BioC 2.14: CHECK report for ShortRead on zin2

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ShortRead.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.22.0’
* 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 ... [25s/27s] OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  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:
  ‘BiocGenerics:::testPackage’ ‘Biostrings:::xscodes’
  See the note in ?`:::` about the use of this operator.
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’
coerce,AlignedRead-GappedReads: no visible global function definition
  for ‘GappedReads’
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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
Snapshot-class   7.925  0.052   8.065
qa2              7.060  0.056   7.103
spViewPerFeature 5.517  0.060   5.665
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘ShortRead_unit_tests.R’ [48s/47s]
 [48s/47s] 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 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-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... /bin/grep
checking for egrep... /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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c io.c -o io.o
io.c: In function ‘write_fastq’:
io.c:113:16: warning: ‘gzbuf_n’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/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  -g -O2  -Wall -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]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/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  -g -O2  -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c sampler.c -o sampler.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c xsnap.c -o xsnap.o
g++ -shared -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 -fopenmp -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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	0.308	0.000	0.309
BAMQA-class	0.004	0.000	0.001
BowtieQA-class	0.000	0.000	0.001
ExperimentPath-class	0.004	0.000	0.001
FastqQA-class	0.000	0.000	0.002
Intensity-class	0.208	0.004	0.213
MAQMapQA-class	0.000	0.000	0.001
QA-class	0.000	0.000	0.001
QualityScore-class	0.012	0.000	0.009
QualityScore	0.008	0.000	0.007
RochePath-class	0.000	0.000	0.001
RocheSet-class	0.000	0.000	0.001
RtaIntensity-class	0.292	0.000	0.290
RtaIntensity	0.028	0.000	0.029
SRFilter-class	0	0	0
SRFilterResult-class	0.060	0.000	0.058
SRSet-class	0.000	0.000	0.001
SRUtil-class	0.008	0.000	0.006
Sampler-class	1.596	0.012	1.300
ShortRead-class	0.084	0.000	0.084
ShortReadQ-class	0.276	0.016	0.293
Snapshot-class	7.925	0.052	8.065
SnapshotFunction-class	0.000	0.000	0.001
SolexaExportQA-class	0.000	0.000	0.001
SolexaIntensity-class	0.124	0.000	0.125
SolexaPath-class	0.112	0.000	0.113
SolexaSet-class	0.100	0.004	0.104
SpTrellis-class	0.624	0.020	0.647
accessors	0.004	0.000	0.005
alphabetByCycle	0.032	0.008	0.037
clean	0.000	0.000	0.002
countLines	0.124	0.004	0.130
deprecated	0.004	0.000	0.001
dotQA-class	0.000	0.000	0.001
dustyScore	0.352	0.000	0.354
filterFastq	0.564	0.008	0.452
polyn	0.004	0.000	0.001
qa	0.836	0.012	0.793
qa2	7.060	0.056	7.103
readAligned	0.284	0.004	0.288
readBaseQuality	0.028	0.004	0.037
readFasta	0.124	0.000	0.147
readFastq	0.092	0.008	0.103
readIntensities	0.088	0.004	0.091
readPrb	0.044	0.000	0.045
readQseq	0.012	0.004	0.015
readXStringColumns	0.108	0.004	0.114
renew	0.088	0.000	0.088
report	0.008	0.000	0.008
spViewPerFeature	5.517	0.060	5.665
srFilter	0.612	0.004	0.618
srapply	0	0	0
srdistance	0.160	0.044	0.219
srduplicated	0.088	0.012	0.101
tables	0.232	0.032	0.292
trimTails	0.192	0.004	0.095

BioC 2.14: CHECK report for ShortRead on zin2

Summary

Command output