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This page was generated on 2024-03-04 11:38:29 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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

Package 1787/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RRHO 1.43.0  (landing page)
Jonathan Rosenblatt
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/RRHO
git_branch: devel
git_last_commit: 566e1f8
git_last_commit_date: 2023-10-24 09:55:09 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for RRHO on palomino3


To the developers/maintainers of the RRHO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RRHO.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RRHO
Version: 1.43.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RRHO.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings RRHO_1.43.0.tar.gz
StartedAt: 2024-03-02 07:19:15 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 07:19:42 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 27.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RRHO.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RRHO.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings RRHO_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/RRHO.Rcheck'
* using R Under development (unstable) (2024-01-14 r85805 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RRHO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RRHO' version '1.43.0'
* 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 'RRHO' 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 ... NOTE
Problems with news in 'NEWS':
  Cannot process chunk/lines:
    Version 1.6.0  (currently 1.5.xx)
    () Major documentation cleanup.
    () Added two sided hypotheses to RRHO() with signed pvalue plotting.
    () Added comparison of three lists using RRHOCOmparison().
    () Added an option for log10 pvalues in RRHO.
    () Added error handling to RRHO so that failed plotting does not crash the computation.
* 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
RRHO: no visible global function definition for 'p.adjust'
RRHO : color.bar: no visible global function definition for 'mtext'
RRHO : color.bar: no visible global function definition for 'axis'
RRHO : color.bar: no visible global function definition for 'rect'
RRHO: no visible global function definition for 'jpeg'
RRHO: no visible global function definition for 'colorRampPalette'
RRHO: no visible global function definition for 'layout'
RRHO: no visible global function definition for 'image'
RRHO: no visible global function definition for 'mtext'
RRHO: no visible global function definition for 'dev.off'
RRHO: no visible global function definition for 'cor'
RRHO: no visible global function definition for 'lm'
RRHO: no visible global function definition for 'lines'
RRHO: no visible global function definition for 'predict'
RRHO: no visible global function definition for 'write.table'
RRHOComparison: no visible global function definition for 'phyper'
RRHOComparison: no visible global function definition for 'pnorm'
RRHOComparison: no visible global function definition for 'p.adjust'
RRHOComparison : color.bar: no visible global function definition for
  'mtext'
RRHOComparison : color.bar: no visible global function definition for
  'axis'
RRHOComparison : color.bar: no visible global function definition for
  'rect'
RRHOComparison: no visible global function definition for 'pdf'
RRHOComparison: no visible global function definition for
  'colorRampPalette'
RRHOComparison: no visible global function definition for 'layout'
RRHOComparison: no visible global function definition for 'image'
RRHOComparison: no visible global function definition for 'mtext'
RRHOComparison: no visible global function definition for 'dev.off'
numericListOverlap : overlap: no visible global function definition for
  'phyper'
pvalRRHO: no visible global function definition for 'txtProgressBar'
pvalRRHO: no visible global function definition for 'na.omit'
pvalRRHO: no visible global function definition for 'setTxtProgressBar'
pvalRRHO : FUN.ecdf: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  axis colorRampPalette cor dev.off ecdf image jpeg layout lines lm
  mtext na.omit p.adjust pdf phyper pnorm predict rect
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "jpeg", "pdf")
  importFrom("graphics", "axis", "image", "layout", "lines", "mtext",
             "rect")
  importFrom("stats", "cor", "ecdf", "lm", "na.omit", "p.adjust",
             "phyper", "pnorm", "predict")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/RRHO.Rcheck/00check.log'
for details.



Installation output

RRHO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL RRHO
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'RRHO' ...
** using staged installation
** R
** data
** inst
** 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 (RRHO)

Tests output


Example timings

RRHO.Rcheck/RRHO-Ex.timings

nameusersystemelapsed
HNP0.050.020.07
RRHO0.030.000.03
RRHOComparison0.700.140.84
pvalRRHO0.210.020.22