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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
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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 367/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compartmap 1.10.0 (landing page) Benjamin Johnson
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: compartmap |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compartmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings compartmap_1.10.0.tar.gz |
| StartedAt: 2021-10-14 21:27:14 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:35:14 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 479.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: compartmap.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compartmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings compartmap_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/compartmap.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.10.0'
* 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 96.55 1.50 98.06
getDenoisedMatrix 8.23 0.22 8.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
scCompartments 84.49 1.39 85.89
getDenoisedMatrix 7.19 0.14 7.33
* 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-3.13-bioc/meat/compartmap.Rcheck/00check.log'
for details.
compartmap.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/compartmap_1.10.0.tar.gz && rm -rf compartmap.buildbin-libdir && mkdir compartmap.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compartmap.buildbin-libdir compartmap_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL compartmap_1.10.0.zip && rm compartmap_1.10.0.tar.gz compartmap_1.10.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
22 3214k 22 718k 0 0 1007k 0 0:00:03 --:--:-- 0:00:03 1007k
83 3214k 83 2696k 0 0 1546k 0 0:00:02 0:00:01 0:00:01 1546k
100 3214k 100 3214k 0 0 1666k 0 0:00:01 0:00:01 --:--:-- 1666k
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_1.10.0.zip
* DONE (compartmap)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'compartmap' successfully unpacked and MD5 sums checked
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compartmap.Rcheck/examples_i386/compartmap-Ex.timings
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compartmap.Rcheck/examples_x64/compartmap-Ex.timings
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