| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-22 11:35:38 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
| 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 695/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| extraChIPs 1.8.1 (landing page) Stevie Pederson
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the extraChIPs package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/extraChIPs.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: extraChIPs |
| Version: 1.8.1 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:extraChIPs.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings extraChIPs_1.8.1.tar.gz |
| StartedAt: 2024-05-22 01:47:55 -0400 (Wed, 22 May 2024) |
| EndedAt: 2024-05-22 01:57:40 -0400 (Wed, 22 May 2024) |
| EllapsedTime: 585.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: extraChIPs.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:extraChIPs.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings extraChIPs_1.8.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/extraChIPs.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'extraChIPs/DESCRIPTION' ... OK
* this is package 'extraChIPs' version '1.8.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocParallel', 'GenomicRanges', 'ggplot2', 'ggside',
'SummarizedExperiment', 'tibble'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'extraChIPs' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 code 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/extraChIPs/libs/x64/extraChIPs.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
'F:/biocbuild/bbs-3.19-bioc/meat/extraChIPs.Rcheck/00check.log'
for details.
extraChIPs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL extraChIPs ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'extraChIPs' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FMStable.c -o FMStable.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -shared -s -static-libgcc -o extraChIPs.dll tmp.def FMStable.o init.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-extraChIPs/00new/extraChIPs/libs/x64 ** 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 (extraChIPs)
extraChIPs.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(extraChIPs)
Loading required package: BiocParallel
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: ggside
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: tibble
>
> test_check("extraChIPs")
Creating DESeqDataSet...
converting counts to integer mode
Calculating none normalisation factors...
Estimating dispersions using fitType = local...
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Creating DGE list...
Calculating experiment-wide normalisation factors...
Estimating dispersions...
Running glmQLFit...
Creating DGE list...
Calculating experiment-wide normalisation factors...
Estimating dispersions...
Running glmQLFit...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 581 ]
>
> proc.time()
user system elapsed
83.90 3.01 87.40
extraChIPs.Rcheck/extraChIPs-Ex.timings
| name | user | system | elapsed | |
| addDiffStatus-methods | 0.23 | 0.01 | 0.25 | |
| as_tibble | 1.59 | 0.03 | 1.64 | |
| bestOverlap-methods | 0.94 | 0.21 | 1.14 | |
| chopMC | 0.22 | 0.01 | 0.23 | |
| colToRanges-methods | 0.25 | 0.02 | 0.27 | |
| collapseGenes | 0 | 0 | 0 | |
| cytobands | 0.02 | 0.05 | 0.08 | |
| defineRegions | 3.76 | 0.03 | 3.80 | |
| defineSeqinfo | 0.00 | 0.02 | 0.03 | |
| distinctMC | 0.39 | 0.02 | 0.40 | |
| dualFilter | 0 | 0 | 0 | |
| ex_datasets | 0.02 | 0.03 | 0.05 | |
| fitAssayDiff-methods | 0.3 | 0.0 | 0.3 | |
| fixed_width_datasets | 0.06 | 0.00 | 0.08 | |
| getProfileData-methods | 2.33 | 0.05 | 2.56 | |
| grlToSE-methods | 0.58 | 0.00 | 0.58 | |
| importPeaks | 0.17 | 0.01 | 0.20 | |
| makeConsensus | 0.95 | 0.02 | 0.97 | |
| mapByFeature | 0.66 | 0.00 | 0.65 | |
| mapGrlCols | 2.06 | 0.03 | 2.08 | |
| mergeByCol-methods | 0.37 | 0.00 | 0.37 | |
| mergeByHMP-methods | 0.55 | 0.00 | 0.55 | |
| mergeBySig-methods | 0.63 | 0.01 | 0.66 | |
| partitionRanges-methods | 1.32 | 0.02 | 1.34 | |
| plotAssayDensities-methods | 0.91 | 0.01 | 0.97 | |
| plotAssayHeatmap-methods | 0.38 | 0.04 | 0.40 | |
| plotAssayPCA-methods | 0.96 | 0.00 | 0.99 | |
| plotAssayRle-methods | 0.86 | 0.00 | 0.86 | |
| plotGrlCol | 1.55 | 0.03 | 1.58 | |
| plotHFGC | 0 | 0 | 0 | |
| plotOverlaps-methods | 3.57 | 0.04 | 3.66 | |
| plotPairwise | 3.47 | 0.07 | 3.54 | |
| plotPie-methods | 1.83 | 0.03 | 1.90 | |
| plotProfileHeatmap-methods | 0 | 0 | 0 | |
| plotSplitDonut-methods | 1.31 | 0.00 | 1.31 | |
| propOverlap-methods | 0.49 | 0.00 | 0.49 | |
| reduceMC | 0.39 | 0.02 | 0.40 | |
| setoptsMC-methods | 1.23 | 0.00 | 1.24 | |
| stitchRanges | 0.26 | 0.00 | 0.27 | |
| voomWeightsFromCPM | 0.27 | 0.01 | 0.34 | |