BioC 3.1: CHECK report for ShortRead on zin2

Package: ShortRead

Version: 1.26.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.26.0.tar.gz

StartedAt: 2015-10-09 05:29:40 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:32:53 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 193.5 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ShortRead.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.26.0’
* 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 ... [18s/18s] OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  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 object imported by a ':::' call: ‘Biostrings:::xscodes’
  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’
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 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 ... [27s/25s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
Snapshot-class 5.502  0.048   5.589
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘ShortRead_unit_tests.R’ [48s/43s]
 [49s/43s] 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c io_soap.c -o io_soap.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-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]
    int name_len, seq_ori_len, seq_len, status;
                                        ^
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c sampler.c -o sampler.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c xsnap.c -o xsnap.o
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/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 -fopenmp -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/ShortRead.Rcheck/ShortRead/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.219	0.004	0.224
BAMQA-class	0.002	0.000	0.001
BowtieQA-class	0.000	0.000	0.001
ExperimentPath-class	0.001	0.000	0.000
FastqQA-class	0.001	0.000	0.001
Intensity-class	0.379	0.004	0.390
MAQMapQA-class	0.001	0.000	0.000
QA-class	0.000	0.004	0.001
QualityScore-class	0.004	0.000	0.007
QualityScore	0.004	0.000	0.004
RochePath-class	0.001	0.000	0.001
RocheSet-class	0.001	0.000	0.001
RtaIntensity-class	0.052	0.000	0.052
RtaIntensity	0.021	0.000	0.020
SRFilter-class	0	0	0
SRFilterResult-class	0.045	0.000	0.045
SRSet-class	0.001	0.000	0.001
SRUtil-class	0.005	0.000	0.004
Sampler-class	1.006	0.008	0.709
ShortRead-class	0.058	0.000	0.058
ShortReadQ-class	0.238	0.012	0.249
Snapshot-class	5.502	0.048	5.589
SnapshotFunction-class	0.001	0.000	0.001
SolexaExportQA-class	0.001	0.000	0.001
SolexaIntensity-class	0.104	0.000	0.104
SolexaPath-class	0.082	0.000	0.081
SolexaSet-class	0.07	0.00	0.07
SpTrellis-class	0.456	0.004	0.461
accessors	0.002	0.000	0.003
alphabetByCycle	0.018	0.008	0.023
clean	0.000	0.000	0.002
countLines	0.106	0.008	0.114
dotQA-class	0.001	0.000	0.001
dustyScore	0.329	0.000	0.328
filterFastq	0.514	0.052	0.450
polyn	0.001	0.000	0.001
qa	0.516	0.076	0.520
qa2	4.730	0.004	4.674
readAligned	0.160	0.004	0.165
readBaseQuality	0.017	0.000	0.017
readFasta	0.084	0.000	0.103
readFastq	0.059	0.000	0.060
readIntensities	0.071	0.000	0.071
readPrb	0.022	0.000	0.022
readQseq	0.007	0.000	0.007
readXStringColumns	0.044	0.000	0.044
renew	0.054	0.000	0.053
report	0.004	0.000	0.005
spViewPerFeature	3.308	0.052	3.392
srFilter	0.380	0.004	0.384
srapply	0.001	0.000	0.001
srdistance	0.101	0.028	0.972
srduplicated	1.433	0.395	0.059
tables	0.163	0.016	0.179
trimTails	0.153	0.008	0.069