Package: TSSi

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TSSi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TSSi_1.29.0.tar.gz

StartedAt: 2018-11-07 03:54:25 -0500 (Wed, 07 Nov 2018)

EndedAt: 2018-11-07 03:56:34 -0500 (Wed, 07 Nov 2018)

EllapsedTime: 128.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TSSi.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TSSi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TSSi_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TSSi.Rcheck’
* using R Under development (unstable) (2018-04-05 r74542)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.29.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/TSSi.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 ... 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 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/TSSi.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TSSi
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘TSSi’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c assess.c -o assess.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.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 TSSi.so assess.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/TSSi/libs
** R
** data
** byte-compile and prepare package for lazy loading
Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found
Creating a new generic function for ‘segments’ in package ‘TSSi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found
* DONE (TSSi)

name	user	system	elapsed
TSSi-package	2.902	0.056	2.979
TssData-class	0.007	0.001	0.007
TssNorm-class	0.003	0.000	0.004
TssResult-class	0.007	0.000	0.008
asRangedData-methods	0.155	0.003	0.159
get-methods	0.040	0.003	0.044
identify-methods	2.487	0.029	2.535
normalize-methods	2.519	0.021	2.565
physcoCounts-data	0.008	0.001	0.010
plot-methods	2.732	0.029	2.780
segmentize-methods	0.022	0.001	0.028
subtract-functions	0.003	0.000	0.004