Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K [L] M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.6: CHECK report for Linnorm on malbec1

This page was generated on 2017-08-16 13:24:24 -0400 (Wed, 16 Aug 2017).

Package 727/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Linnorm 2.1.5
Ken Shun Hang Yip
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Linnorm
Last Changed Rev: 131462 / Revision: 131943
Last Changed Date: 2017-07-21 07:16:55 -0400 (Fri, 21 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Linnorm
Version: 2.1.5
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Linnorm_2.1.5.tar.gz
StartedAt: 2017-08-16 00:18:37 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:24:44 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 366.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Linnorm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Linnorm_2.1.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Linnorm.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Linnorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Linnorm’ version ‘2.1.5’
* 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 ‘Linnorm’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    1.9Mb
* 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 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 ... NOTE
Linnorm.HClust: no visible binding for global variable ‘x’
Linnorm.HClust: no visible binding for global variable ‘y’
Linnorm.HClust: no visible binding for global variable ‘xend’
Linnorm.HClust: no visible binding for global variable ‘yend’
Linnorm.HClust: no visible binding for global variable ‘cluster’
Linnorm.HClust: no visible binding for global variable ‘X1’
Linnorm.HClust: no visible binding for global variable ‘X2’
Linnorm.HVar: no visible binding for global variable ‘SD’
Linnorm.HVar: no visible binding for global variable ‘group’
Undefined global functions or variables:
  SD X1 X2 cluster group x xend y yend
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
RnaXSim       83.148  0.024  83.230
Linnorm.Cor   51.916  0.188  52.129
Linnorm.limma 35.252  0.004  35.277
Linnorm       34.020  0.012  34.047
Linnorm.Norm  33.180  0.020  33.217
Linnorm.tSNE   5.148  0.012   5.165
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/Linnorm.Rcheck/00check.log’
for details.


Linnorm.Rcheck/00install.out:

* installing *source* package ‘Linnorm’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Misc.cpp -o Misc.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o Linnorm.so Misc.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/Linnorm.Rcheck/Linnorm/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Linnorm)

Linnorm.Rcheck/Linnorm-Ex.timings:

nameusersystemelapsed
LinearRegression0.0000.0040.001
LinearRegressionFP0.0000.0000.001
Linnorm.Cor51.916 0.18852.129
Linnorm.DataImput2.0000.1562.162
Linnorm.HClust3.3600.0763.113
Linnorm.HVar1.4320.0961.528
Linnorm.Norm33.180 0.02033.217
Linnorm.PCA3.8120.1763.993
Linnorm34.020 0.01234.047
Linnorm.SGenes0.3440.0080.352
Linnorm.limma35.252 0.00435.277
Linnorm.tSNE5.1480.0125.165
RnaXSim83.148 0.02483.230