Matt Settles
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/rSFFreader |
| Branch: RELEASE_3_8 |
| Last Commit: fdcb055 |
| Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:36 -0400 (Tue, 16 Apr 2019).
| Package 1355/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rSFFreader 0.30.0 Matt Settles
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: rSFFreader |
| Version: 0.30.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rSFFreader.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rSFFreader_0.30.0.tar.gz |
| StartedAt: 2019-04-16 02:31:13 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:34:13 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 180.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rSFFreader.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rSFFreader.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rSFFreader_0.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/rSFFreader.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘0.30.0’
* 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 8.8Mb
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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/rSFFreader.Rcheck/00check.log’
for details.
rSFFreader.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rSFFreader ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘rSFFreader’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rSFFreader/libs ** R ** inst ** byte-compile and prepare 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
| name | user | system | elapsed | |
| SffHeader-class | 0.463 | 0.052 | 0.553 | |
| SffReads-class | 0.426 | 0.014 | 0.444 | |
| SffReadsQ-class | 0.390 | 0.015 | 0.405 | |
| availableClipModes | 0.214 | 0.011 | 0.225 | |
| load454SampleData | 0.384 | 0.014 | 0.400 | |
| loadIonSampleData | 0.182 | 0.007 | 0.189 | |
| readsff | 0.312 | 0.010 | 0.324 | |
| readsffgeometry | 0.006 | 0.007 | 0.013 | |
| readsffheader | 0.004 | 0.001 | 0.004 | |