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BioC 2.12: CHECK report for ShortRead on george2

This page was generated on 2013-10-09 09:37:30 -0700 (Wed, 09 Oct 2013).

Package 592/671HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.18.0
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/ShortRead
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: ShortRead
Version: 1.18.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.18.0.tar.gz
StartedAt: 2013-10-09 04:54:50 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 05:03:26 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 516.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ShortRead.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ShortRead.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.18.0’
* 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 ... [44s/48s] OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   1.4Mb
* checking package 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 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’
.readQual: no visible global function definition for ‘readFASTA’
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 for portable 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 examples ... [60s/63s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
Snapshot-class 17.169  0.176  17.987
qa2             8.305  0.064   8.719
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘ShortRead_unit_tests.R’ [96s/98s]
 [97s/99s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/ShortRead.Rcheck/00check.log’
for details.

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... /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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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:35:59: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readBfaToc.cc:36:55: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readBfaToc.cc:37:51: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c sampler.c -o sampler.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.12-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 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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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:

nameusersystemelapsed
AlignedRead-class0.6160.0000.617
BAMQA-class0.0240.0000.026
BowtieQA-class0.0160.0040.017
ExperimentPath-class0.020.000.02
FastqQA-class0.0120.0000.013
GappedReads-class1.0360.0041.052
Intensity-class0.4850.0160.498
MAQMapQA-class0.0240.0000.024
QA-class0.0280.0000.029
QualityScore-class0.0440.0000.043
QualityScore0.0520.0000.053
RochePath-class0.0240.0000.024
RocheSet-class0.0320.0000.031
RtaIntensity-class0.1480.0000.147
RtaIntensity0.0920.0000.092
SRFilter-class0.0240.0000.021
SRFilterResult-class0.1520.0040.160
SRSet-class0.0280.0000.042
SRUtil-class0.080.000.14
Sampler-class3.7120.0203.598
ShortRead-class0.1680.0040.174
ShortReadQ-class0.4080.0560.503
Snapshot-class17.169 0.17617.987
SnapshotFunction-class0.0320.0040.034
SolexaExportQA-class0.0080.0040.012
SolexaIntensity-class0.2520.0080.259
SolexaPath-class0.2240.0080.233
SolexaSet-class0.1960.0000.196
SpTrellis-class1.2320.0081.267
accessors0.0120.0040.017
alphabetByCycle0.0520.0080.059
clean0.0240.0000.022
countLines0.0240.0040.024
deprecated0.0120.0000.010
dotQA-class0.0160.0000.018
dustyScore1.0080.0001.016
polyn0.0160.0000.018
qa0.6280.0000.645
qa28.3050.0648.719
readAligned0.4240.0280.458
readBaseQuality0.0480.0120.059
readFasta0.1880.0120.222
readFastq0.1760.0040.183
readIntensities0.1440.0280.175
readPrb0.0720.0080.077
readQseq0.0280.0000.028
readXStringColumns0.1600.0080.170
renew0.1560.0040.169
report0.0160.0040.017
spViewPerFeature3.8360.0284.060
srFilter0.7120.0040.724
srapply0.0160.0000.019
srdistance0.220.000.24
srduplicated0.1280.0000.129
tables0.2040.0040.210
trimTails0.2560.0040.151