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CHECK report for rSFFreader on veracruz1

This page was generated on 2018-04-12 13:36:11 -0400 (Thu, 12 Apr 2018).

Package 1218/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rSFFreader 0.26.0
Matt Settles
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/rSFFreader
Branch: RELEASE_3_6
Last Commit: 46a46c3
Last Changed Date: 2017-10-30 12:39:54 -0400 (Mon, 30 Oct 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 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: rSFFreader
Version: 0.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rSFFreader_0.26.0.tar.gz
StartedAt: 2018-04-12 09:03:38 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 09:06:27 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 168.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: rSFFreader.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rSFFreader_0.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/rSFFreader.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘0.26.0’
* 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 ... 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 ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘S4Vectors’ is only usable in R >= 3.0.2
* 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’
Undefined global functions or variables:
  isTRUEorFALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'SffReads,ANY,ANY,ANY'
  generic '[' and siglist 'SffReads,ANY,missing,ANY'
  generic '[' and siglist 'SffReads,missing,ANY,ANY'
  generic '[' and siglist 'SffReads,missing,missing,ANY'
  generic '[' and siglist 'SffReadsQ,ANY,ANY,ANY'
  generic '[' and siglist 'SffReadsQ,ANY,missing,ANY'
  generic '[' and siglist 'SffReadsQ,missing,ANY,ANY'
  generic '[' and siglist 'SffReadsQ,missing,missing,ANY'
All user-level objects in a package (including S4 classes and methods)
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 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 ... 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/rSFFreader.Rcheck/00check.log’
for details.



Installation output

rSFFreader.Rcheck/00install.out

* installing *source* package ‘rSFFreader’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_rSFFreader.c -o R_init_rSFFreader.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SFF-io.c -o SFF-io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I/usr/local/include   -fPIC  -Wall -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-3.6-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)

Tests output


Example timings

rSFFreader.Rcheck/rSFFreader-Ex.timings

nameusersystemelapsed
SffHeader-class0.8090.0200.833
SffReads-class0.5910.0390.634
SffReadsQ-class0.4200.0120.440
availableClipModes0.2250.0090.236
load454SampleData0.3580.0150.376
loadIonSampleData0.1700.0070.181
readsff0.2980.0090.308
readsffgeometry0.0060.0050.011
readsffheader0.0030.0010.004