Multiple platform build/check report for BioC 3.8 - CHECK report for TSSi on tokay1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TSSi.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TSSi_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/TSSi.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 'TSSi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TSSi' version '1.28.0'
* 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 'TSSi' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TSSi-package.Rd:54: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TSSi-package.Rd:54: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TSSi-package.Rd:55: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TSSi-package.Rd:66: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssData-class.Rd:144: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssData-class.Rd:144: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssData-class.Rd:145: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssData-class.Rd:152: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssNorm-class.Rd:74: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssNorm-class.Rd:74: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssNorm-class.Rd:75: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssNorm-class.Rd:82: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssResult-class.Rd:86: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssResult-class.Rd:86: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssResult-class.Rd:87: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssResult-class.Rd:94: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/asRangedData-methods.Rd:89: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/asRangedData-methods.Rd:89: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/asRangedData-methods.Rd:90: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/asRangedData-methods.Rd:97: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/get-methods.Rd:160: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/get-methods.Rd:160: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/get-methods.Rd:161: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/get-methods.Rd:168: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/identify-methods.Rd:101: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/identify-methods.Rd:101: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/identify-methods.Rd:102: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/identify-methods.Rd:109: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/normalize-methods.Rd:112: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/normalize-methods.Rd:112: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/normalize-methods.Rd:113: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/normalize-methods.Rd:120: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/physcoCounts-data.Rd:49: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/physcoCounts-data.Rd:49: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/physcoCounts-data.Rd:50: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/physcoCounts-data.Rd:57: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/plot-methods.Rd:154: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/plot-methods.Rd:154: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/plot-methods.Rd:155: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/plot-methods.Rd:162: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/segmentize-methods.Rd:91: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/segmentize-methods.Rd:91: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/segmentize-methods.Rd:92: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/segmentize-methods.Rd:99: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/subtract-functions.Rd:50: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/subtract-functions.Rd:50: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/subtract-functions.Rd:51: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/subtract-functions.Rd:58: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-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
* 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 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-3.8-bioc/R/library/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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
TSSi-package     5.42   0.11    5.58
plot-methods     5.10   0.02    5.11
identify-methods 5.02   0.02    5.04
** 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-3.8-bioc/meat/TSSi.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/TSSi_1.28.0.tar.gz && rm -rf TSSi.buildbin-libdir && mkdir TSSi.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TSSi.buildbin-libdir TSSi_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL TSSi_1.28.0.zip && rm TSSi_1.28.0.tar.gz TSSi_1.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 24061  100 24061    0     0   671k      0 --:--:-- --:--:-- --:--:--  757k

install for i386

* installing *source* package 'TSSi' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o TSSi.dll tmp.def assess.o init.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/TSSi.buildbin-libdir/TSSi/libs/i386
** R
** data
** byte-compile and prepare 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-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TSSi-package.Rd:54: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TSSi-package.Rd:54: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TSSi-package.Rd:55: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TSSi-package.Rd:66: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    TssData-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssData-class.Rd:144: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssData-class.Rd:144: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssData-class.Rd:145: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssData-class.Rd:152: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    TssNorm-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssNorm-class.Rd:74: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssNorm-class.Rd:74: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssNorm-class.Rd:75: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssNorm-class.Rd:82: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    TssResult-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssResult-class.Rd:86: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssResult-class.Rd:86: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssResult-class.Rd:87: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/TssResult-class.Rd:94: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    asRangedData-methods                    html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/asRangedData-methods.Rd:89: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/asRangedData-methods.Rd:89: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/asRangedData-methods.Rd:90: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/asRangedData-methods.Rd:97: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    get-methods                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/get-methods.Rd:160: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/get-methods.Rd:160: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/get-methods.Rd:161: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/get-methods.Rd:168: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    identify-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/identify-methods.Rd:101: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/identify-methods.Rd:101: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/identify-methods.Rd:102: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/identify-methods.Rd:109: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    normalize-methods                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/normalize-methods.Rd:112: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/normalize-methods.Rd:112: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/normalize-methods.Rd:113: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/normalize-methods.Rd:120: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    physcoCounts-data                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/physcoCounts-data.Rd:49: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/physcoCounts-data.Rd:49: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/physcoCounts-data.Rd:50: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/physcoCounts-data.Rd:57: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    plot-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/plot-methods.Rd:154: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/plot-methods.Rd:154: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
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    segmentize-methods                      html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/segmentize-methods.Rd:91: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/segmentize-methods.Rd:91: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/segmentize-methods.Rd:99: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
    subtract-functions                      html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/subtract-functions.Rd:50: file link 'segmentizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/subtract-functions.Rd:50: file link 'normalizeCounts' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/subtract-functions.Rd:51: file link 'identifyStartSites' in package 'TSSi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpKEAJmO/R.INSTALL10b867e53735/TSSi/man/subtract-functions.Rd:58: file link 'physcoCounts' in package 'TSSi' does not exist and so has been treated as a topic
** 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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o TSSi.dll tmp.def assess.o init.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/TSSi.buildbin-libdir/TSSi/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TSSi' as TSSi_1.28.0.zip
* DONE (TSSi)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'TSSi' successfully unpacked and MD5 sums checked
In R CMD INSTALL

CHECK report for TSSi on tokay1

Summary

Command output

Installation output

Tests output

Example timings