Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:40 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 684/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
extraChIPs 1.6.0  (landing page)
Stephen Pederson
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/extraChIPs
git_branch: RELEASE_3_18
git_last_commit: 5a8ce24
git_last_commit_date: 2023-10-24 11:41:36 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for extraChIPs on kunpeng2


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.

raw results


Summary

Package: extraChIPs
Version: 1.6.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings extraChIPs_1.6.0.tar.gz
StartedAt: 2023-11-02 10:26:26 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 10:37:21 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 654.7 seconds
RetCode: 0
Status:   OK  
CheckDir: extraChIPs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings extraChIPs_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/extraChIPs.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘1.6.0’
* 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 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 ... 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 5.429  0.063   5.508
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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
  ‘/home/biocbuild/bbs-3.18-bioc/meat/extraChIPs.Rcheck/00check.log’
for details.



Installation output

extraChIPs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL extraChIPs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘extraChIPs’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o extraChIPs.so FMStable.o init.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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)

Tests output

extraChIPs.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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, sort, 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 
 94.465   2.040  96.826 

Example timings

extraChIPs.Rcheck/extraChIPs-Ex.timings

nameusersystemelapsed
addDiffStatus-methods1.6410.0321.676
as_tibble0.6510.0080.662
bestOverlap-methods1.2160.1481.367
chopMC0.2340.0000.234
colToRanges-methods0.2850.0190.306
collapseGenes0.0040.0010.010
cytobands0.0130.0000.014
defineRegions5.4290.0635.508
defineSeqinfo0.0140.0000.015
distinctMC0.5200.0000.521
dualFilter000
ex_datasets0.0190.0020.021
fitAssayDiff-methods0.2950.0040.301
fixed_width_datasets0.0720.0040.076
getProfileData-methods2.1070.0842.198
grlToSE-methods0.6950.0040.704
importPeaks0.2050.0030.210
makeConsensus1.3410.0201.366
mapByFeature0.9680.0040.979
mapGrlCols2.3210.0202.348
mergeByCol-methods0.4690.0040.474
mergeByHMP-methods0.6720.0040.678
mergeBySig-methods0.6570.0160.676
partitionRanges-methods1.6170.0161.637
plotAssayDensities-methods1.1830.0201.206
plotAssayHeatmap-methods0.5320.0160.549
plotAssayPCA-methods1.3270.0281.357
plotAssayRle-methods1.2540.0081.264
plotGrlCol2.0680.0402.112
plotHFGC0.0000.0000.001
plotOverlaps-methods3.9560.0354.006
plotPairwise4.2270.0284.262
plotPie-methods2.0610.0082.082
plotProfileHeatmap-methods000
plotSplitDonut-methods1.6540.0081.666
propOverlap-methods0.4180.0000.419
reduceMC0.3430.0000.343
setoptsMC-methods1.2930.0041.299
stitchRanges0.3840.0000.384
voomWeightsFromCPM0.3070.0160.337