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BioC 2.13: CHECK report for rSFFreader on zin1

This page was generated on 2014-04-05 09:48:27 -0700 (Sat, 05 Apr 2014).

Package 627/750HostnameOS / ArchBUILDCHECKBUILD BIN
rSFFreader 0.10.0
Matt Settles
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/rSFFreader
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: rSFFreader
Version: 0.10.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings rSFFreader_0.10.0.tar.gz
StartedAt: 2014-04-05 03:44:47 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:47:15 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 148.2 seconds
RetCode: 0
Status:  OK 
CheckDir: rSFFreader.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/rSFFreader.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rSFFreader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rSFFreader’ version ‘0.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rSFFreader’ can be installed ... [16s/17s] OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘IRanges’ ‘XVector’ ‘Biostrings’ ‘ShortRead’ ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘GenomicRanges’ ‘ShortRead’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GenomicRanges’ ‘ShortRead’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... OK
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘rSFFreader.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [9s/9s] 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 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/rSFFreader.Rcheck/00check.log’
for details.

rSFFreader.Rcheck/00install.out:

* installing *source* package ‘rSFFreader’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c R_init_rSFFreader.c -o R_init_rSFFreader.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c SFF-io.c -o SFF-io.o
SFF-io.c: In function ‘readCommonHeader’:
SFF-io.c:281:10: warning: value computed is not used [-Wunused-value]
SFF-io.c:259:9: warning: unused variable ‘size’ [-Wunused-variable]
SFF-io.c:251:13: warning: unused variable ‘uint8’ [-Wunused-variable]
SFF-io.c:250:14: warning: unused variable ‘uint16’ [-Wunused-variable]
SFF-io.c:248:14: warning: unused variable ‘padding_size’ [-Wunused-variable]
SFF-io.c: In function ‘readSFF’:
SFF-io.c:602:26: warning: variable ‘fres’ set but not used [-Wunused-but-set-variable]
SFF-io.c: In function ‘sff_geometry’:
SFF-io.c:739:53: warning: variable ‘fres’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -shared -L/usr/local/lib -o rSFFreader.so Biostrings_stubs.o IRanges_stubs.o R_init_rSFFreader.o SFF-io.o XVector_stubs.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/rSFFreader.Rcheck/rSFFreader/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 (rSFFreader)

rSFFreader.Rcheck/rSFFreader-Ex.timings:

nameusersystemelapsed
SffHeader-class0.1960.0120.456
SffReads-class0.4080.0080.429
SffReadsQ-class0.2160.0040.221
availableClipModes0.1480.0080.159
load454SampleData0.4040.0040.409
loadIonSampleData0.1360.0000.137
readsff0.1200.0040.124
readsffgeometry0.0000.0080.009
readsffheader0.0080.0000.007