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CHECK report for TSSi on malbec2

This page was generated on 2018-11-07 14:48:45 -0500 (Wed, 07 Nov 2018).

Package 1584/1636HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TSSi 1.29.0
Julian Gehring
Snapshot Date: 2018-11-06 16:46:33 -0500 (Tue, 06 Nov 2018)
URL: https://git.bioconductor.org/packages/TSSi
Branch: master
Last Commit: 7dbde71
Last Changed Date: 2018-10-30 11:54:29 -0500 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: TSSi
Version: 1.29.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TSSi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TSSi_1.29.0.tar.gz
StartedAt: 2018-11-07 08:31:27 -0500 (Wed, 07 Nov 2018)
EndedAt: 2018-11-07 08:33:27 -0500 (Wed, 07 Nov 2018)
EllapsedTime: 120.0 seconds
RetCode: 0
Status:  OK 
CheckDir: TSSi.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TSSi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TSSi_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TSSi.Rcheck’
* using R Under development (unstable) (2018-10-16 r75448)
* using platform: x86_64-pc-linux-gnu (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 ... OK
* 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 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 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/TSSi.Rcheck/00check.log’
for details.



Installation output

TSSi.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TSSi
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘TSSi’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c assess.c -o assess.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o TSSi.so assess.o init.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/TSSi/libs
** R
** data
** byte-compile and prepare package for lazy loading
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
* DONE (TSSi)

Tests output


Example timings

TSSi.Rcheck/TSSi-Ex.timings

nameusersystemelapsed
TSSi-package2.9120.0162.933
TssData-class0.0010.0000.001
TssNorm-class0.0000.0000.001
TssResult-class000
asRangedData-methods0.1910.0000.228
get-methods0.0200.0000.021
identify-methods2.6000.0002.606
normalize-methods2.4470.0002.454
physcoCounts-data0.0020.0000.001
plot-methods2.7870.0042.795
segmentize-methods0.0120.0000.012
subtract-functions000