Benjamin Johnson
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 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 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:14 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 377/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compartmap 1.13.0 (landing page) Benjamin Johnson
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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: 2022-03-17 18:47:16 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:51:39 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 262.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: compartmap.Rcheck |
| Warnings: 0 |
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###
### 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
###
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* 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 64.66 6.15 70.81
getDenoisedMatrix 5.41 0.23 5.65
* 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.
compartmap.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL compartmap
###
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* 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 'Pigengene' is missing or broken
done
compartmap.Rcheck/compartmap-Ex.timings
| name | user | system | elapsed | |
| agrestiCoullCI | 0 | 0 | 0 | |
| bootstrapCompartments | 0 | 0 | 0 | |
| checkAssayType | 0.61 | 0.02 | 0.62 | |
| condenseRE | 0.29 | 0.03 | 0.33 | |
| condenseSE | 0.24 | 0.09 | 0.33 | |
| estRMT | 0.06 | 0.06 | 0.12 | |
| extractOpenClosed | 0.03 | 0.00 | 0.03 | |
| fexpit | 0 | 0 | 0 | |
| fisherZ | 0 | 0 | 0 | |
| flogit | 0 | 0 | 0 | |
| getABSignal | 0.30 | 0.10 | 0.39 | |
| getATACABsignal | 1.70 | 0.22 | 1.93 | |
| getAssayNames | 0.09 | 0.03 | 0.12 | |
| getBinMatrix | 0.14 | 0.04 | 0.19 | |
| getChrs | 0.11 | 0.00 | 0.11 | |
| getCorMatrix | 0.13 | 0.07 | 0.18 | |
| getDenoisedMatrix | 5.41 | 0.23 | 5.65 | |
| getDomainInflections | 1.00 | 0.22 | 1.21 | |
| getGlobalMeans | 0.18 | 0.03 | 0.22 | |
| getMatrixBlocks | 0.02 | 0.00 | 0.02 | |
| getSVD | 0 | 0 | 0 | |
| getSeqLengths | 0 | 0 | 0 | |
| getShrinkageTargets | 0 | 0 | 0 | |
| hdf5TFIDF | 0.21 | 0.02 | 0.22 | |
| ifisherZ | 0 | 0 | 0 | |
| meanSmoother | 1.12 | 0.04 | 1.17 | |
| plotAB | 0.21 | 0.07 | 0.27 | |
| plotCorMatrix | 0.01 | 0.00 | 0.02 | |
| precomputeBootstrapMeans | 0.45 | 0.06 | 0.51 | |
| scCompartments | 64.66 | 6.15 | 70.81 | |
| shrinkBins | 1.08 | 0.15 | 1.22 | |
| sparseToDenseMatrix | 0.03 | 0.00 | 0.03 | |
| transformTFIDF | 0.02 | 0.00 | 0.02 | |