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BioC 3.5: CHECK report for Linnorm on toluca2

This page was generated on 2017-04-23 14:41:32 -0400 (Sun, 23 Apr 2017).

Package 715/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Linnorm 1.99.19
Ken Shun Hang Yip
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Linnorm
Last Changed Rev: 128516 / Revision: 129046
Last Changed Date: 2017-04-11 00:05:06 -0400 (Tue, 11 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Linnorm
Version: 1.99.19
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Linnorm_1.99.19.tar.gz
StartedAt: 2017-04-23 05:52:59 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 06:00:20 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 440.5 seconds
RetCode: 0
Status:  OK 
CheckDir: Linnorm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Linnorm_1.99.19.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Linnorm.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.99.19’
* 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 ... 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 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 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        140.187  2.577 146.251
Linnorm.Cor     90.295  4.212  95.465
Linnorm.tSNE     6.510  0.162   6.739
Linnorm.Norm     6.393  0.063   6.538
Linnorm.limma    6.282  0.066   6.596
Linnorm          6.019  0.041   6.078
Linnorm.PCA      5.001  0.280   5.320
Linnorm.HClust   4.831  0.200   4.570
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Linnorm.Rcheck/00check.log’
for details.


Linnorm.Rcheck/00install.out:

* installing *source* package ‘Linnorm’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Misc.cpp -o Misc.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 Linnorm.so Misc.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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
LinearRegression0.0010.0000.001
LinearRegressionFP0.0010.0010.001
Linnorm.Cor90.295 4.21295.465
Linnorm.DataImput2.8810.2133.104
Linnorm.HClust4.8310.2004.570
Linnorm.HVar1.9530.1182.085
Linnorm.Norm6.3930.0636.538
Linnorm.PCA5.0010.2805.320
Linnorm6.0190.0416.078
Linnorm.SGenes0.5920.0600.654
Linnorm.limma6.2820.0666.596
Linnorm.tSNE6.5100.1626.739
RnaXSim140.187 2.577146.251