Multiple platform build/check report for BioC 3.9 - CHECK report for ShortRead on tokay2

Package: ShortRead

Version: 1.42.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ShortRead.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ShortRead_1.42.0.tar.gz

StartedAt: 2019-10-16 07:04:48 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:16:49 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 721.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: ShortRead.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ShortRead.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ShortRead_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ShortRead.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.42.0'
* 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 'ShortRead' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsRaqiY/R.INSTALL1abc5407d81/ShortRead/man/AlignedRead-class.Rd:119: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsRaqiY/R.INSTALL1abc5407d81/ShortRead/man/AlignedRead-class.Rd:120: file link 'RangedData' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsRaqiY/R.INSTALL1abc5407d81/ShortRead/man/AlignedRead-class.Rd:121: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsRaqiY/R.INSTALL1abc5407d81/ShortRead/man/AlignedRead-class.Rd:124: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    extdata   4.0Mb
    libs      1.2Mb
* 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
':::' call which should be '::': 'Biostrings:::xscodes'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'S4Vectors:::V_recycle'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotCycleBaseCall: no visible binding for global variable 'Base'
flag,QAReadQuality: no visible binding for global variable 'Score'
flag,QAReadQuality: no visible binding for global variable 'Id'
flag,QAReadQuality: no visible binding for global variable 'Density'
report,QAFrequentSequence: no visible binding for global variable
  'TopCount'
report,QAFrequentSequence: no visible binding for global variable 'Id'
report,QANucleotideByCycle: no visible binding for global variable
  'Base'
report,QANucleotideUse: no visible binding for global variable
  'Nucleotide'
report,QAQualityUse: no visible binding for global variable 'Count'
report,QAQualityUse: no visible binding for global variable 'Id'
report,QAQualityUse: no visible binding for global variable 'Quality'
report,QAReadQuality: no visible binding for global variable 'Id'
report,QASequenceUse: no visible binding for global variable
  'Occurrences'
report,QASequenceUse: no visible binding for global variable 'Id'
report,QASequenceUse: no visible binding for global variable 'Reads'
Undefined global functions or variables:
  Base Count Density Id Nucleotide Occurrences Quality Reads Score
  TopCount
* 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 shell scripts ... 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-3.9-bioc/R/library/ShortRead/libs/i386/ShortRead.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/ShortRead/libs/x64/ShortRead.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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
Snapshot-class 6.67   1.03    8.45
srdistance     0.90   0.25   13.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
Snapshot-class 8.77   0.36    9.14
srdistance     1.02   0.19   10.67
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'ShortRead_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'ShortRead_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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ShortRead.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ShortRead_1.42.0.tar.gz && rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ShortRead.buildbin-libdir ShortRead_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ShortRead_1.42.0.zip && rm ShortRead_1.42.0.tar.gz ShortRead_1.42.0.zip
###
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  % 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 4895k  100 4895k    0     0  39.4M      0 --:--:-- --:--:-- --:--:-- 41.9M

install for i386

* installing *source* package 'ShortRead' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_ShortRead.c -o R_init_ShortRead.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/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/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c alphabet.c -o alphabet.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c io.c -o io.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c io_bowtie.c -o io_bowtie.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c io_soap.c -o io_soap.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c readBfaToc.cc -o readBfaToc.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c read_maq_map.cc -o read_maq_map.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c sampler.c -o sampler.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c trim.c -o trim.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c util.c -o util.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c xsnap.c -o xsnap.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ShortRead'
    finding HTML links ... done
    AlignedDataFrame-class                  html  
    AlignedDataFrame                        html  
    AlignedRead-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsRaqiY/R.INSTALL1abc5407d81/ShortRead/man/AlignedRead-class.Rd:119: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsRaqiY/R.INSTALL1abc5407d81/ShortRead/man/AlignedRead-class.Rd:120: file link 'RangedData' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsRaqiY/R.INSTALL1abc5407d81/ShortRead/man/AlignedRead-class.Rd:121: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsRaqiY/R.INSTALL1abc5407d81/ShortRead/man/AlignedRead-class.Rd:124: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    AlignedRead                             html  
    BowtieQA-class                          html  
    ExperimentPath-class                    html  
    FastqQA-class                           html  
    Intensity-class                         html  
    MAQMapQA-class                          html  
    QA-class                                html  
    QualityScore-class                      html  
    QualityScore                            html  
    RochePath-class                         html  
    RocheSet-class                          html  
    RtaIntensity-class                      html  
    RtaIntensity                            html  
    SRFilter-class                          html  
    SRFilterResult-class                    html  
    SRSet-class                             html  
    finding level-2 HTML links ... done

    SRUtil-class                            html  
    Sampler-class                           html  
    ShortRead-class                         html  
    ShortRead-deprecated                    html  
    ShortRead-package                       html  
    ShortReadQ-class                        html  
    Snapshot-class                          html  
    SnapshotFunction-class                  html  
    SolexaExportQA-class                    html  
    SolexaIntensity-class                   html  
    SolexaIntensity                         html  
    SolexaPath-class                        html  
    SolexaSet-class                         html  
    SpTrellis-class                         html  
    accessors                               html  
    alphabetByCycle                         html  
    alphabetScore                           html  
    clean                                   html  
    countLines                              html  
    deprecated                              html  
    dotQA-class                             html  
    dustyScore                              html  
    filterFastq                             html  
    polyn                                   html  
    qa                                      html  
    qa2                                     html  
    readAligned                             html  
    readBaseQuality                         html  
    readBfaToc                              html  
    readFasta                               html  
    readFastq                               html  
    readIntensities                         html  
    readPrb                                 html  
    readQseq                                html  
    readXStringColumns                      html  
    renew                                   html  
    report                                  html  
    spViewPerFeature                        html  
    srFilter                                html  
    srdistance                              html  
    srduplicated                            html  
    tables                                  html  
    trimTails                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ShortRead' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_ShortRead.c -o R_init_ShortRead.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/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/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c alphabet.c -o alphabet.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c io.c -o io.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c io_bowtie.c -o io_bowtie.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c io_soap.c -o io_soap.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c readBfaToc.cc -o readBfaToc.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c read_maq_map.cc -o read_maq_map.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sampler.c -o sampler.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c trim.c -o trim.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c xsnap.c -o xsnap.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ShortRead' as ShortRead_1.42.0.zip
* DONE (ShortRead)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ShortRead' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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("ShortRead")

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    type

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

    aperm, apply, rowsum



RUNIT TEST PROTOCOL -- Wed Oct 16 07:13:47 2019 
*********************************************** 
Number of test functions: 103 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ShortRead RUnit Tests - 103 test functions, 0 errors, 0 failures
Number of test functions: 103 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In for (i in seq_along(slots)) { :
  closing unused connection 6 (C:/Users/biocbuild/bbs-3.9-bioc/R/library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
2: In for (i in seq_along(slots)) { :
  closing unused connection 5 (C:/Users/biocbuild/bbs-3.9-bioc/R/library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
> 
> proc.time()
   user  system elapsed 
  30.09   26.93  167.07


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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("ShortRead")

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    type

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

    aperm, apply, rowsum



RUNIT TEST PROTOCOL -- Wed Oct 16 07:16:36 2019 
*********************************************** 
Number of test functions: 103 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ShortRead RUnit Tests - 103 test functions, 0 errors, 0 failures
Number of test functions: 103 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In for (i in seq_along(defined)) { :
  closing unused connection 6 (C:/Users/biocbuild/bbs-3.9-bioc/R/library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
2: In for (i in seq_along(defined)) { :
  closing unused connection 5 (C:/Users/biocbuild/bbs-3.9-bioc/R/library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
> 
> proc.time()
   user  system elapsed 
  37.48   30.31  168.45

name	user	system	elapsed
AlignedRead-class	0.52	0.51	1.19
BowtieQA-class	0	0	0
ExperimentPath-class	0	0	0
FastqQA-class	0	0	0
Intensity-class	0.22	0.00	0.60
MAQMapQA-class	0	0	0
QA-class	0	0	0
QualityScore-class	0.02	0.00	0.01
QualityScore	0	0	0
RochePath-class	0	0	0
RocheSet-class	0	0	0
RtaIntensity-class	0.07	0.00	0.06
RtaIntensity	0.03	0.00	0.03
SRFilter-class	0	0	0
SRFilterResult-class	0.06	0.00	0.07
SRSet-class	0	0	0
SRUtil-class	0.02	0.00	0.01
Sampler-class	1.03	0.43	1.45
ShortRead-class	0.04	0.00	0.05
ShortReadQ-class	0.33	0.31	0.64
Snapshot-class	6.67	1.03	8.45
SnapshotFunction-class	0	0	0
SolexaExportQA-class	0	0	0
SolexaIntensity-class	0.09	0.00	0.09
SolexaPath-class	0.25	0.47	0.72
SolexaSet-class	0.07	0.00	0.07
SpTrellis-class	0.54	0.00	0.54
accessors	0	0	0
alphabetByCycle	0.16	0.30	0.45
clean	0	0	0
countLines	0.15	0.01	0.89
dotQA-class	0	0	0
dustyScore	0.22	0.39	0.61
filterFastq	0.84	0.02	0.88
polyn	0	0	0
qa	0.58	0.06	0.64
qa2	3.58	0.11	3.71
readAligned	0.59	1.01	1.60
readBaseQuality	0.81	0.13	0.94
readFasta	0.27	0.28	0.55
readFastq	0.23	0.77	1.00
readIntensities	0.05	0.00	0.05
readPrb	0.03	0.00	0.03
readQseq	0.06	0.26	0.33
readXStringColumns	0.41	0.55	0.95
renew	0.16	0.19	0.34
report	0.00	0.01	0.02
spViewPerFeature	3.54	0.24	3.78
srFilter	0.41	0.57	0.98
srdistance	0.90	0.25	13.50
srduplicated	0.24	0.36	0.60
tables	0.30	0.18	0.47
trimTails	0.18	0.26	0.45

name	user	system	elapsed
AlignedRead-class	0.61	0.34	0.95
BowtieQA-class	0	0	0
ExperimentPath-class	0	0	0
FastqQA-class	0	0	0
Intensity-class	0.82	0.02	0.83
MAQMapQA-class	0	0	0
QA-class	0	0	0
QualityScore-class	0	0	0
QualityScore	0.01	0.00	0.01
RochePath-class	0	0	0
RocheSet-class	0	0	0
RtaIntensity-class	0.05	0.00	0.05
RtaIntensity	0.02	0.00	0.01
SRFilter-class	0	0	0
SRFilterResult-class	0.06	0.00	0.07
SRSet-class	0	0	0
SRUtil-class	0	0	0
Sampler-class	1.39	0.34	1.73
ShortRead-class	0.09	0.00	0.10
ShortReadQ-class	0.61	0.46	1.06
Snapshot-class	8.77	0.36	9.14
SnapshotFunction-class	0	0	0
SolexaExportQA-class	0	0	0
SolexaIntensity-class	0.1	0.0	0.1
SolexaPath-class	0.22	0.54	0.78
SolexaSet-class	0.06	0.02	0.08
SpTrellis-class	0.73	0.00	0.73
accessors	0	0	0
alphabetByCycle	0.19	0.61	0.83
clean	0	0	0
countLines	0.16	0.01	0.17
dotQA-class	0	0	0
dustyScore	0.21	0.52	0.72
filterFastq	1.43	0.00	1.43
polyn	0	0	0
qa	0.66	0.02	0.68
qa2	3.45	0.15	3.70
readAligned	0.61	1.02	1.62
readBaseQuality	1.14	0.17	1.32
readFasta	0.35	0.37	0.72
readFastq	0.34	0.85	1.18
readIntensities	0.09	0.00	0.10
readPrb	0.05	0.00	0.04
readQseq	0.11	0.29	0.41
readXStringColumns	0.34	0.74	1.08
renew	0.13	0.23	0.36
report	0.01	0.00	0.01
spViewPerFeature	3.04	0.19	3.22
srFilter	0.46	0.58	1.05
srdistance	1.02	0.19	10.67
srduplicated	0.20	0.53	0.74
tables	0.32	0.25	0.56
trimTails	0.07	0.45	0.53

CHECK report for ShortRead on tokay2

Summary

Command output

Installation output

Tests output

Example timings