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BioC 3.2: CHECK report for rSFFreader on oaxaca

This page was generated on 2016-04-23 10:26:13 -0700 (Sat, 23 Apr 2016).

Package 918/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rSFFreader 0.18.0
Matt Settles
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/rSFFreader
Last Changed Rev: 111517 / Revision: 116712
Last Changed Date: 2015-12-15 11:30:26 -0800 (Tue, 15 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: rSFFreader
Version: 0.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rSFFreader_0.18.0.tar.gz
StartedAt: 2016-04-23 04:04:22 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:07:05 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 162.5 seconds
RetCode: 0
Status:  OK 
CheckDir: rSFFreader.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rSFFreader_0.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rSFFreader.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘0.18.0’
* 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 ... [18s/19s] OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readSff: no visible global function definition for ‘isTRUEorFALSE’
readSffHeader: no visible global function definition for
  ‘isTRUEorFALSE’
* 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 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 ... [10s/10s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/rSFFreader.Rcheck/00check.log’
for details.


rSFFreader.Rcheck/00install.out:

* installing *source* package ‘rSFFreader’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_rSFFreader.c -o R_init_rSFFreader.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c SFF-io.c -o SFF-io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rSFFreader.so Biostrings_stubs.o IRanges_stubs.o R_init_rSFFreader.o S4Vectors_stubs.o SFF-io.o XVector_stubs.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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-class0.6020.0170.619
SffReads-class0.5690.0140.583
SffReadsQ-class0.5360.0100.544
availableClipModes0.2670.0100.278
load454SampleData0.4770.0110.504
loadIonSampleData0.2140.0050.220
readsff0.3530.0060.360
readsffgeometry0.0040.0030.007
readsffheader0.0030.0010.004