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This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).

CHECK results for gaia on nebbiolo1

To the developers/maintainers of the gaia package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gaia.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 687/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaia 2.36.0  (landing page)
S. Morganella
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/gaia
git_branch: RELEASE_3_13
git_last_commit: 4524f5d
git_last_commit_date: 2021-05-19 11:46:53 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: gaia
Version: 2.36.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:gaia.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings gaia_2.36.0.tar.gz
StartedAt: 2021-10-14 09:54:13 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:54:36 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 23.2 seconds
RetCode: 0
Status:   OK  
CheckDir: gaia.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:gaia.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings gaia_2.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/gaia.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaia/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gaia’ version ‘2.36.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/gaia.Rcheck/00check.log’
for details.



Installation output

gaia.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL gaia
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘gaia’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (gaia)

Tests output


Example timings

gaia.Rcheck/gaia-Ex.timings

nameusersystemelapsed
crc0.0150.0000.016
crc_markers0.0660.0000.066
gaia-package3.1250.0323.157
load_cnv0.1130.0000.113
load_markers0.0060.0040.011
runGAIA4.6070.0204.628
synthCNV_Matrix0.0010.0000.001
synthMarkers_Matrix0.0020.0000.002