Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-21 11:07:16 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 compartmap on riesling1


To the developers/maintainers of the compartmap package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/compartmap.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 376/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compartmap 1.13.0  (landing page)
Benjamin Johnson
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/compartmap
git_branch: master
git_last_commit: 087d134
git_last_commit_date: 2021-10-26 12:48:10 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: compartmap
Version: 1.13.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:compartmap.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings compartmap_1.13.0.tar.gz
StartedAt: 2022-01-20 18:34:09 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:38:33 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 263.8 seconds
RetCode: 0
Status:   OK  
CheckDir: compartmap.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:compartmap.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings compartmap_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/compartmap.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'compartmap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compartmap' version '1.13.0'
* package encoding: UTF-8
* 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 'compartmap' 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 dependencies in R code ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.ebayes: no visible global function definition for 'sd'
.jse: no visible global function definition for 'sd'
.unitarize: no visible global function definition for 'median'
.window.mean: no visible global function definition for 'weighted.mean'
.window.mean.rcpp: no visible global function definition for
  'weighted.mean'
.window.mean.rcpp: no visible binding for global variable 'x'
checkAssayType: no visible global function definition for 'is'
condenseRE: no visible global function definition for 'is'
condenseSE: no visible global function definition for 'is'
estRMT: no visible global function definition for 'cov'
estRMT : <anonymous>: no visible global function definition for 'optim'
extractOpenClosed: no visible global function definition for 'is'
filterCompartments: no visible global function definition for 'is'
fixCompartments: no visible global function definition for 'is'
getATACABsignal : atacCompartments: no visible global function
  definition for 'keepSeqlevels'
getATACABsignal : atacCompartments: no visible global function
  definition for 'as'
getATACABsignal : <anonymous>: no visible global function definition
  for 'as'
getATACABsignal: no visible global function definition for 'as'
getBinMatrix: no visible global function definition for 'IRanges'
getCorMatrix: no visible global function definition for 'cor'
getDenoisedCorMatrix: no visible global function definition for
  'keepSeqlevels'
getDomainInflections: no visible global function definition for 'is'
getDomainInflections: no visible global function definition for 'data'
getDomainInflections: no visible global function definition for
  'seqlengths'
getDomainInflections: no visible global function definition for
  'queryHits'
getDomainInflections: no visible global function definition for
  'subjectHits'
getDomainInflections : .getInflections: no visible global function
  definition for 'IRanges'
getDomainInflections: no visible global function definition for 'as'
getRNAABsignal : atacCompartments: no visible global function
  definition for 'keepSeqlevels'
getRNAABsignal : atacCompartments: no visible global function
  definition for 'as'
getRNAABsignal : <anonymous>: no visible global function definition for
  'as'
getRNAABsignal: no visible global function definition for 'as'
getSVD: no visible global function definition for 'cor'
getSeqLengths: no visible global function definition for 'data'
getSeqLengths: no visible global function definition for 'seqlevels'
getSeqLengths: no visible global function definition for 'seqlengths'
hdf5TFIDF: no visible global function definition for 'is'
hdf5TFIDF: no visible global function definition for 'as'
importBigWig: no visible global function definition for
  'seqlevelsStyle<-'
importBigWig: no visible global function definition for 'seqlengths'
importBigWig: no visible global function definition for
  'keepStandardChromosomes'
importBigWig: no visible global function definition for 'keepSeqlevels'
importBigWig: no visible global function definition for 'seqlevels'
importBigWig: no visible global function definition for 'SimpleList'
meanSmoother: no visible global function definition for 'median'
plotAB: no visible global function definition for 'is'
plotAB: no visible global function definition for 'keepSeqlevels'
plotAB: no visible global function definition for 'as'
plotAB: no visible global function definition for 'par'
plotAB: no visible global function definition for 'barplot'
plotAB: no visible global function definition for 'abline'
plotAB: no visible global function definition for 'median'
plotCorMatrix: no visible binding for global variable 'Var2'
plotCorMatrix: no visible binding for global variable 'Var1'
plotCorMatrix: no visible binding for global variable 'value'
precomputeBootstrapMeans : <anonymous>: no visible global function
  definition for 'SimpleList'
sparseToDenseMatrix: no visible global function definition for 'as'
sparseToDenseMatrix : <anonymous>: no visible global function
  definition for 'as'
summarizeBootstraps : <anonymous>: no visible global function
  definition for 'subjectHits'
summarizeBootstraps : <anonymous>: no visible global function
  definition for 'queryHits'
transformTFIDF: no visible global function definition for 'is'
as.matrix,GRanges: no visible global function definition for 'as'
coerce,GRanges-matrix: no visible global function definition for 'as'
coerce,matrix-GRanges: no visible global function definition for 'as'
granges,matrix: no visible global function definition for 'as'
Undefined global functions or variables:
  IRanges SimpleList Var1 Var2 abline as barplot cor cov data is
  keepSeqlevels keepStandardChromosomes median optim par queryHits sd
  seqlengths seqlevels seqlevelsStyle<- subjectHits value weighted.mean
  x
Consider adding
  importFrom("graphics", "abline", "barplot", "par")
  importFrom("methods", "as", "is")
  importFrom("stats", "cor", "cov", "median", "optim", "sd",
             "weighted.mean")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: filterCompartments.Rd:22-24: Dropping empty section \examples
prepare_Rd: fixCompartments.Rd:24-26: Dropping empty section \examples
prepare_Rd: summarizeBootstraps.Rd:24-26: Dropping empty section \examples
* 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
scCompartments    72.38   5.64   78.01
getDenoisedMatrix  7.00   0.22    7.22
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/compartmap.Rcheck/00check.log'
for details.



Installation output

compartmap.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL compartmap
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'compartmap' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'compartmap'
    finding HTML links ... done
    agrestiCoullCI                          html  
    bootstrapCompartments                   html  
    checkAssayType                          html  
    condenseRE                              html  
    condenseSE                              html  
    dot-n_approx                            html  
    dot-p_approx                            html  
    dot-z                                   html  
    estRMT                                  html  
    extractOpenClosed                       html  
    fexpit                                  html  
    filterCompartments                      html  
    fisherZ                                 html  
    fixCompartments                         html  
    flogit                                  html  
    getABSignal                             html  
    getATACABsignal                         html  
    getAssayNames                           html  
    getBinMatrix                            html  
    getChrs                                 html  
    getCorMatrix                            html  
    getDenoisedMatrix                       html  
    getDomainInflections                    html  
    getGlobalMeans                          html  
    getMatrixBlocks                         html  
    getSVD                                  html  
    getSeqLengths                           html  
    getShrinkageTargets                     html  
    hdf5TFIDF                               html  
    hg19.gr                                 html  
    hg38.gr                                 html  
    ifisherZ                                html  
    importBigWig                            html  
    k562_scatac_chr14                       html  
    k562_scrna_chr14                        html  
    k562_scrna_se_chr14                     html  
    meanSmoother                            html  
    mm10.gr                                 html  
    mm9.gr                                  html  
    plotAB                                  html  
    plotCorMatrix                           html  
    precomputeBootstrapMeans                html  
    removeEmptyBoots                        html  
    scCompartments                          html  
    shrinkBins                              html  
    sparseToDenseMatrix                     html  
    ss3_umi_sce                             html  
    summarizeBootstraps                     html  
    transformTFIDF                          html  
*** copying figures
** 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 (compartmap)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'RTN' is missing or broken
 done

Tests output


Example timings

compartmap.Rcheck/compartmap-Ex.timings

nameusersystemelapsed
agrestiCoullCI000
bootstrapCompartments000
checkAssayType0.720.050.76
condenseRE0.360.030.39
condenseSE0.420.050.47
estRMT0.140.060.21
extractOpenClosed0.010.000.01
fexpit000
fisherZ000
flogit000
getABSignal0.330.080.40
getATACABsignal1.840.192.04
getAssayNames0.110.010.12
getBinMatrix0.110.080.19
getChrs0.090.060.15
getCorMatrix0.180.080.25
getDenoisedMatrix7.000.227.22
getDomainInflections1.700.141.85
getGlobalMeans0.210.020.22
getMatrixBlocks0.000.010.02
getSVD000
getSeqLengths000
getShrinkageTargets000
hdf5TFIDF0.210.050.28
ifisherZ000
meanSmoother1.110.001.11
plotAB0.260.030.30
plotCorMatrix0.030.000.03
precomputeBootstrapMeans0.500.050.55
scCompartments72.38 5.6478.01
shrinkBins0.670.040.72
sparseToDenseMatrix0.030.000.03
transformTFIDF0.020.000.02