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This page was generated on 2024-04-17 11:36:59 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1239/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mfuzz 2.62.0  (landing page)
Matthias Futschik
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/Mfuzz
git_branch: RELEASE_3_18
git_last_commit: b17f5af
git_last_commit_date: 2023-10-24 09:36:17 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for Mfuzz on palomino4


To the developers/maintainers of the Mfuzz package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Mfuzz.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: Mfuzz
Version: 2.62.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Mfuzz.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings Mfuzz_2.62.0.tar.gz
StartedAt: 2024-04-16 02:34:59 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 02:35:49 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 50.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Mfuzz.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Mfuzz.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings Mfuzz_2.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/Mfuzz.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* 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 'Mfuzz/DESCRIPTION' ... OK
* this is package 'Mfuzz' version '2.62.0'
* 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 'Mfuzz' can be installed ... WARNING
Found the following significant warnings:
  Warning: cselection.Rd:25: unexpected '}'
  Warning: cselection.Rd:25: All text must be in a section
See 'F:/biocbuild/bbs-3.18-bioc/meat/Mfuzz.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to 'marray' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Biobase' 'e1071'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Dmin: warning in mfuzz(eset, c = i, m = m): partial argument match of
  'c' to 'centers'
Mfuzzgui : objectBrowser2 : viewEnv: warning in ls(env = env, all =
  TRUE): partial argument match of 'env' to 'envir'
Mfuzzgui : objectBrowser2 : viewEnv: warning in ls(env = env, all =
  TRUE): partial argument match of 'all' to 'all.names'
kmeans2.plot: no visible global function definition for 'X11'
mfuzz: no visible global function definition for 'cmeans'
mfuzz.plot: no visible global function definition for 'X11'
mfuzz.plot2: no visible global function definition for 'rgb'
mfuzz.plot2: no visible global function definition for 'X11'
mfuzzColorBar: no visible global function definition for 'rgb'
mfuzzColorBar: no visible global function definition for 'maColorBar'
Undefined global functions or variables:
  X11 cmeans maColorBar rgb
Consider adding
  importFrom("grDevices", "X11", "rgb")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: cselection.Rd:25: unexpected '}'
prepare_Rd: cselection.Rd:25: All text must be in a section
* 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 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 WARNINGs, 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/Mfuzz.Rcheck/00check.log'
for details.



Installation output

Mfuzz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL Mfuzz
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'Mfuzz' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: cselection.Rd:25: unexpected '}'
Warning: cselection.Rd:25: All text must be in a section
*** 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 (Mfuzz)

Tests output


Example timings

Mfuzz.Rcheck/Mfuzz-Ex.timings

nameusersystemelapsed
Dmin000
acore000
cselection0.020.000.02
fill.NA000
filter.NA000
filter.std0.300.020.31
kmeans2000
kmeans2.plot000
membership000
mestimate000
mfuzz000
mfuzz.plot000
mfuzz.plot2000
mfuzzColorBar000
overlap000
overlap.plot000
partcoef0.010.000.01
randomise0.070.020.08
standardise000
standardise2000
top.count000