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BioC 3.4: CHECK report for gaia on tokay1

This page was generated on 2017-04-15 16:16:26 -0400 (Sat, 15 Apr 2017).

Package 463/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaia 2.18.0
S. Morganella
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/gaia
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gaia
Version: 2.18.0
Command: rm -rf gaia.buildbin-libdir gaia.Rcheck && mkdir gaia.buildbin-libdir gaia.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gaia.buildbin-libdir gaia_2.18.0.tar.gz >gaia.Rcheck\00install.out 2>&1 && cp gaia.Rcheck\00install.out gaia-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=gaia.buildbin-libdir --install="check:gaia-install.out" --force-multiarch --no-vignettes --timings gaia_2.18.0.tar.gz
StartedAt: 2017-04-14 22:25:45 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:26:23 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 37.9 seconds
RetCode: 0
Status:  OK  
CheckDir: gaia.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gaia.buildbin-libdir gaia.Rcheck && mkdir gaia.buildbin-libdir gaia.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gaia.buildbin-libdir gaia_2.18.0.tar.gz >gaia.Rcheck\00install.out 2>&1 && cp gaia.Rcheck\00install.out gaia-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=gaia.buildbin-libdir --install="check:gaia-install.out" --force-multiarch --no-vignettes --timings gaia_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/gaia.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gaia/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gaia' version '2.18.0'
* 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 whether package 'gaia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
generate_approx_null_hypothesis: no visible global function definition
  for 'rbinom'
qvalue: no visible global function definition for 'smooth.spline'
qvalue: no visible global function definition for 'predict'
runGAIA: no visible global function definition for 'write.table'
write_significant_regions: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  predict rbinom smooth.spline write.table
Consider adding
  importFrom("stats", "predict", "rbinom", "smooth.spline")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
runGAIA 5.21   0.01    5.22
* 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
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/gaia.Rcheck/00check.log'
for details.


gaia.Rcheck/00install.out:


install for i386

* installing *source* package 'gaia' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'gaia' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gaia' as gaia_2.18.0.zip
* DONE (gaia)

gaia.Rcheck/examples_i386/gaia-Ex.timings:

nameusersystemelapsed
crc0.020.000.01
crc_markers0.080.010.10
gaia-package2.980.033.01
load_cnv0.170.000.18
load_markers0.020.000.01
runGAIA4.780.024.80
synthCNV_Matrix000
synthMarkers_Matrix0.000.010.01

gaia.Rcheck/examples_x64/gaia-Ex.timings:

nameusersystemelapsed
crc0.020.000.02
crc_markers0.070.000.07
gaia-package3.550.023.57
load_cnv0.190.000.18
load_markers0.010.000.02
runGAIA5.210.015.22
synthCNV_Matrix0.010.000.01
synthMarkers_Matrix000