| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:16 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 406/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compartmap 1.18.0 (landing page) Benjamin Johnson
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the compartmap package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: compartmap |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:compartmap.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings compartmap_1.18.0.tar.gz |
| StartedAt: 2023-10-15 20:17:12 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 20:22:27 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 314.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: compartmap.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:compartmap.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings compartmap_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/compartmap.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘compartmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compartmap’ version ‘1.18.0’
* 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 loading without being on the library search path ... 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 ... WARNING
Error loading dataset 'k562_scatac_chr14':
Error in .requirePackage(package) :
unable to find required package 'csaw'
Error loading dataset 'ss3_umi_sce':
Error in .requirePackage(package) :
unable to find required package 'SingleCellExperiment'
The dataset(s) may use package(s) not declared in Depends/Imports.
* 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 106.50 1.168 107.668
getDenoisedMatrix 7.46 0.144 7.604
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘compartmap_vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘compartmap_vignette.Rmd’ using rmarkdown
Quitting from lines 2-16 (compartmap_vignette.Rmd)
Error: processing vignette 'compartmap_vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘compartmap_vignette.Rmd’
SUMMARY: processing the following file failed:
‘compartmap_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/compartmap.Rcheck/00check.log’
for details.
compartmap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL compartmap ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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)
compartmap.Rcheck/compartmap-Ex.timings
| name | user | system | elapsed | |
| agrestiCoullCI | 0.001 | 0.000 | 0.001 | |
| bootstrapCompartments | 0 | 0 | 0 | |
| checkAssayType | 0.124 | 0.008 | 0.132 | |
| condenseRE | 0.413 | 0.004 | 0.417 | |
| condenseSE | 0.331 | 0.012 | 0.343 | |
| estRMT | 0.119 | 0.032 | 0.151 | |
| extractOpenClosed | 0.014 | 0.012 | 0.026 | |
| fexpit | 0.000 | 0.004 | 0.005 | |
| fisherZ | 0.002 | 0.000 | 0.003 | |
| flogit | 0.002 | 0.000 | 0.002 | |
| getABSignal | 0.222 | 0.060 | 0.280 | |
| getATACABsignal | 2.526 | 0.156 | 2.682 | |
| getAssayNames | 0.110 | 0.028 | 0.136 | |
| getBinMatrix | 0.152 | 0.024 | 0.176 | |
| getChrs | 0.139 | 0.004 | 0.143 | |
| getCorMatrix | 0.166 | 0.008 | 0.175 | |
| getDenoisedMatrix | 7.460 | 0.144 | 7.604 | |
| getDomainInflections | 1.929 | 0.184 | 2.112 | |
| getGlobalMeans | 0.264 | 0.008 | 0.271 | |
| getMatrixBlocks | 0.010 | 0.000 | 0.009 | |
| getSVD | 0.007 | 0.000 | 0.006 | |
| getSeqLengths | 0.002 | 0.000 | 0.001 | |
| getShrinkageTargets | 0.000 | 0.000 | 0.001 | |
| hdf5TFIDF | 0.208 | 0.000 | 0.208 | |
| ifisherZ | 0.002 | 0.000 | 0.002 | |
| meanSmoother | 1.135 | 0.008 | 1.143 | |
| plotAB | 0.193 | 0.028 | 0.221 | |
| plotCorMatrix | 0.039 | 0.004 | 0.043 | |
| precomputeBootstrapMeans | 0.491 | 0.007 | 0.500 | |
| scCompartments | 106.500 | 1.168 | 107.668 | |
| shrinkBins | 1.307 | 0.008 | 1.315 | |
| sparseToDenseMatrix | 0.020 | 0.000 | 0.021 | |
| transformTFIDF | 0.016 | 0.000 | 0.016 | |