Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

BioC 3.6: CHECK report for ShortRead on malbec1

This page was generated on 2017-08-16 13:18:17 -0400 (Wed, 16 Aug 2017).

Package 1236/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ShortRead 1.35.1
Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead
Last Changed Rev: 129294 / Revision: 131943
Last Changed Date: 2017-04-29 17:21:50 -0400 (Sat, 29 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ShortRead
Version: 1.35.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.35.1.tar.gz
StartedAt: 2017-08-16 02:23:54 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:28:05 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 250.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ShortRead.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.35.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ShortRead.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.35.1’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    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:
  ‘Biostrings:::xscodes’ ‘S4Vectors:::V_recycle’
  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’
.readAligned_bam: no visible global function definition for
  ‘.readAligned_bamWhat’
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’
Undefined global functions or variables:
  .readAligned_bamWhat Base Count Density Id Nucleotide Occurrences
  Quality Reads Score TopCount
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'AlignedRead-class.Rd':
  ‘[IRanges:IntervalTree-class]{overlap}’

Missing link or links in documentation object 'SRFilter-class.Rd':
  ‘[IRanges]{FilterRules}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘left’ ‘right’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
Snapshot-class 6.04   0.06   6.173
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘ShortRead_unit_tests.R’
 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: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-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 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c alphabet.c -o alphabet.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c io.c -o io.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c io_bowtie.c -o io_bowtie.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c io_soap.c -o io_soap.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/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 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c sampler.c -o sampler.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c xsnap.c -o xsnap.o
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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-class0.8800.0120.893
BowtieQA-class0.0000.0000.001
ExperimentPath-class0.0000.0000.001
FastqQA-class0.0000.0040.001
Intensity-class0.1440.0160.162
MAQMapQA-class0.0040.0000.001
QA-class0.0000.0000.001
QualityScore-class0.0120.0040.016
QualityScore0.0080.0000.005
RochePath-class0.0000.0000.001
RocheSet-class0.0040.0000.000
RtaIntensity-class0.0520.0000.052
RtaIntensity0.0280.0000.027
SRFilter-class0.0000.0000.001
SRFilterResult-class0.0680.0000.068
SRSet-class000
SRUtil-class0.0040.0000.004
Sampler-class1.1880.0001.189
ShortRead-class0.0520.0000.049
ShortReadQ-class0.2760.0000.276
Snapshot-class6.0400.0606.173
SnapshotFunction-class0.0000.0000.001
SolexaExportQA-class0.0000.0000.001
SolexaIntensity-class0.1720.0000.175
SolexaPath-class0.0640.0000.067
SolexaSet-class0.0680.0000.065
SpTrellis-class0.4160.0040.421
accessors0.0000.0000.002
alphabetByCycle0.0160.0000.016
clean0.0000.0040.001
countLines0.1120.0000.114
dotQA-class0.0000.0000.001
dustyScore0.0400.0080.048
filterFastq0.1200.0000.121
polyn0.0000.0000.001
qa0.4480.0040.453
qa24.1240.0164.145
readAligned0.2120.0040.218
readBaseQuality0.0680.0600.143
readFasta0.1360.0080.167
readFastq0.0360.0080.044
readIntensities0.0520.0080.062
readPrb0.0440.0080.052
readQseq0.0080.0000.007
readXStringColumns0.0360.0000.037
renew0.0320.0000.031
report0.0040.0000.005
spViewPerFeature2.8960.0442.942
srFilter0.30.00.3
srdistance0.2040.0280.354
srduplicated0.0520.0040.052
tables0.1320.0040.136
trimTails0.0480.0040.050