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This page was generated on 2015-10-22 17:52:26 -0400 (Thu, 22 Oct 2015).
| Package 967/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| ShortRead 1.29.0 Bioconductor Package Maintainer
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | ||||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: ShortRead |
| Version: 1.29.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ShortRead_1.29.0.tar.gz |
| StartedAt: 2015-10-22 11:16:47 -0400 (Thu, 22 Oct 2015) |
| EndedAt: 2015-10-22 11:20:09 -0400 (Thu, 22 Oct 2015) |
| EllapsedTime: 201.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ShortRead.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ShortRead_1.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ShortRead/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ShortRead’ version ‘1.29.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ShortRead’ can be installed ... [19s/20s] OK
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
extdata 4.0Mb
* 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
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ShortRead-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AlignedRead-class
> ### Title: (Legacy) "AlignedRead" class for aligned short reads
> ### Aliases: AlignedRead-class [,AlignedRead,ANY,ANY-method
> ### [,AlignedRead,ANY,missing-method [,AlignedRead,missing,ANY-method
> ### [,AlignedRead,missing,missing-method
> ### [,AlignedRead,missing,missing,ANY-method
> ### [,AlignedRead,missing,ANY,ANY-method [,AlignedRead,ANY,ANY,ANY-method
> ### [,AlignedRead,ANY,missing,ANY-method
> ### append,AlignedRead,AlignedRead-method
> ### coerce,PairwiseAlignments,AlignedRead-method
> ### coerce,AlignedRead,RangesList-method
> ### coerce,AlignedRead,RangedData-method
> ### coerce,AlignedRead,GRanges-method
> ### coerce,AlignedRead,GAlignments-method
> ### coerce,AlignedRead,GappedReads-method chromosome,AlignedRead-method
> ### position,AlignedRead-method strand,AlignedRead-method
> ### coverage,AlignedRead-method srrank,AlignedRead-method
> ### srorder,AlignedRead-method srduplicated,AlignedRead-method
> ### %in%,AlignedRead,RangesList-method detail,AlignedRead-method
> ### show,AlignedRead-method
> ### Keywords: classes
>
> ### ** Examples
>
> showMethods(class="AlignedRead", where=getNamespace("ShortRead"))
Function: %in% (package base)
x="AlignedRead", table="RangesList"
Function: .bowtie_mismatches (package ShortRead)
object="AlignedRead"
Function: .srValidity (package ShortRead)
object="AlignedRead"
Function: [ (package base)
x="AlignedRead", i="ANY", j="ANY"
x="AlignedRead", i="ANY", j="missing"
x="AlignedRead", i="missing", j="ANY"
x="AlignedRead", i="missing", j="missing"
Function: append (package BiocGenerics)
x="AlignedRead", values="AlignedRead"
Function: chromosome (package ShortRead)
object="AlignedRead"
Function: coerce (package methods)
from="AlignedRead", to="GAlignments"
from="AlignedRead", to="GRanges"
from="AlignedRead", to="GappedReads"
from="AlignedRead", to="RangedData"
from="AlignedRead", to="RangesList"
from="PairwiseAlignments", to="AlignedRead"
Function: coverage (package IRanges)
x="AlignedRead"
Function: detail (package Biostrings)
x="AlignedRead"
Function: position (package ShortRead)
object="AlignedRead"
Function: show (package methods)
object="AlignedRead"
Function: srduplicated (package ShortRead)
x="AlignedRead"
Function: srorder (package ShortRead)
x="AlignedRead"
Function: srrank (package ShortRead)
x="AlignedRead"
Function: strand (package BiocGenerics)
x="AlignedRead"
> dirPath <- system.file('extdata', 'maq', package='ShortRead')
> (aln <- readAligned(dirPath, 'out.aln.1.txt', type="MAQMapview"))
Warning in read.table(file = file, header = header, sep = sep, quote = quote, :
not all columns named in 'colClasses' exist
Error: Input/Output
'readAligned' failed to parse files
dirPath: '/Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck/ShortRead/extdata/maq'
pattern: 'out.aln.1.txt'
type: 'MAQMapview'
error: invalid class “IntegerQuality” object: invalid object for slot "quality" in class "IntegerQuality": got class "character", should be or extend class "integer"
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘ShortRead_unit_tests.R’ [54s/49s]
ERROR
Running the tests in ‘tests/ShortRead_unit_tests.R’ failed.
Last 13 lines of output:
Error in BiocGenerics:::testPackage("ShortRead") :
unit tests failed for package ShortRead
In addition: Warning messages:
1: closing unused connection 6 (/Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
2: closing unused connection 5 (/Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
3: closing unused connection 3 (/tmp/RtmpkpHos0/file397b431548ee)
4: In NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript is an array, passing it thru as.vector() first
5: In NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript is an array, passing it thru as.vector() first
Execution halted
* 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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck/00check.log’
for details.
ShortRead.Rcheck/tests/ShortRead_unit_tests.Rout.fail:
R Under development (unstable) (2015-10-08 r69496) -- "Unsuffered Consequences"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Timing stopped at: 0.059 0.001 0.061
Error : Input/Output
'readAligned' failed to parse files
dirPath: '/Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck/ShortRead/extdata/maq'
pattern: '.*aln.*'
type: 'MAQMapview'
error: invalid class "IntegerQuality" object: invalid object for slot "quality" in class "IntegerQuality": got class "character", should be or extend class "integer"
In addition: Warning messages:
1: In read.table(file = file, header = header, sep = sep, quote = quote, :
not all columns named in 'colClasses' exist
2: In read.table(file = file, header = header, sep = sep, quote = quote, :
not all columns named in 'colClasses' exist
RUNIT TEST PROTOCOL -- Thu Oct 22 11:19:59 2015
***********************************************
Number of test functions: 103
Number of errors: 1
Number of failures: 0
1 Test Suite :
ShortRead RUnit Tests - 103 test functions, 1 error, 0 failures
ERROR in test_AlignedRead_readAligned_MAQMapview: Error : Input/Output
'readAligned' failed to parse files
dirPath: '/Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck/ShortRead/extdata/maq'
pattern: '.*aln.*'
type: 'MAQMapview'
error: invalid class "IntegerQuality" object: invalid object for slot "quality" in class "IntegerQuality": got class "character", should be or extend class "integer"
Test files with failing tests
test_AlignedRead.R
test_AlignedRead_readAligned_MAQMapview
Error in BiocGenerics:::testPackage("ShortRead") :
unit tests failed for package ShortRead
In addition: Warning messages:
1: closing unused connection 6 (/Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
2: closing unused connection 5 (/Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
3: closing unused connection 3 (/tmp/RtmpkpHos0/file397b431548ee)
4: In NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript is an array, passing it thru as.vector() first
5: In NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript is an array, passing it thru as.vector() first
Execution halted
ShortRead.Rcheck/00install.out:
* installing *source* package ‘ShortRead’ ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of unsigned long... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c R_init_ShortRead.c -o R_init_ShortRead.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c alphabet.c -o alphabet.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c io.c -o io.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c io_bowtie.c -o io_bowtie.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c io_soap.c -o io_soap.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC -Wall -mtune=core2 -g -O2 -c readBfaToc.cc -o readBfaToc.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC -Wall -mtune=core2 -g -O2 -c read_maq_map.cc -o read_maq_map.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c sampler.c -o sampler.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c trim.c -o trim.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c util.c -o util.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -fPIC -Wall -mtune=core2 -g -O2 -c xsnap.c -o xsnap.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ShortRead.so 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 -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.3-bioc/meat/ShortRead.Rcheck/ShortRead/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ShortRead)
ShortRead.Rcheck/ShortRead-Ex.timings:
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