BioC 2.13: CHECK report for ShortRead on perceval

Package: ShortRead

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ShortRead_1.20.0.tar.gz

StartedAt: 2014-04-05 04:19:40 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:27:15 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 454.7 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ShortRead.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘Rmpi’
* 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 ... [37s/39s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 object imported by a ‘:::’ call: ‘Biostrings:::xscodes’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.readAligned_character’ ‘.readBaseQuality_character’
  ‘.readIntensities_character’ ‘.readPrb_character’
  ‘.readQseq_character’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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’
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘ShortRead_and_HilbertVis.pdf’ from 1277Kb to 598Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Overview.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [67s/68s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Snapshot-class   13.838  0.465  14.536
spViewPerFeature 12.807  1.105  14.059
qa2               9.179  0.331   9.792
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘ShortRead_unit_tests.R’ [83s/86s]
 [83s/86s] 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

NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/ShortRead.Rcheck/00check.log’
for details.

* 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Biostrings_stubs.c -o Biostrings_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_ShortRead.c -o R_init_ShortRead.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XVector_stubs.c -o XVector_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c alphabet.c -o alphabet.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c io.c -o io.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c io_bowtie.c -o io_bowtie.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c io_soap.c -o io_soap.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c pileup.c -o pileup.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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  -mtune=core2 -g -O2 -Wall  -c readBfaToc.cc -o readBfaToc.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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  -mtune=core2 -g -O2 -Wall  -c read_maq_map.cc -o read_maq_map.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c sampler.c -o sampler.o
sampler.c: In function ‘_records_status’:
sampler.c:25: warning: unused variable ‘len’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c trim.c -o trim.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c util.c -o util.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c xsnap.c -o xsnap.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o pileup.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-2.13-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)

name	user	system	elapsed
AlignedRead-class	0.503	0.023	0.529
BAMQA-class	0.013	0.002	0.016
BowtieQA-class	0.013	0.002	0.014
ExperimentPath-class	0.015	0.002	0.016
FastqQA-class	0.013	0.002	0.015
GappedReads-class	0.489	0.015	0.505
Intensity-class	0.379	0.024	0.404
MAQMapQA-class	0.008	0.001	0.010
QA-class	0.015	0.001	0.016
QualityScore-class	0.024	0.009	0.032
QualityScore	0.018	0.003	0.021
RochePath-class	0.010	0.004	0.013
RocheSet-class	0.009	0.002	0.012
RtaIntensity-class	0.120	0.004	0.124
RtaIntensity	0.049	0.003	0.053
SRFilter-class	0.006	0.002	0.008
SRFilterResult-class	0.098	0.005	0.103
SRSet-class	0.008	0.003	0.011
SRUtil-class	0.021	0.005	0.026
Sampler-class	2.177	0.045	2.247
ShortRead-class	0.107	0.014	0.121
ShortReadQ-class	0.320	0.058	0.378
Snapshot-class	13.838	0.465	14.536
SnapshotFunction-class	0.014	0.007	0.019
SolexaExportQA-class	0.004	0.004	0.008
SolexaIntensity-class	0.175	0.022	0.198
SolexaPath-class	0.184	0.019	0.207
SolexaSet-class	0.167	0.017	0.185
SpTrellis-class	0.946	0.041	0.998
accessors	0.010	0.008	0.020
alphabetByCycle	0.064	0.017	0.082
clean	0.004	0.005	0.008
countLines	0.020	0.013	0.034
deprecated	0.015	0.013	0.029
dotQA-class	0.005	0.006	0.012
dustyScore	0.899	0.018	0.920
filterFastq	3.165	0.037	3.224
polyn	0.008	0.009	0.017
qa	0.653	0.022	0.675
qa2	9.179	0.331	9.792
readAligned	0.431	0.042	0.489
readBaseQuality	0.055	0.013	0.069
readFasta	0.160	0.026	0.203
readFastq	0.139	0.026	0.166
readIntensities	0.144	0.031	0.174
readPrb	0.059	0.009	0.069
readQseq	0.024	0.010	0.034
readXStringColumns	0.147	0.018	0.167
renew	0.132	0.022	0.154
report	0.012	0.008	0.021
spViewPerFeature	12.807	1.105	14.059
srFilter	0.799	0.038	0.836
srapply	0.023	0.008	0.032
srdistance	0.262	0.015	0.278
srduplicated	0.142	0.021	0.164
tables	0.292	0.034	0.347
trimTails	0.064	0.012	0.076