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This page was generated on 2024-03-04 11:36:35 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1126/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
macat 1.76.0  (landing page)
Joern Toedling
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/macat
git_branch: RELEASE_3_18
git_last_commit: eb279b2
git_last_commit_date: 2023-10-24 09:34:20 -0500 (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
lconwaymacOS 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 macat on palomino4


To the developers/maintainers of the macat package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/macat.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: macat
Version: 1.76.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:macat.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings macat_1.76.0.tar.gz
StartedAt: 2024-03-04 03:15:58 -0500 (Mon, 04 Mar 2024)
EndedAt: 2024-03-04 03:17:37 -0500 (Mon, 04 Mar 2024)
EllapsedTime: 99.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: macat.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:macat.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings macat_1.76.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/macat.Rcheck'
* using R version 4.3.2 (2023-10-31 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 'macat/DESCRIPTION' ... OK
* this is package 'macat' version '1.76.0'
* 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 'macat' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'macat' is deprecated and will be removed from Bioconductor
See 'F:/biocbuild/bbs-3.18-bioc/meat/macat.Rcheck/00install.out' for details.
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'annotate' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'annotate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'annotate:::getTDRows'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
evalScoring : computePermSlideScores: warning in compute.sliding(permM,
  chrom = chromosome, sample = 1, kernel, kernelparams, step.width =
  step.width): partial argument match of 'chrom' to 'chromosome'
preprocessedLoader: warning in require(chip, character.only = TRUE,
  quiet = TRUE): partial argument match of 'quiet' to 'quietly'
.onAttach: no visible global function definition for 'addVigs2WinMenu'
buildMACAT: no visible global function definition for 'featureNames'
buildMACAT: no visible global function definition for 'sampleNames'
buildMACAT: no visible global function definition for 'exprs'
compare.gammas: no visible global function definition for 'x11'
compare.gammas: no visible global function definition for 'lines'
compare.gammas: no visible global function definition for 'legend'
discreteKernelize: no visible binding for global variable 'quantile'
discretize: no visible binding for global variable 'quantile'
discretizeChromosome: no visible binding for global variable 'quantile'
discretizeOne: no visible binding for global variable 'quantile'
evalScoring: no visible binding for global variable 'quantile'
getHtml: no visible global function definition for 'browseURL'
loaddatapkg: no visible global function definition for
  'install.packages'
loaddatapkg: no visible global function definition for 'contrib.url'
plot.MACATevalScoring: no visible global function definition for 'x11'
plot.MACATevalScoring: no visible global function definition for 'png'
plot.MACATevalScoring: no visible global function definition for 'par'
plot.MACATevalScoring: no visible global function definition for
  'points'
plot.MACATevalScoring: no visible global function definition for
  'lines'
plot.MACATevalScoring: no visible global function definition for
  'title'
plot.MACATevalScoring: no visible global function definition for 'axis'
plot.MACATevalScoring: no visible global function definition for
  'mtext'
plot.MACATevalScoring: no visible global function definition for
  'dev.off'
plotSliding: no visible global function definition for 'lines'
preprocessedLoader: no visible global function definition for
  'read.delim'
preprocessedLoader: no visible global function definition for
  'read.table'
preprocessedLoader: no visible global function definition for
  'buildChromLocation'
preprocessedLoader: no visible global function definition for 'new'
preprocessedLoader: no visible global function definition for 'pData<-'
preprocessedLoader: no visible global function definition for
  'varLabels<-'
preprocessedLoader: no visible global function definition for
  'chromLocs'
preprocessedLoader : usedChromGenes2: no visible global function
  definition for 'chromLocs'
preprocessedLoader : usedChromGenes2: no visible global function
  definition for 'featureNames'
scoring : tscore: no visible global function definition for 'median'
scoring : tscoremat: no visible binding for global variable 'median'
scoring : pval: no visible binding for global variable 'pt'
scoring: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  addVigs2WinMenu axis browseURL buildChromLocation chromLocs
  contrib.url dev.off exprs featureNames install.packages legend lines
  median mtext new pData<- par png points pt quantile read.delim
  read.table sampleNames title varLabels<- x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "x11")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "points", "title")
  importFrom("methods", "new")
  importFrom("stats", "median", "pt", "quantile")
  importFrom("utils", "browseURL", "contrib.url", "install.packages",
             "read.delim", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
discretize_tscores 13.68   0.75   14.43
get_results         6.83   0.16    6.99
* 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: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/macat.Rcheck/00check.log'
for details.



Installation output

macat.Rcheck/00install.out

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


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'macat' ...
** using staged installation
** R
** data
** demo
** 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
Warning: Package 'macat' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'macat' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (macat)

Tests output


Example timings

macat.Rcheck/macat-Ex.timings

nameusersystemelapsed
buildMACAT1.270.081.35
compute_sliding0.970.131.09
discreteKernelize1.070.041.11
discretizeAll000
discretize_tscores13.68 0.7514.43
evalScoring2.300.112.41
evaluateParameters0.280.030.31
get_results6.830.166.99
kernelize0.300.020.31
kernelizeAll000
kernelizeToPython000
kernels0.030.000.03
loaddatapkg000
plot_MACATevalScoring000
preprocessedLoader000
pythondata000
scoring0.010.000.02
stjd0.000.010.01