BioC 2.14: CHECK report for TSSi on petty

Package: TSSi

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TSSi_1.10.0.tar.gz

StartedAt: 2014-10-08 00:30:51 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:34:07 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 196.0 seconds

RetCode: 0

Status:  OK

CheckDir: TSSi.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TSSi_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/TSSi.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TSSi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSSi’ version ‘1.10.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TSSi’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’
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 loading without being on the library search path ... 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/27s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plot-methods     9.418  0.690   4.882
TSSi-package     6.577  0.579   5.460
identify-methods 6.381  0.555   4.886
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/TSSi.Rcheck/00check.log’
for details.

* installing *source* package ‘TSSi’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c assess.c -o assess.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o TSSi.so assess.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/TSSi.Rcheck/TSSi/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘start’ from package ‘stats’ in package ‘TSSi’
Creating a generic function for ‘end’ from package ‘stats’ in package ‘TSSi’
Creating a new generic function for ‘segments’ in package ‘TSSi’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘TSSi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TSSi)

name	user	system	elapsed
TSSi-package	6.577	0.579	5.460
TssData-class	0.003	0.001	0.004
TssNorm-class	0.003	0.001	0.003
TssResult-class	0.002	0.001	0.002
asRangedData-methods	0.663	0.036	0.702
get-methods	0.074	0.005	0.087
identify-methods	6.381	0.555	4.886
normalize-methods	2.942	0.352	4.676
physcoCounts-data	0.003	0.002	0.006
plot-methods	9.418	0.690	4.882
segmentize-methods	0.049	0.009	0.058
subtract-functions	0.001	0.001	0.001