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Package 390/444HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.9.16
Biocore Team c/o BioC user list
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead
Last Changed Rev: 53541 / Revision: 53825
Last Changed Date: 2011-03-09 04:47:01 -0800 (Wed, 09 Mar 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ WARNINGS ] OK 

Summary

Package: ShortRead
Version: 1.9.16
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ShortRead_1.9.16.tar.gz
StartedAt: 2011-03-17 17:31:38 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 17:34:49 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 190.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ShortRead.Rcheck
Warnings: 2

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/ShortRead.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.9.16'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ShortRead' can be installed ... WARNING
Found the following significant warnings:
  Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported?  Making a copy in package 'ShortRead'
See '/Users/biocbuild/bbs-2.8-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotCycleBaseCall: no visible binding for global variable 'Base'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  AssayData
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'ShortRead_unit_tests.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/ShortRead.Rcheck/00check.log'
for details

ShortRead.Rcheck/00install.out:

* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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 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
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c alphabet.c -o alphabet.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c io.c -o io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c io_bowtie.c -o io_bowtie.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c io_soap.c -o io_soap.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c pileup.c -o pileup.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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 -DHAVE_LIBZ=1 -fPIC  -g -O2 -Wall -fasm-blocks -c readBfaToc.cc -o readBfaToc.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -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 -DHAVE_LIBZ=1 -fPIC  -g -O2 -Wall -fasm-blocks -c read_maq_map.cc -o read_maq_map.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c sampler.c -o sampler.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c util.c -o util.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -pedantic -c xsnap.c -o xsnap.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/ShortRead.Rcheck/ShortRead/libs/i386
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported?  Making a copy in package 'ShortRead'
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ShortRead)

ShortRead.Rcheck/ShortRead-Ex.timings:

nameusersystemelapsed
AlignedRead-class0.4540.0090.465
BAMQA-class0.0020.0010.001
BowtieQA-class0.0010.0000.001
ExperimentPath-class0.0010.0010.001
FastqQA-class0.0010.0000.001
Intensity-class0.5160.0140.529
MAQMapQA-class0.0010.0000.001
QA-class0.0010.0010.001
QualityScore-class0.0010.0000.001
QualityScore0.0070.0010.008
RochePath-class0.0010.0000.001
RocheSet-class0.0000.0010.001
RtaIntensity-class0.0630.0000.063
RtaIntensity0.0440.0030.047
SRFilter-class000
SRFilterResult-class0.0850.0020.088
SRSet-class0.0010.0000.001
SRUtil-class0.0050.0010.005
Sampler-class0.2920.0030.295
ShortRead-class0.0660.0010.067
ShortReadQ-class0.1350.0040.139
SolexaExportQA-class0.0000.0000.001
SolexaIntensity-class0.150.010.16
SolexaPath-class0.0910.0050.095
SolexaSet-class0.0820.0010.083
accessors0.0040.0000.005
alphabetByCycle0.0280.0040.032
clean0.0010.0000.001
countLines0.0100.0040.014
deprecated0.0010.0000.001
dustyScore0.1850.0020.187
polyn0.0010.0000.001
qa0.0010.0000.001
readAligned0.3270.0090.337
readBaseQuality0.0360.0010.038
readFasta0.0790.0030.094
readFastq0.3000.0050.305
readIntensities0.1240.0120.136
readPrb0.0780.0020.080
readQseq0.0160.0010.018
readXStringColumns0.1940.0080.202
renew0.0890.0030.092
report0.0040.0010.004
srFilter0.3550.0090.364
srapply0.0070.0000.007
srdistance0.2570.0060.263
srduplicated0.1350.0030.137
tables0.1600.0020.162