: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/get-methods.Rd:160: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/get-methods.Rd:160: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/get-methods.Rd:161: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/get-methods.Rd:168: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/identify-methods.Rd:101: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/identify-methods.Rd:101: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/identify-methods.Rd:102: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/identify-methods.Rd:109: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/normalize-methods.Rd:112: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/normalize-methods.Rd:112: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/normalize-methods.Rd:113: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/normalize-methods.Rd:120: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/physcoCounts-data.Rd:49: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/physcoCounts-data.Rd:49: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/physcoCounts-data.Rd:50: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/physcoCounts-data.Rd:57: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/plot-methods.Rd:154: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/plot-methods.Rd:154: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/plot-methods.Rd:155: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/plot-methods.Rd:162: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/segmentize-methods.Rd:91: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/segmentize-methods.Rd:91: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/segmentize-methods.Rd:92: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/segmentize-methods.Rd:99: missing file link 'physcoCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/subtract-functions.Rd:50: missing file link 'segmentizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/subtract-functions.Rd:50: missing file link 'normalizeCounts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/subtract-functions.Rd:51: missing file link 'identifyStartSites'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/subtract-functions.Rd:58: missing file link 'physcoCounts'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TSSi.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
** 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 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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TSSi.buildbin-libdir/TSSi/libs/i386/TSSi.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
Examples with CPU or elapsed time > 5s
                  user system elapsed
identify-methods  6.34   0.00    6.35
TSSi-package      6.03   0.03    6.06
plot-methods      5.42   0.02    5.44
normalize-methods 5.20   0.00    5.21
** 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/TSSi.Rcheck/00check.log'
for details.

Installation output

TSSi.Rcheck/00install.out


install for i386

* installing *source* package 'TSSi' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c assess.c -o assess.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o TSSi.dll tmp.def assess.o init.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/TSSi.buildbin-libdir/TSSi/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'segments' in package 'TSSi'
** help
*** installing help indices
  converting help for package 'TSSi'
    finding HTML links ... done
    TSSi-package                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TSSi-package.Rd:54: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TSSi-package.Rd:54: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TSSi-package.Rd:55: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TSSi-package.Rd:66: missing file link 'physcoCounts'
    TssData-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssData-class.Rd:144: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssData-class.Rd:144: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssData-class.Rd:145: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssData-class.Rd:152: missing file link 'physcoCounts'
    TssNorm-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssNorm-class.Rd:74: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssNorm-class.Rd:74: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssNorm-class.Rd:75: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssNorm-class.Rd:82: missing file link 'physcoCounts'
    TssResult-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssResult-class.Rd:86: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssResult-class.Rd:86: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssResult-class.Rd:87: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/TssResult-class.Rd:94: missing file link 'physcoCounts'
    asRangedData-methods                    html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/asRangedData-methods.Rd:89: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/asRangedData-methods.Rd:89: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/asRangedData-methods.Rd:90: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/asRangedData-methods.Rd:97: missing file link 'physcoCounts'
    get-methods                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/get-methods.Rd:160: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/get-methods.Rd:160: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/get-methods.Rd:161: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/get-methods.Rd:168: missing file link 'physcoCounts'
    identify-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/identify-methods.Rd:101: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/identify-methods.Rd:101: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/identify-methods.Rd:102: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/identify-methods.Rd:109: missing file link 'physcoCounts'
    normalize-methods                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/normalize-methods.Rd:112: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/normalize-methods.Rd:112: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/normalize-methods.Rd:113: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/normalize-methods.Rd:120: missing file link 'physcoCounts'
    physcoCounts-data                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/physcoCounts-data.Rd:49: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/physcoCounts-data.Rd:49: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/physcoCounts-data.Rd:50: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/physcoCounts-data.Rd:57: missing file link 'physcoCounts'
    plot-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/plot-methods.Rd:154: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/plot-methods.Rd:154: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/plot-methods.Rd:155: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/plot-methods.Rd:162: missing file link 'physcoCounts'
    segmentize-methods                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/segmentize-methods.Rd:91: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/segmentize-methods.Rd:91: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/segmentize-methods.Rd:92: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/segmentize-methods.Rd:99: missing file link 'physcoCounts'
    subtract-functions                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/subtract-functions.Rd:50: missing file link 'segmentizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/subtract-functions.Rd:50: missing file link 'normalizeCounts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/subtract-functions.Rd:51: missing file link 'identifyStartSites'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuMugI8/R.INSTALLfc8799c151c/TSSi/man/subtract-functions.Rd:58: missing file link 'physcoCounts'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TSSi' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c assess.c -o assess.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o TSSi.dll tmp.def assess.o init.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/TSSi.buildbin-libdir/TSSi/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TSSi' as TSSi_1.24.0.zip
* DONE (TSSi)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

TSSi.Rcheck/examples_i386/TSSi-Ex.timings

nameusersystemelapsed
TSSi-package6.030.036.06
TssData-class000
TssNorm-class000
TssResult-class000
asRangedData-methods0.50.00.5
get-methods0.020.010.04
identify-methods6.340.006.35
normalize-methods5.200.005.21
physcoCounts-data000
plot-methods5.420.025.44
segmentize-methods0.000.010.02
subtract-functions000

TSSi.Rcheck/examples_x64/TSSi-Ex.timings

nameusersystemelapsed
TSSi-package3.690.013.70
TssData-class000
TssNorm-class000
TssResult-class000
asRangedData-methods0.670.020.69
get-methods0.030.000.03
identify-methods2.560.002.58
normalize-methods3.090.003.32
physcoCounts-data0.000.020.02
plot-methods2.820.002.84
segmentize-methods0.000.010.02
subtract-functions000