Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:19:13 -0400 (Thu, 12 Apr 2018).
Package 1287/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ShortRead 1.36.1 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | ![]() |
Package: ShortRead |
Version: 1.36.1 |
Command: rm -rf ShortRead.buildbin-libdir ShortRead.Rcheck && mkdir ShortRead.buildbin-libdir ShortRead.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ShortRead.buildbin-libdir ShortRead_1.36.1.tar.gz >ShortRead.Rcheck\00install.out 2>&1 && cp ShortRead.Rcheck\00install.out ShortRead-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ShortRead.buildbin-libdir --install="check:ShortRead-install.out" --force-multiarch --no-vignettes --timings ShortRead_1.36.1.tar.gz |
StartedAt: 2018-04-12 03:10:04 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 03:22:44 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 760.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ShortRead.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ShortRead.buildbin-libdir ShortRead.Rcheck && mkdir ShortRead.buildbin-libdir ShortRead.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ShortRead.buildbin-libdir ShortRead_1.36.1.tar.gz >ShortRead.Rcheck\00install.out 2>&1 && cp ShortRead.Rcheck\00install.out ShortRead-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ShortRead.buildbin-libdir --install="check:ShortRead-install.out" --force-multiarch --no-vignettes --timings ShortRead_1.36.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ShortRead.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 'ShortRead/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ShortRead' version '1.36.1' * 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-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:119: missing file link 'RangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:120: missing file link 'RangedData' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:121: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:124: missing file link 'Ranges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:182: file link 'IntervalTree-class' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/SRFilter-class.Rd:76: file link 'FilterRules' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/SRFilter-class.Rd:80: file link 'FilterRules' in package 'IRanges' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ShortRead.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: 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 Unexported objects imported by ':::' calls: 'Biostrings:::xscodes' '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' .readAligned_bam: no visible global function definition for '.readAligned_bamWhat' 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: .readAligned_bamWhat Base Count Density Id Nucleotide Occurrences Quality Reads Score TopCount * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'AlignedRead-class.Rd': '[IRanges:IntervalTree-class]{overlap}' Missing link or links in documentation object 'SRFilter-class.Rd': '[IRanges]{FilterRules}' See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: 'left' 'right' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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-3.6-bioc/meat/ShortRead.buildbin-libdir/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) 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 Snapshot-class 7.45 0.30 9.00 srdistance 0.57 0.38 8.56 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed Snapshot-class 9.80 0.16 9.95 qa2 7.00 0.24 7.23 srdistance 0.54 0.15 9.36 * 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: 3 WARNINGs, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ShortRead.Rcheck/00check.log' for details.
ShortRead.Rcheck/00install.out
install for i386 * installing *source* package 'ShortRead' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c alphabet.c -o alphabet.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c io.c -o io.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXP)': readBfaToc.cc:19:40: warning: variable 'status' set but not used [-Wunused-but-set-variable] int name_len, seq_ori_len, seq_len, status; ^ C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c sampler.c -o sampler.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c trim.c -o trim.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c util.c -o util.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/ShortRead.buildbin-libdir/ShortRead/libs/i386 ** R ** inst ** preparing 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-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:119: missing file link 'RangesList' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:120: missing file link 'RangedData' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:121: missing file link 'GRanges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:124: missing file link 'Ranges' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/AlignedRead-class.Rd:182: file link 'IntervalTree-class' 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 Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/SRFilter-class.Rd:76: file link 'FilterRules' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmytSOB/R.INSTALL29687dfe6aee/ShortRead/man/SRFilter-class.Rd:80: file link 'FilterRules' in package 'IRanges' does not exist and so has been treated as a topic 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 In R CMD INSTALL 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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c alphabet.c -o alphabet.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c io.c -o io.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXP)': readBfaToc.cc:19:40: warning: variable 'status' set but not used [-Wunused-but-set-variable] int name_len, seq_ori_len, seq_len, status; ^ C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c sampler.c -o sampler.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c trim.c -o trim.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c util.c -o util.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/local323/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-3.6-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/ShortRead.buildbin-libdir/ShortRead/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'ShortRead' as ShortRead_1.36.1.zip * DONE (ShortRead) In R CMD INSTALL In R CMD INSTALL
ShortRead.Rcheck/tests_i386/ShortRead_unit_tests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid 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 object is masked from 'package:base': apply RUNIT TEST PROTOCOL -- Thu Apr 12 03:19:20 2018 *********************************************** 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 .Internal(gc(verbose, reset)) : closing unused connection 6 (C:/Users/biocbuild/bbs-3.6-bioc/meat/ShortRead.buildbin-libdir/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt) 2: In .Internal(gc(verbose, reset)) : closing unused connection 5 (C:/Users/biocbuild/bbs-3.6-bioc/meat/ShortRead.buildbin-libdir/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt) 3: In .Internal(gc(verbose, reset)) : closing unused connection 3 (C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpQzEZTr\file2f88761f6302) > > proc.time() user system elapsed 74.37 26.89 169.21 |
ShortRead.Rcheck/tests_x64/ShortRead_unit_tests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid 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 object is masked from 'package:base': apply RUNIT TEST PROTOCOL -- Thu Apr 12 03:22:36 2018 *********************************************** 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 .Internal(gc(verbose, reset)) : closing unused connection 6 (C:/Users/biocbuild/bbs-3.6-bioc/meat/ShortRead.buildbin-libdir/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt) 2: In .Internal(gc(verbose, reset)) : closing unused connection 5 (C:/Users/biocbuild/bbs-3.6-bioc/meat/ShortRead.buildbin-libdir/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt) 3: In .Internal(gc(verbose, reset)) : closing unused connection 3 (C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpKioeVs\file389c5faa79d8) > > proc.time() user system elapsed 88.26 23.87 194.73 |
ShortRead.Rcheck/examples_i386/ShortRead-Ex.timings
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ShortRead.Rcheck/examples_x64/ShortRead-Ex.timings
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