Linnorm 1.1.14
Ken Shun Hang Yip
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Linnorm | | Last Changed Rev: 120534 / Revision: 121152 | | Last Changed Date: 2016-08-27 01:03:03 -0700 (Sat, 27 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Linnorm_1.1.14.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Linnorm.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.14’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘Linnorm’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘Linnorm’
See ‘/home/biocbuild/bbs-3.4-bioc/meat/Linnorm.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
data 3.6Mb
doc 1.8Mb
* 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.HVar: no visible binding for global variable ‘SD’
Linnorm.HVar: no visible binding for global variable ‘group’
Undefined global functions or variables:
SD group
* 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 sizes of PDF files under ‘inst/doc’ ... 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 152.708 1.900 155.086
Linnorm.Cor 31.996 2.224 34.222
Linnorm.PCA 11.380 0.004 11.387
Linnorm 8.408 0.004 8.412
* 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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/Linnorm.Rcheck/00check.log’
for details.
* installing *source* package ‘Linnorm’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c Misc.cpp -o Misc.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o Linnorm.so Misc.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/Linnorm.Rcheck/Linnorm/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘Linnorm’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘Linnorm’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘Linnorm’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘Linnorm’
* DONE (Linnorm)