Stevie Pederson
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/extraChIPs |
| git_branch: devel |
| git_last_commit: 100cd56 |
| git_last_commit_date: 2024-03-04 21:19:47 -0400 (Mon, 04 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:42 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 689/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| extraChIPs 1.7.5 (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 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: extraChIPs |
| Version: 1.7.5 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings extraChIPs_1.7.5.tar.gz |
| StartedAt: 2024-03-28 05:17:01 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 05:27:31 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 629.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: extraChIPs.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings extraChIPs_1.7.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/extraChIPs.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘extraChIPs/DESCRIPTION’ ... OK
* this is package ‘extraChIPs’ version ‘1.7.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘extraChIPs’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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 loading without being on the library search path ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
defineRegions 5.324 0.1 5.435
* 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
‘/home/biocbuild/bbs-3.19-bioc/meat/extraChIPs.Rcheck/00check.log’
for details.
extraChIPs.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL extraChIPs
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘extraChIPs’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c FMStable.c -o FMStable.o
FMStable.c: In function ‘setalpha’:
FMStable.c:4835:22: warning: unused variable ‘sinhalfangle’ [-Wunused-variable]
4835 | double sinangle, sinhalfangle;
| ^~~~~~~~~~~~
FMStable.c: In function ‘tailsMSS’:
FMStable.c:4924:21: warning: unused variable ‘temp’ [-Wunused-variable]
4924 | double z,y,dy,t,temp,scale;
| ^~~~
At top level:
FMStable.c:231:35: warning: ‘alphalarge’ defined but not used [-Wunused-variable]
231 | static int distributiontabulated, alphalarge;
| ^~~~~~~~~~
FMStable.c:227:52: warning: ‘C4’ defined but not used [-Wunused-variable]
227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
| ^~
FMStable.c:227:49: warning: ‘C3’ defined but not used [-Wunused-variable]
227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
| ^~
FMStable.c:227:46: warning: ‘C2’ defined but not used [-Wunused-variable]
227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
| ^~
FMStable.c:227:43: warning: ‘C1’ defined but not used [-Wunused-variable]
227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
| ^~
FMStable.c:227:37: warning: ‘angle’ defined but not used [-Wunused-variable]
227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
| ^~~~~
FMStable.c:227:31: warning: ‘ratio’ defined but not used [-Wunused-variable]
227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
| ^~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o extraChIPs.so FMStable.o init.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-extraChIPs/00new/extraChIPs/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
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 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 575 ]
>
> proc.time()
user system elapsed
96.158 2.377 98.721
extraChIPs.Rcheck/extraChIPs-Ex.timings
| name | user | system | elapsed | |
| addDiffStatus-methods | 0.326 | 0.036 | 0.363 | |
| as_tibble | 2.045 | 0.096 | 2.146 | |
| bestOverlap-methods | 1.342 | 0.072 | 1.416 | |
| chopMC | 0.267 | 0.020 | 0.287 | |
| colToRanges-methods | 0.321 | 0.000 | 0.322 | |
| collapseGenes | 0.003 | 0.000 | 0.003 | |
| cytobands | 0.013 | 0.000 | 0.013 | |
| defineRegions | 5.324 | 0.100 | 5.435 | |
| defineSeqinfo | 0.013 | 0.000 | 0.014 | |
| distinctMC | 0.474 | 0.004 | 0.479 | |
| dualFilter | 0 | 0 | 0 | |
| ex_datasets | 0.020 | 0.000 | 0.021 | |
| fitAssayDiff-methods | 0.328 | 0.000 | 0.329 | |
| fixed_width_datasets | 0.073 | 0.004 | 0.077 | |
| getProfileData-methods | 2.572 | 0.091 | 2.671 | |
| grlToSE-methods | 0.657 | 0.000 | 0.658 | |
| importPeaks | 0.195 | 0.000 | 0.197 | |
| makeConsensus | 1.264 | 0.008 | 1.274 | |
| mapByFeature | 0.908 | 0.012 | 0.922 | |
| mapGrlCols | 2.249 | 0.008 | 2.263 | |
| mergeByCol-methods | 0.434 | 0.000 | 0.436 | |
| mergeByHMP-methods | 0.659 | 0.004 | 0.665 | |
| mergeBySig-methods | 0.662 | 0.000 | 0.663 | |
| partitionRanges-methods | 1.508 | 0.012 | 1.524 | |
| plotAssayDensities-methods | 1.596 | 0.028 | 1.628 | |
| plotAssayHeatmap-methods | 0.567 | 0.012 | 0.581 | |
| plotAssayPCA-methods | 1.113 | 0.016 | 1.132 | |
| plotAssayRle-methods | 1.271 | 0.028 | 1.302 | |
| plotGrlCol | 2.042 | 0.023 | 2.071 | |
| plotHFGC | 0 | 0 | 0 | |
| plotOverlaps-methods | 4.168 | 0.032 | 4.210 | |
| plotPairwise | 4.319 | 0.020 | 4.349 | |
| plotPie-methods | 2.166 | 0.004 | 2.176 | |
| plotProfileHeatmap-methods | 0 | 0 | 0 | |
| plotSplitDonut-methods | 2.082 | 0.004 | 2.091 | |
| propOverlap-methods | 0.385 | 0.000 | 0.385 | |
| reduceMC | 0.355 | 0.000 | 0.355 | |
| setoptsMC-methods | 1.369 | 0.016 | 1.388 | |
| stitchRanges | 0.427 | 0.004 | 0.432 | |
| voomWeightsFromCPM | 0.296 | 0.004 | 0.301 | |