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This page was generated on 2023-04-12 11:05:12 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for occugene on nebbiolo2


To the developers/maintainers of the occugene package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/occugene.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1372/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
occugene 1.58.0  (landing page)
Oliver Will
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/occugene
git_branch: RELEASE_3_16
git_last_commit: 4eb81e1
git_last_commit_date: 2022-11-01 10:42:38 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: occugene
Version: 1.58.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:occugene.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings occugene_1.58.0.tar.gz
StartedAt: 2023-04-10 22:24:57 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:25:18 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 20.7 seconds
RetCode: 0
Status:   OK  
CheckDir: occugene.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:occugene.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings occugene_1.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/occugene.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘occugene/DESCRIPTION’ ... OK
* this is package ‘occugene’ version ‘1.58.0’
* 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 ‘occugene’ 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
binInsertHist: no visible global function definition for ‘hist’
delta0: no visible global function definition for ‘coef’
eMult : unequalApproxEMult: no visible global function definition for
  ‘runif’
eMult : unequalApproxEMult: no visible binding for global variable
  ‘hist’
fFit : expModel: no visible global function definition for ‘nls’
loadAnnotation: no visible global function definition for ‘read.table’
loadInsertions: no visible global function definition for ‘read.table’
unbiasB0 : simB0: no visible global function definition for ‘coef’
unbiasB0: no visible global function definition for ‘coef’
varMult : unequalApproxVarMult: no visible global function definition
  for ‘runif’
varMult : unequalApproxVarMult: no visible binding for global variable
  ‘hist’
varMult : unequalApproxVarMult: no visible global function definition
  for ‘var’
Undefined global functions or variables:
  coef hist nls read.table runif var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coef", "nls", "runif", "var")
  importFrom("utils", "read.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 ...
  ‘occugene.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/occugene.Rcheck/00check.log’
for details.



Installation output

occugene.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL occugene
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘occugene’ ...
** 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 (occugene)

Tests output


Example timings

occugene.Rcheck/occugene-Ex.timings

nameusersystemelapsed
binHist000
binInsert000
binInsertHist000
checkFormat0.0180.0000.018
delta00.0370.0000.037
eMult0.3380.0000.337
etDelta0.0030.0000.002
fCumul0.0010.0000.000
fFit0.0330.0000.034
loadAnnotation000
loadInsertions000
occup2Negenes0.0050.0000.005
unbiasB00.2790.0000.278
unbiasDelta00.3620.0000.361
varMult0.3440.0000.343