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CHECK report for gaia on tokay2

This page was generated on 2020-10-17 11:56:37 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE gaia PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 651/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaia 2.32.0
S. Morganella
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/gaia
Branch: RELEASE_3_11
Last Commit: e91de1f
Last Changed Date: 2020-04-27 14:23:46 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gaia
Version: 2.32.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaia.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gaia_2.32.0.tar.gz
StartedAt: 2020-10-17 04:12:42 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:13:42 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 60.1 seconds
RetCode: 0
Status:  OK  
CheckDir: gaia.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaia.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gaia_2.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/gaia.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '2.32.0'
* 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
* 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
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
runGAIA 6.11   0.05    6.15
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
runGAIA 6.24   0.04    6.26
* 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-3.11-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://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/gaia_2.32.0.tar.gz && rm -rf gaia.buildbin-libdir && mkdir gaia.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gaia.buildbin-libdir gaia_2.32.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL gaia_2.32.0.zip && rm gaia_2.32.0.tar.gz gaia_2.32.0.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  455k  100  455k    0     0  7897k      0 --:--:-- --:--:-- --:--:-- 8925k

install for i386

* installing *source* package 'gaia' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'gaia' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gaia' as gaia_2.32.0.zip
* DONE (gaia)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'gaia' successfully unpacked and MD5 sums checked

Tests output


Example timings

gaia.Rcheck/examples_i386/gaia-Ex.timings

nameusersystemelapsed
crc0.030.000.03
crc_markers0.110.000.11
gaia-package4.190.004.19
load_cnv0.120.000.12
load_markers0.000.010.02
runGAIA6.110.056.15
synthCNV_Matrix000
synthMarkers_Matrix000

gaia.Rcheck/examples_x64/gaia-Ex.timings

nameusersystemelapsed
crc0.040.000.03
crc_markers0.060.020.08
gaia-package4.670.044.71
load_cnv0.190.000.19
load_markers0.010.000.02
runGAIA6.240.046.26
synthCNV_Matrix000
synthMarkers_Matrix000