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CHECK report for gaia on tokay1

This page was generated on 2019-04-13 11:21:27 -0400 (Sat, 13 Apr 2019).

Package 570/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaia 2.26.0
S. Morganella
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/gaia
Branch: RELEASE_3_8
Last Commit: da890c8
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gaia
Version: 2.26.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaia.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gaia_2.26.0.tar.gz
StartedAt: 2019-04-13 02:22:29 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:24:08 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 99.0 seconds
RetCode: 0
Status:  OK  
CheckDir: gaia.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaia.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gaia_2.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/gaia.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.26.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/gaia.Rcheck/00check.log'
for details.



Installation output

gaia.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/gaia_2.26.0.tar.gz && rm -rf gaia.buildbin-libdir && mkdir gaia.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gaia.buildbin-libdir gaia_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL gaia_2.26.0.zip && rm gaia_2.26.0.tar.gz gaia_2.26.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  456k  100  456k    0     0  10.4M      0 --:--:-- --:--:-- --:--:-- 11.7M

install for i386

* installing *source* package 'gaia' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gaia'
    finding HTML links ... done
    crc                                     html  
    crc_markers                             html  
    gaia-package                            html  
    generate_approx_null_hypothesis         html  
    generate_null_hypothesis                html  
    load_cnv                                html  
    load_markers                            html  
    peel_off                                html  
    qvalue                                  html  
    runGAIA                                 html  
    search_peaks_in_regions                 html  
    synthCNV_Matrix                         html  
    synthMarkers_Matrix                     html  
    write_significant_regions               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'gaia' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gaia' as gaia_2.26.0.zip
* DONE (gaia)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'gaia' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

gaia.Rcheck/examples_i386/gaia-Ex.timings

nameusersystemelapsed
crc0.020.000.01
crc_markers0.090.000.10
gaia-package3.410.023.42
load_cnv0.110.010.13
load_markers0.010.000.01
runGAIA4.710.024.72
synthCNV_Matrix000
synthMarkers_Matrix0.000.010.02

gaia.Rcheck/examples_x64/gaia-Ex.timings

nameusersystemelapsed
crc0.000.010.01
crc_markers0.080.000.08
gaia-package2.980.033.01
load_cnv0.110.030.14
load_markers0.020.000.02
runGAIA4.480.044.51
synthCNV_Matrix000
synthMarkers_Matrix0.000.010.02