Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-29 15:05:17 -0500 (Mon, 29 Nov 2021).

CHECK results for compartmap on tokay2

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 376/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compartmap 1.12.0  (landing page)
Benjamin Johnson
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/compartmap
git_branch: RELEASE_3_14
git_last_commit: 3fce1b6
git_last_commit_date: 2021-10-26 12:48:10 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: compartmap
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compartmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings compartmap_1.12.0.tar.gz
StartedAt: 2021-11-28 20:05:58 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 20:14:29 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 512.0 seconds
RetCode: 0
Status:   OK  
CheckDir: compartmap.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compartmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings compartmap_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/compartmap.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.12.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
scCompartments    97.11   1.58   98.70
getDenoisedMatrix  8.17   0.10    8.27
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
scCompartments    92.12   1.70   93.84
getDenoisedMatrix  9.25   0.11    9.36
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/compartmap.Rcheck/00check.log'
for details.



Installation output

compartmap.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/compartmap_1.12.0.tar.gz && rm -rf compartmap.buildbin-libdir && mkdir compartmap.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compartmap.buildbin-libdir compartmap_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL compartmap_1.12.0.zip && rm compartmap_1.12.0.tar.gz compartmap_1.12.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 3215k    0 14875    0     0   126k      0  0:00:25 --:--:--  0:00:25  126k
 94 3215k   94 3024k    0     0  2768k      0  0:00:01  0:00:01 --:--:-- 2767k
100 3215k  100 3215k    0     0  2844k      0  0:00:01  0:00:01 --:--:-- 2845k

install for i386

* 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

install for x64

* installing *source* package 'compartmap' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'compartmap' as compartmap_1.12.0.zip
* DONE (compartmap)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'compartmap' successfully unpacked and MD5 sums checked

Tests output


Example timings

compartmap.Rcheck/examples_i386/compartmap-Ex.timings

nameusersystemelapsed
agrestiCoullCI000
bootstrapCompartments000
checkAssayType0.780.000.79
condenseRE0.50.00.5
condenseSE0.630.140.76
estRMT0.120.000.13
extractOpenClosed0.030.000.03
fexpit000
fisherZ000
flogit000
getABSignal0.380.060.43
getATACABsignal2.230.142.38
getAssayNames0.170.020.19
getBinMatrix0.220.030.25
getChrs0.160.030.18
getCorMatrix0.220.030.25
getDenoisedMatrix8.170.108.27
getDomainInflections2.910.072.98
getGlobalMeans0.460.020.49
getMatrixBlocks0.020.000.01
getSVD0.020.000.02
getSeqLengths000
getShrinkageTargets000
hdf5TFIDF0.290.030.33
ifisherZ000
meanSmoother1.380.001.37
plotAB0.260.060.33
plotCorMatrix0.030.000.03
precomputeBootstrapMeans0.770.030.80
scCompartments97.11 1.5898.70
shrinkBins1.270.051.32
sparseToDenseMatrix0.030.000.03
transformTFIDF0.010.000.01

compartmap.Rcheck/examples_x64/compartmap-Ex.timings

nameusersystemelapsed
agrestiCoullCI000
bootstrapCompartments000
checkAssayType0.900.020.92
condenseRE0.920.000.92
condenseSE0.710.090.80
estRMT0.220.040.25
extractOpenClosed0.030.000.03
fexpit0.010.000.02
fisherZ000
flogit000
getABSignal0.60.10.7
getATACABsignal3.860.083.94
getAssayNames0.200.030.23
getBinMatrix0.240.100.33
getChrs0.110.030.14
getCorMatrix0.230.060.29
getDenoisedMatrix9.250.119.36
getDomainInflections2.390.062.46
getGlobalMeans0.280.020.29
getMatrixBlocks0.020.000.02
getSVD0.020.000.01
getSeqLengths000
getShrinkageTargets000
hdf5TFIDF0.260.010.29
ifisherZ000
meanSmoother1.590.001.59
plotAB0.270.100.36
plotCorMatrix0.050.000.05
precomputeBootstrapMeans0.580.050.62
scCompartments92.12 1.7093.84
shrinkBins1.580.031.61
sparseToDenseMatrix0.030.000.04
transformTFIDF0.030.000.03