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This page was generated on 2021-11-29 15:05:50 -0500 (Mon, 29 Nov 2021).

CHECK results for compartmap on machv2

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:compartmap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings compartmap_1.12.0.tar.gz
StartedAt: 2021-11-28 15:00:08 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 15:07:14 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 425.9 seconds
RetCode: 0
Status:   OK  
CheckDir: compartmap.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:compartmap.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings compartmap_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/compartmap.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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    120.745  4.572 125.379
getDenoisedMatrix  14.804  0.212  15.021
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/compartmap.Rcheck/00check.log’
for details.



Installation output

compartmap.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL compartmap
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘compartmap’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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)

Tests output


Example timings

compartmap.Rcheck/compartmap-Ex.timings

nameusersystemelapsed
agrestiCoullCI0.0020.0000.002
bootstrapCompartments000
checkAssayType0.2790.0310.310
condenseRE0.8640.0060.871
condenseSE1.2700.0031.273
estRMT0.2910.0280.319
extractOpenClosed0.0370.0030.041
fexpit0.0060.0010.007
fisherZ0.0030.0010.002
flogit0.0010.0010.002
getABSignal0.5870.0990.686
getATACABsignal3.0730.1633.237
getAssayNames0.2740.0100.284
getBinMatrix0.2670.0480.315
getChrs0.2340.0140.248
getCorMatrix0.2760.0440.318
getDenoisedMatrix14.804 0.21215.021
getDomainInflections2.5450.1032.650
getGlobalMeans0.3880.0020.390
getMatrixBlocks0.0150.0010.017
getSVD0.0110.0000.012
getSeqLengths0.0020.0000.003
getShrinkageTargets0.0020.0000.002
hdf5TFIDF0.2690.0110.280
ifisherZ0.0030.0000.003
meanSmoother3.3230.0783.404
plotAB0.4080.0490.458
plotCorMatrix0.0450.0010.047
precomputeBootstrapMeans0.6970.0030.701
scCompartments120.745 4.572125.379
shrinkBins1.8930.0311.927
sparseToDenseMatrix0.0440.0010.045
transformTFIDF0.0190.0000.020